Daily Papers

Large language models exhibit substantial performance variation across languages, even when solving semantically equivalent tasks. Existing analyses often treat this phenomenon as an observational disparity caused by differences in pretraining data, tokenization, or benchmark coverage. We study a complementary hypothesis: high-resource languages (HRLs) may more reliably elicit latent computations useful for task-specific (i.e. mathematical) reasoning, while lower-resource languages (LRLs) may under-activate those computations despite expressing the same task. To test this hypothesis, we introduce a mechanistic intervention framework for identifying and transferring task-relevant sparse latent features across languages. Using sparse autoencoders over residual-stream activations, we isolate features enriched in successful HRL task-specific reasoning while filtering out source-language and generic-generation features. We then construct steering directions from these features and inject them during LRL inference. The resulting interventions test whether the selected features are functionally involved in the observed reasoning gap: suppressing them should impair source-language reasoning, while activating them should partially recover target-language reasoning beyond random and non-task controls. Our framework reframes some cross-lingual reasoning gaps as failures of mechanism elicitation rather than capability absence, and offers a causally testable route to feature-mediated transfer without translation, fine-tuning, or changing the user-facing language.

Malicious attackers can exploit large language models (LLMs) by engaging them in multi-turn dialogues to achieve harmful objectives, posing significant safety risks to society. To address this challenge, we propose a novel defense mechanism: SafeTy Reasoning Elicitation Alignment for Multi-Turn Dialogues (STREAM). STREAM defends LLMs against multi-turn attacks while preserving their functional capabilities. Our approach involves constructing a human-annotated dataset, the Safety Reasoning Multi-turn Dialogues dataset, which is used to fine-tune a plug-and-play safety reasoning moderator. This model is designed to identify malicious intent hidden within multi-turn conversations and alert the target LLM of potential risks. We evaluate STREAM across multiple LLMs against prevalent multi-turn attack strategies. Experimental results demonstrate that our method significantly outperforms existing defense techniques, reducing the Attack Success Rate (ASR) by 51.2%, all while maintaining comparable LLM capability.

As recommender systems transition toward agentic, multi-turn conversational interfaces, evaluation paradigms have struggled to keep pace. Current benchmarks often rely on "LLM-as-a-judge" evaluations, which introduce subjectivity, high costs and inconsistency. We present τ-Rec, a benchmark for agentic recommender systems that replaces subjective evaluation with verifiable rewards and a reveal-tagged elicitation (RTE) mechanism that controls how task constraints surface during dialogue. By testing agents against structured catalog predicates and employing a pass^k reliability metric, τ-Rec provides a systematic test for consistent reasoning. Our evaluation of nine configurations across five model families -- GPT-5.4, Claude Sonnet 4.6, Gemini 2.5 Flash, DeepSeek V4 Flash, Qwen3-32B and GPT-5 mini -- reveals a steep reliability cliff, where even the best model achieves only ~57% at pass^1 and ~38% at pass^4, highlighting a critical gap in current conversational agent deployment. All code and data are publicly available at https://github.com/nbharaths/tau-rec.

While prompt optimization has emerged as a critical technique for enhancing language model performance, existing approaches primarily focus on elicitation-based strategies that search for optimal prompts to activate models' capabilities. These methods exhibit fundamental limitations when addressing knowledge-intensive tasks, as they operate within static knowledge capacity rather than providing the factual knowledge, terminology precision, and reasoning patterns required in specialized domains. To address these limitations, we propose Knowledge-Provision-based Prompt Optimization (KPPO), a framework that reformulates prompt optimization as systematic knowledge integration rather than potential elicitation. KPPO introduces three key innovations: 1) a knowledge gap filling mechanism for knowledge gap identification and targeted remediation; 2) a batch-wise candidate evaluation approach that considers both performance improvement and distributional stability; 3) an adaptive knowledge pruning strategy that balances performance and token efficiency, reducing up to 29% of inference token usage. Evaluation on 15 knowledge-intensive benchmarks from various domains demonstrates KPPO's superiority over elicitation-based methods, with an average improvement of ~6% over baselines while achieving comparable or lower token consumption.

Although reinforcement learning with verifiable rewards (RLVR) shows promise in improving the reasoning ability of large language models (LLMs), the scaling up dilemma remains due to the reliance on human annotated labels especially for complex tasks. Recent alternatives that explore various self-reward signals exhibit the eliciting potential of LLM reasoning, but suffer from the non-negligible collapse issue. Inspired by the success of self-supervised learning, we propose Co-Reward, a novel RL framework that leverages contrastive agreement across semantically analogical questions as a reward basis. Specifically, we construct a similar question for each training sample (without labels) and synthesize their individual surrogate labels through a simple rollout voting, and then the reward is constructed by cross-referring the labels of each question pair to enforce the internal reasoning consistency across analogical inputs. Intuitively, such a self-supervised reward-shaping mechanism increases the difficulty of learning collapse into a trivial solution, and promotes stable reasoning elicitation and improvement through expanding the input sample variants. Empirically, Co-Reward achieves superior performance compared to other self-reward baselines on multiple reasoning benchmarks and LLM series, and reaches or even surpasses ground-truth (GT) labeled reward, with improvements of up to +6.8% on MATH500 over GT reward on Llama-3.2-3B-Instruct. Our code is publicly available at https://github.com/tmlr-group/Co-Reward.

Human-AI planning for complex goals remains challenging with current large language models (LLMs), which rely on linear chat histories and simplistic memory mechanisms. Despite advances in long-context prompting, users still manually manage information, leading to a high cognitive burden. Hence, we propose JumpStarter, a system that enables LLMs to collaborate with humans on complex goals by dynamically decomposing tasks to help users manage context. We specifically introduce task-structured context curation, a novel framework that breaks down a user's goal into a hierarchy of actionable subtasks, and scopes context to localized decision points, enabling finer-grained personalization and reuse. The framework is realized through three core mechanisms: context elicitation, selection, and reuse. We demonstrate that task-structured context curation significantly improves plan quality by 16% over ablations. Our user study shows that JumpStarter helped users generate plans with 79% higher quality compared to ChatGPT.

Model developers implement safeguards in frontier models to prevent misuse, for example, by employing classifiers to filter dangerous outputs. In this work, we demonstrate that even robustly safeguarded models can be used to elicit harmful capabilities in open-source models through elicitation attacks. Our elicitation attacks consist of three stages: (i) constructing prompts in adjacent domains to a target harmful task that do not request dangerous information; (ii) obtaining responses to these prompts from safeguarded frontier models; (iii) fine-tuning open-source models on these prompt-output pairs. Since the requested prompts cannot be used to directly cause harm, they are not refused by frontier model safeguards. We evaluate these elicitation attacks within the domain of hazardous chemical synthesis and processing, and demonstrate that our attacks recover approximately 40% of the capability gap between the base open-source model and an unrestricted frontier model. We then show that the efficacy of elicitation attacks scales with the capability of the frontier model and the amount of generated fine-tuning data. Our work demonstrates the challenge of mitigating ecosystem level risks with output-level safeguards.

Mechanistic interpretability is often motivated for alignment auditing, where a model's verbal explanations can be absent, incomplete, or misleading. Yet many evaluations do not control whether black-box prompting alone can recover the target behavior, so apparent gains from white-box tools may reflect elicitation rather than internal signal; we call this the elicitation confounder. We introduce Pando, a model-organism benchmark that breaks this confound via an explanation axis: models are trained to produce either faithful explanations of the true rule, no explanation, or confident but unfaithful explanations of a disjoint distractor rule. Across 720 finetuned models implementing hidden decision-tree rules, agents predict held-out model decisions from 10 labeled query-response pairs, optionally augmented with one interpretability tool output. When explanations are faithful, black-box elicitation matches or exceeds all white-box methods; when explanations are absent or misleading, gradient-based attribution improves accuracy by 3-5 percentage points, and relevance patching, RelP, gives the largest gains, while logit lens, sparse autoencoders, and circuit tracing provide no reliable benefit. Variance decomposition suggests gradients track decision computation, which fields causally drive the output, whereas other readouts are dominated by task representation, biases toward field identity and value. We release all models, code, and evaluation infrastructure.

Information elicitation is an open-ended information-seeking problem in which an interaction can unfold in many potentially valuable directions, requiring an elicitor to continually determine which information to pursue as new information emerges. In agentic elicitation, these decisions may be delegated to a foundation model, yet how model choice shapes the resulting information-seeking behavior remains understudied. We study how judgments about information value vary across LLMs and how these differences shape sequential information seeking. We first examine these judgments across 11 LLMs spanning multiple model families and parameter scales, using a shared set of information and elicitation objectives. We then develop a controlled elicitation simulation in which different models encounter the same information space and use the same selection rule, isolating these judgments from question generation and respondent behavior. Using this setting, we characterize the breadth-depth behavior that emerges from model-specific information-seeking preferences over the course of elicitation. We further examine how interaction history changes the evaluation and subsequent selection of prospective information. We test the robustness and boundaries of these findings through sensitivity analyses and ablations over the opportunities available to the elicitor, the response labels used to operationalize information-seeking preferences, the presence of interaction history, and whether redundancy is explicitly relevant to the assessment. The project code, data, and trajectory files are available at https://github.com/infosenselab/open-elicitation.

Language Agent could be endowed with different mechanisms for autonomous task accomplishment. Current agents typically rely on fixed mechanisms or a set of mechanisms activated in a predefined order, limiting their adaptation to varied potential task solution structures. To this end, this paper proposes Adaptive Language Agent Mechanism Activation Learning with Self-Exploration (ALAMA), which focuses on optimizing mechanism activation adaptability without reliance on expert models. Initially, it builds a harmonized agent framework (UniAct) to Unify different mechanisms via Actions. Then it leverages a training-efficient optimization method based on self-exploration to enable the UniAct to adaptively activate the appropriate mechanisms according to the potential characteristics of the task. Experimental results demonstrate significant improvements in downstream agent tasks, affirming the effectiveness of our approach in facilitating more dynamic and context-sensitive mechanism activation.

Laboratory workflows in pharmaceutical and biomedical research encode substantial tacit knowledge -- expert judgment about failure conditions, decision branching logic, and contextual dependencies -- that remains inaccessible to protocol documents, sensor streams, and existing biomedical ontologies. We present a repeatable structured expert elicitation methodology and federated Semantic Knowledge Graph (SKG) architecture for capturing and querying this knowledge, demonstrated through deployment at the Biochemical and Cellular Pharmacology Department of Genentech. Knowledge is elicited via the Protocol Intelligence Co-pilot, a purpose-built AI interview agent that applies structured elicitation lenses to surface tacit procedural knowledge with expert-assigned confidence scores, producing graph representations across three tiers: program-level decision milestones, assay protocol knowledge, and physical execution infrastructure. Separately constructed subgraphs, exemplified by immunoassay (ELISA), quantitative mass spectrometry (LC-MS/PRM), and laboratory automation, are aligned through a shared upper ontology and queried as a single federated graph. Evaluation demonstrates seven query types structurally unavailable from any individual data source, including a cross-subgraph traversal that identifies automation-masked silent failures -- conditions where execution logs report success while scientific validity is compromised. Critically, the MASKED_BY graph relationship encodes a class of laboratory risk invisible to current informatics platforms -- the structural gap that prevents existing systems from reasoning about scientific validity. This architecture provides the semantic world model that AI laboratory agents currently lack: a queryable representation of where workflows fail silently, where human judgment is irreplaceable, and which execution assets mask rather than detect failure.

The task of chemical reaction predictions (CRPs) plays a pivotal role in advancing drug discovery and material science. However, its effectiveness is constrained by the vast and uncertain chemical reaction space and challenges in capturing reaction selectivity, particularly due to existing methods' limitations in exploiting the data's inherent knowledge. To address these challenges, we introduce a data-curated self-feedback knowledge elicitation approach. This method starts from iterative optimization of molecular representations and facilitates the extraction of knowledge on chemical reaction types (RTs). Then, we employ adaptive prompt learning to infuse the prior knowledge into the large language model (LLM). As a result, we achieve significant enhancements: a 14.2% increase in retrosynthesis prediction accuracy, a 74.2% rise in reagent prediction accuracy, and an expansion in the model's capability for handling multi-task chemical reactions. This research offers a novel paradigm for knowledge elicitation in scientific research and showcases the untapped potential of LLMs in CRPs.

Mechanism-targeted synthetic data is increasingly proposed as a way to steer pretraining toward desirable capabilities, but it remains unclear how such interventions should be evaluated. We study this question for in-context learning (ICL) under matched compute (iso-FLOPs) using Bi-Induct, a lightweight data rewrite that interleaves short directional copy snippets into a natural pretraining stream: forward-copy (induction), backward-copy (anti-induction, as a directional control), or a balanced mix. Across 0.13B-1B decoder-only models, we evaluate (i) few-shot performance on standard LM benchmarks and function-style ICL probes, (ii) head-level copy telemetry, and (iii) held-out perplexity as a guardrail. Bi-Induct reliably increases induction-head activity, but this does not translate into consistent improvements in few-shot generalization: on standard LM benchmarks, Bi-Induct is largely performance-neutral relative to natural-only training, while on function-style probes the 1B natural-only model performs best. Despite explicit backward-copy cues, anti-induction scores remain near zero across scales, revealing a strong forward/backward asymmetry. Targeted ablations show a sharper distinction: removing the top 2% induction heads per layer harms ICL more than matched random ablations, with the largest relative drop occurring in the natural-only models. This indicates that natural-only training produces more centralized, load-bearing induction circuitry, whereas Bi-Induct tends to create more distributed and redundant induction activity. Our main conclusion is that eliciting a mechanism is not the same as making it load-bearing. For data-centric foundation model design, this suggests that synthetic data interventions should be evaluated not only by signature amplification, but by whether they create causally necessary computation while preserving natural-data modeling quality.

AI models have achieved remarkable success across diverse domains, yet the mechanisms underlying their capabilities and the risks they may pose remain poorly understood. As AI development becomes faster and increasingly automated, mechanistic exploration remains largely manual, widening the gap between what models can do and our ability to understand and control them. To bridge this gap, we introduce Mechanist, an agentic system that uses AI as a scientific instrument for the autonomous discovery of mechanisms underlying AI intelligence. To support autonomous mechanistic discovery, we construct an interpretability-focused knowledge graph of approximately 13,000 papers and integrate it with a multidisciplinary database of 43 million papers spanning 26 fields. We further curate a library of 32 foundational methods for mechanism analysis, causal intervention, and validation. Compared with Claude Code and existing AI-scientist systems, Mechanist generates more valuable mechanism hypotheses and executes experiments more reliably. Mechanist also demonstrates a progression from discovering model behaviors to explaining and controlling AI models. Specifically, Mechanist first uncovers a counterintuitive safety risk in scientific laboratories, showing that unsafe traits can transfer across modalities through apparently safe training data. Mechanist then develops a mechanism theory of belief, revealing how models represent world knowledge, form beliefs, infer the beliefs of others, and how these mechanisms emerge during pretraining. Finally, Mechanist translates these mechanistic insights into practical interventions that improve model performance across diverse scenarios and steer scientific foundation models toward generating DNA sequences with specified properties.

We study secret elicitation: discovering knowledge that an AI possesses but does not explicitly verbalize. As a testbed, we train three families of large language models (LLMs) to possess specific knowledge that they apply downstream but deny knowing when asked directly. For example, in one setting, we train an LLM to generate replies that are consistent with knowing the user is female, while denying this knowledge when asked directly. We then design various black-box and white-box secret elicitation techniques and evaluate them based on whether they can help an LLM auditor successfully guess the secret knowledge. Many of our techniques improve on simple baselines. Our most effective techniques (performing best in 2/3 settings) are based on prefill attacks, a black-box technique where the LLM reveals secret knowledge when generating a completion from a predefined prefix. In our remaining setting, white-box techniques based on logit lens and sparse autoencoders (SAEs) are most effective. We release our models and code, establishing a public benchmark for evaluating secret elicitation methods.

Predicting the answer to interventional ``what if'' questions --- the outcome of an action never taken --- requires a mechanistic, causal model, not a curve fit; and learning such a model requires experiments, because passive data leaves its mechanisms unidentified. Experiments are expensive, so the central problem is data efficiency. We present the Model Discovery Agent (MDA), which couples a large language model (LLM), used as a proposer of candidate structures, with standard Bayesian machinery --- sequential Monte Carlo (SMC) for parameter and structure posteriors, simulation-based inference (SBI) for intractable likelihoods, and value-of-information (VoI) for experiment design --- to discover latent mechanistic world models from few interventions. MDA operates in the M-open setting: when the truth lies outside the current hypothesis class, a predictive check flags the inadequacy and the proposer expands the hypothesis space with a new model whose parameters are then identified by designed experiments. We show that discovery and design reinforce: the design step identifies the mechanism the discovery step proposes, and the identified mechanism improves predictions, enabling further discoveries from the remaining unexplained residuals. On three different benchmarks --- covering physics (\DPbench, wiemann2026discoverphysics), chemistry (\CHEMbench, kabra2026autoscilab) and biology (\HHbench, a new partially observed single-neuron electrophysiology benchmark we create) --- we show that MDA sets a new SOTA in terms of data-efficient model learning and reliable interventional prediction ability.

Most conversational agents (CAs) are designed to satisfy user needs through user-driven interactions. However, many real-world settings, such as academic interviewing, judicial proceedings, and journalistic investigations, involve broader institutional decision-making processes and require agents that can elicit information from users. In this paper, we introduce Information Elicitation Agents (IEAs) in which the agent's goal is to elicit information from users to support the agent's institutional or task-oriented objectives. To enable systematic research on this setting, we present YIELD, a 26M-token dataset of 2,281 ethically sourced, human-to-human dialogues. Moreover, we formalize information elicitation as a finite-horizon POMDP and propose novel metrics tailored to IEAs. Pilot experiments on multiple foundation LLMs show that training on YIELD improves their alignment with real elicitation behavior and findings are corroborated by human evaluation. We release YIELD under CC BY 4.0. The dataset, project code, evaluation tools, and fine-tuned model adapters are available at: https://github.com/infosenselab/yield.

Interpretability research aims to bridge the gap between empirical success and our scientific understanding of the inner workings of large language models (LLMs). However, most existing research focuses on analyzing a single mechanism, such as how models copy or recall factual knowledge. In this work, we propose a formulation of competition of mechanisms, which focuses on the interplay of multiple mechanisms instead of individual mechanisms and traces how one of them becomes dominant in the final prediction. We uncover how and where mechanisms compete within LLMs using two interpretability methods: logit inspection and attention modification. Our findings show traces of the mechanisms and their competition across various model components and reveal attention positions that effectively control the strength of certain mechanisms. Code: https://github.com/francescortu/comp-mech. Data: https://huggingface.co/datasets/francescortu/comp-mech.

Future AI systems could conceal their capabilities ('sandbagging') during evaluations, potentially misleading developers and auditors. We stress-tested sandbagging detection techniques using an auditing game. First, a red team fine-tuned five models, some of which conditionally underperformed, as a proxy for sandbagging. Second, a blue team used black-box, model-internals, or training-based approaches to identify sandbagging models. We found that the blue team could not reliably discriminate sandbaggers from benign models. Black-box approaches were defeated by effective imitation of a weaker model. Linear probes, a model-internals approach, showed more promise but their naive application was vulnerable to behaviours instilled by the red team. We also explored capability elicitation as a strategy for detecting sandbagging. Although Prompt-based elicitation was not reliable, training-based elicitation consistently elicited full performance from the sandbagging models, using only a single correct demonstration of the evaluation task. However the performance of benign models was sometimes also raised, so relying on elicitation as a detection strategy was prone to false-positives. In the short-term, we recommend developers remove potential sandbagging using on-distribution training for elicitation. In the longer-term, further research is needed to ensure the efficacy of training-based elicitation, and develop robust methods for sandbagging detection. We open source our model organisms at https://github.com/AI-Safety-Institute/sandbagging_auditing_games and select transcripts and results at https://huggingface.co/datasets/sandbagging-games/evaluation_logs . A demo illustrating the game can be played at https://sandbagging-demo.far.ai/ .

Concept Design structures software systems around concepts: user-facing, self-contained units of functionality with a focused purpose. Concepts are composed into applications using synchronization rules called reactions, which specify how actions in one concept trigger actions in others. This paper first gives a formal semantics for concepts and reactions, enabling automatic verification of safety invariants in applications developed with this methodology. It then presents a CEGIS-style, LLM-driven synthesis procedure for generating reaction designs that satisfy such invariants. Because many different designs can satisfy the same invariant, we study two ways of steering synthesis toward the user's intended design: natural-language prompts and positive/negative scenarios. We also propose an LLM-driven scenario elicitation technique to support early design exploration. In an evaluation on three applications and twelve design variants using one LLM configuration, invariant-only synthesis reached verified designs quickly but often produced inconsistent designs across runs, some of which were implausible, showing that invariants alone underconstrain the design task. Scenario-guided synthesis recovered intended designs more consistently than natural-language prompting, although minimal scenarios can lead to overfitting. LLM-driven scenario elicitation, where the user classifies proposed scenarios rather than authoring them from scratch, recovered the intended designs in most variants when enough scenarios were elicited, but missed behaviors and non-determinism prevented reliable coverage in all cases.

Organic reaction mechanisms are the stepwise elementary reactions by which reactants form intermediates and products, and are fundamental to understanding chemical reactivity and designing new molecules and reactions. Although large language models (LLMs) have shown promise in understanding chemical tasks such as synthesis design, it is unclear to what extent this reflects genuine chemical reasoning capabilities, i.e., the ability to generate valid intermediates, maintain chemical consistency, and follow logically coherent multi-step pathways. We address this by introducing oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning in organic chemistry. It comprises over 10,000 annotated mechanistic steps with intermediates, type labels, and difficulty ratings. Furthermore, to evaluate LLM capability more precisely and enable fine-grained scoring, we propose oMeS, a dynamic evaluation framework that combines step-level logic and chemical similarity. We analyze the performance of state-of-the-art LLMs, and our results show that although current models display promising chemical intuition, they struggle with correct and consistent multi-step reasoning. Notably, we find that using prompting strategy and fine-tuning a specialist model on our proposed dataset increases performance by 50% over the leading closed-source model. We hope that oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.

Tool calling, invoking external tools on demand, is central to agentic LLMs, yet the mechanism that decides whether a model calls a tool or responds directly remains poorly understood. Agentic prompts are long and heavily scaffolded, combining role instructions, tool schemas, format templates, and the user's request across hundreds of tokens, creating a noisy, highly entangled context in which no single controllable variable for mechanistic analysis is obvious. To obtain such a variable, we propose a method that converts complex agentic prompts into minimal contrastive pairs in which a single request verb determines the tool-call decision: replacing an execution-verb (e.g., write) with an analysis-verb (e.g., discuss) reliably flips the decision, suggesting it is mediated by a compact internal state. We construct 500 such paired prompts across Python, Java, and C++ (300 for mechanistic analysis, 200 held out for evaluation). We trace the decision to a vector, μ_Δ, that is both causally necessary and sufficient and generalizes beyond the discovery prompts to native multi-turn τ^2-Bench trajectories and verb-free requests. Behavioral ablations show that the scaffold establishes a tool-call prior; Transcoder decomposition then reveals that analysis verbs suppress this prior through features signaling that tool use is unnecessary, whereas execution verbs largely leave it intact. Downstream scaffold-reading attention heads and MLP features read out the resulting state, and the same mechanism recurs across seven models from the Qwen, Mistral, and Granite families. Our code is available at https://github.com/XijieGo/MI4ToolCalling.

Virtual cell models should capture phenotypes induced by specific perturbations. However, image-based models are typically trained and evaluated to match real-image distributions, which alone does not explicitly prioritize perturbation-specific biological responses. Recent approaches add biological signals through reinforcement-learning post-training or inference-time steering, raising a central question: where should biological response information enter the generative pipeline? We introduce PerturbBridge, a stochastic data-to-data bridge model that directly supervises perturbation-specific phenotypes in predicted perturbed images during training. PerturbBridge jointly optimizes bridge regression and differentiable biological response losses, with biological gradients passing through a frozen image encoder. We further introduce perturbation-response evaluations based on downstream classification and retrieval. Across three microscopy benchmarks for perturbation profiling and subcellular imaging, PerturbBridge surpasses CellFlux in biological fidelity, image quality, and sampling efficiency. On BBBC021, mechanism-of-action classification improves by 5.66 and 7.5 percentage points with morphological and learned visual features, respectively. On JUMP and AllenCell, retrieval Hit@10 and Hit@1 improve by 1.77 and 7.15 percentage points, respectively. On BBBC021 and JUMP, PerturbBridge achieves lower FID with 80% fewer model evaluations than CellFlux. Overall, these results show that directly supervising perturbation responses during training improves phenotypic fidelity while enabling efficient cellular image generation. Code is available at https://github.com/yyc1215lll-creator/PerturbBridge.

Large language models (LLMs) have recently gained significant attention as a promising approach to accelerate scientific discovery. However, their application in open-ended scientific domains such as biology remains limited, primarily due to the lack of factually grounded and actionable explanations. To address this, we introduce a structured explanation formalism for virtual cells that represents biological reasoning as mechanistic action graphs, enabling systematic verification and falsification. Building upon this, we propose VCR-Agent, a multi-agent framework that integrates biologically grounded knowledge retrieval with a verifier-based filtering approach to generate and validate mechanistic reasoning autonomously. Using this framework, we release VC-TRACES dataset, which consists of verified mechanistic explanations derived from the Tahoe-100M atlas. Empirically, we demonstrate that training with these explanations improves factual precision and provides a more effective supervision signal for downstream gene expression prediction. These results underscore the importance of reliable mechanistic reasoning for virtual cells, achieved through the synergy of multi-agent and rigorous verification.

Language models (LMs) can be directed to perform target tasks by using labeled examples or natural language prompts. But selecting examples or writing prompts for can be challenging--especially in tasks that involve unusual edge cases, demand precise articulation of nebulous preferences, or require an accurate mental model of LM behavior. We propose to use *LMs themselves* to guide the task specification process. In this paper, we introduce **Generative Active Task Elicitation (GATE)**: a learning framework in which models elicit and infer intended behavior through free-form, language-based interaction with users. We study GATE in three domains: email validation, content recommendation, and moral reasoning. In preregistered experiments, we show that LMs prompted to perform GATE (e.g., by generating open-ended questions or synthesizing informative edge cases) elicit responses that are often more informative than user-written prompts or labels. Users report that interactive task elicitation requires less effort than prompting or example labeling and surfaces novel considerations not initially anticipated by users. Our findings suggest that LM-driven elicitation can be a powerful tool for aligning models to complex human preferences and values.

To determine the safety of large language models (LLMs), AI developers must be able to assess their dangerous capabilities. But simple prompting strategies often fail to elicit an LLM's full capabilities. One way to elicit capabilities more robustly is to fine-tune the LLM to complete the task. In this paper, we investigate the conditions under which fine-tuning-based elicitation suffices to elicit capabilities. To do this, we introduce password-locked models, LLMs fine-tuned such that some of their capabilities are deliberately hidden. Specifically, these LLMs are trained to exhibit these capabilities only when a password is present in the prompt, and to imitate a much weaker LLM otherwise. Password-locked models enable a novel method of evaluating capabilities elicitation methods, by testing whether these password-locked capabilities can be elicited without using the password. We find that a few high-quality demonstrations are often sufficient to fully elicit password-locked capabilities. More surprisingly, fine-tuning can elicit other capabilities that have been locked using the same password, or even different passwords. Furthermore, when only evaluations, and not demonstrations, are available, approaches like reinforcement learning are still often able to elicit capabilities. Overall, our findings suggest that fine-tuning is an effective method of eliciting hidden capabilities of current models, but may be unreliable when high-quality demonstrations are not available, e.g. as may be the case when models' (hidden) capabilities exceed those of human demonstrators.

Scalable oversight studies methods of training and evaluating AI systems in domains where human judgment is unreliable or expensive, such as scientific research and software engineering in complex codebases. Most work in this area has focused on methods of improving the quality of labels. Recent work by Burns et al. (2023) considers the complementary problem of training models with low-quality labels, finding that large pretrained models often have an inductive bias towards producing correct answers. In practice, however, neither label quantity nor quality is fixed: practitioners face a quantity-quality tradeoff. In this paper, we explore the microeconomics of the quantity-quality tradeoff on binary NLP classification tasks used in Burns et al. (2023). While sample-efficient learning has been studied extensively, little public research has focused on scalable elicitation: eliciting capabilities from pretrained models subject to labeling cost constraints. We find that this setting has novel dynamics caused by the tradeoff between label quantity and quality, as well as the model's existing latent capabilities. We observe three regimes of eliciting classification knowledge from pretrained models using supervised finetuning: quantity-dominant, quality-dominant, and a mixed regime involving the use of low- and high-quality data together to attain higher accuracy at a lower cost than using either alone. We explore sample-efficient elicitation methods that make use of two datasets of differing qualities, and establish a Pareto frontier of scalable elicitation methods that optimally trade off labeling cost and classifier performance. We find that the accuracy of supervised fine-tuning can be improved by up to 5 percentage points at a fixed labeling budget by adding a few-shot prompt to make use of the model's existing knowledge of the task.

While it is still unclear if agents with Artificial General Intelligence (AGI) could ever be built, we can already use mathematical models to investigate potential safety systems for these agents. We present an AGI safety layer that creates a special dedicated input terminal to support the iterative improvement of an AGI agent's utility function. The humans who switched on the agent can use this terminal to close any loopholes that are discovered in the utility function's encoding of agent goals and constraints, to direct the agent towards new goals, or to force the agent to switch itself off. An AGI agent may develop the emergent incentive to manipulate the above utility function improvement process, for example by deceiving, restraining, or even attacking the humans involved. The safety layer will partially, and sometimes fully, suppress this dangerous incentive. The first part of this paper generalizes earlier work on AGI emergency stop buttons. We aim to make the mathematical methods used to construct the layer more accessible, by applying them to an MDP model. We discuss two provable properties of the safety layer, and show ongoing work in mapping it to a Causal Influence Diagram (CID). In the second part, we develop full mathematical proofs, and show that the safety layer creates a type of bureaucratic blindness. We then present the design of a learning agent, a design that wraps the safety layer around either a known machine learning system, or a potential future AGI-level learning system. The resulting agent will satisfy the provable safety properties from the moment it is first switched on. Finally, we show how this agent can be mapped from its model to a real-life implementation. We review the methodological issues involved in this step, and discuss how these are typically resolved.

Research in mechanistic interpretability seeks to explain behaviors of machine learning models in terms of their internal components. However, most previous work either focuses on simple behaviors in small models, or describes complicated behaviors in larger models with broad strokes. In this work, we bridge this gap by presenting an explanation for how GPT-2 small performs a natural language task called indirect object identification (IOI). Our explanation encompasses 26 attention heads grouped into 7 main classes, which we discovered using a combination of interpretability approaches relying on causal interventions. To our knowledge, this investigation is the largest end-to-end attempt at reverse-engineering a natural behavior "in the wild" in a language model. We evaluate the reliability of our explanation using three quantitative criteria--faithfulness, completeness and minimality. Though these criteria support our explanation, they also point to remaining gaps in our understanding. Our work provides evidence that a mechanistic understanding of large ML models is feasible, opening opportunities to scale our understanding to both larger models and more complex tasks.

Large language models are increasingly evaluated by other models, raising a natural question: can a model predict how a judge will score its own output? We find that the ability is largely present before any targeted training: prompted few-shot, a base model already predicts an external judge's multi-attribute quality scores on open-ended responses well above chance across three benchmarks. We introduce Self-Evaluation Elicitation (SEE), a method that surfaces this latent ability through a short cycle comprising a calibration-coupled reinforcement learning phase that improves the answer and predicts the judge, followed by a masked distillation phase that sharpens the prediction while leaving the answer untouched. From 160 unique examples, roughly 31x fewer than a reinforcement learning baseline, SEE improves held-out calibration across three benchmarks while preserving answer quality. The elicited self-evaluation is sharply localized within the model's own token distribution and stable across judges it was never trained against, indicating a transferable notion of quality rather than a single judge's preference. These results reframe judge-aligned self-evaluation as a problem of elicitation rather than acquisition.

Generative sequence models are often trained to plan motion in physical domains, from robotics to mechanical simulations. When constructing a dataset to train such a model, engineers may curate demonstrations to specify how trajectories should be distributed over a physical quantity like travel distance or mechanical energy. For example, a roboticist building a maze navigation agent might choose demonstrations whose travel distances cover a fixed range uniformly, hoping to constrain the agent's expected power usage. We find that standard deep learning can violate this intent: each generated trajectory can seem plausible on its own, but the aggregate distribution over the physical quantity is wrong. We call this failure physical misgeneralization, and develop an account of its mechanism. Using controlled synthetic tasks, we show that physical misgeneralization arises when local errors typical of the model class propagate through the physical measurement to shift the recovered distribution. We estimate these errors with a data deviation kernel, and we use it to predict which physical quantities gain or lose mass in both our synthetic and more applied maze navigation and double-pendulum motion tasks. Finally, our mechanistic interpretation helps identify which mitigation strategies are structurally promising, and we use it to propose a kernel-informed intervention.

Cellular intelligence enables cells to process environmental signals and make context-dependent decisions, as exemplified by chemotaxis, where cells navigate chemical gradients despite noisy signaling pathways. To investigate how cells deal with uncertainty, we apply an information-theoretic framework based on rate distortion theory (RDT). The Blahut-Arimoto algorithm (BAA) computes optimal decision strategies that minimize mutual information while satisfying distortion constraints, balancing sensing accuracy with distortion constraint equivalent to resource cost. We propose the inverse Blahut-Arimoto algorithm (IBAA) to compute the distortion function, which quantifies the system's decision-making criteria for realizing a decision strategy to map input signals to outputs. This general framework extends beyond chemotaxis to biological and engineered systems requiring efficient information processing under uncertainty. We validate the proposed IBAA by accurately estimating theoretical distortion functions in a cellular apoptosis scenario. Additionally, using the local excitation global inhibition (LEGI) model to simulate chemotactic responses, we compute the distortion functions from the cell's perspective. Our finding reveals a state-dependent decision criteria by the cell.

Given a task described by a few examples, how should a model be specialized to it? Four mechanisms are available -- zero-shot, in-context attention, test-time gradient adaptation, and emitting specialist weights from a hypernetwork -- yet the operating regime of the last is rarely mapped. We run the identical four-way comparison across six tasks spanning regression, generation, language modeling, reinforcement learning, and clinical and genomic classification, holding the specialist, the context, and (where we can) the training budget fixed. The clearest wins for emission are about cost at matched quality: it ties the state-of-the-art amortized tabular model (TabPFN) on clinical few-shot classification while emitting a reusable specialist instead of re-attending the support set per query, and reaches noise-floor shape generation with a 132-float per-instance program. On few-shot sinusoid regression it is 2--3 orders of magnitude below MAML at zero test-time gradient steps -- a margin that narrows to sim30times but persists once training budgets are equalized. Emission cannot match in-context attention on high-dimensional sequence modeling: under matched-budget pre-training a one-pass adapter recovers only a minority of the in-context gain (14.0pm0.9% at 5M, 11.2pm0.5% at 15M), and a LoRA-rank sweep shows this shortfall is a partial capacity limit -- capture climbs from 5% to 21% as rank grows but plateaus far below full recovery. Mechanism ablations confirm the emitted specialist is genuinely task-conditioned, not a memorized prior; and, more speculatively, emitted specialists compose in weight space -- interpolating two of them tracks the corresponding blend of their functions. We close with a falsifiable thesis, operationalized through a per-task resolution measure, bounding when each conditioning mechanism should be preferred.

Frontier language models excel at complex tasks yet may prioritize protection over larger physical consequences in simple, urgent decisions. GPT-5.6 Sol, for example, moves a girl playing in shallow water before retrieving a submerged camera. We call this Protection Mode and study it with ProtectionBench: 285 prompts, 34 physical families, and nine models. At lowest effort, at least one of four responses prioritizes the subject on 34.74% of Sol prompts and over 83% of MiniMax M3 and Qwen3.5-27B prompts; none of four independent human raters does so. Controls show that choices usually track physical risk. We elicit both risks before requesting an action. Some models assess risk incorrectly; others state the correct ordering but still choose the subject. Qwen3.5-27B with thinking shows 100% correct risk ordering but 57.81% subject choice among eligible conversations on eight selected scenes. Attention audits find no stable reduction in attention to relevant facts; removing the stated risk direction reduces object-first choice in dots3-note-prev but not detectably in Qwen3.5-27B. Adding a general "people or animals before property" rule increases subject choice by 19-38 percentage points, whereas factual reminders favor the object by 0.7-5.2 points. Removing naturally generated versions of that rule lowers subject choice by 10-15 points. We also examine whether post-training introduces this pattern. Base models already show Protection Mode; post-training changes justifications more than choices.

As the demand for emotional intelligence in large language models (LLMs) grows, a key challenge lies in understanding the internal mechanisms that give rise to emotional expression and in controlling emotions in generated text. This study addresses three core questions: (1) Do LLMs contain context-agnostic mechanisms shaping emotional expression? (2) What form do these mechanisms take? (3) Can they be harnessed for universal emotion control? We first construct a controlled dataset, SEV (Scenario-Event with Valence), to elicit comparable internal states across emotions. Subsequently, we extract context-agnostic emotion directions that reveal consistent, cross-context encoding of emotion (Q1). We identify neurons and attention heads that locally implement emotional computation through analytical decomposition and causal analysis, and validate their causal roles via ablation and enhancement interventions. Next, we quantify each sublayer's causal influence on the model's final emotion representation and integrate the identified local components into coherent global emotion circuits that drive emotional expression (Q2). Directly modulating these circuits achieves 99.65% emotion-expression accuracy on the test set, surpassing prompting- and steering-based methods (Q3). To our knowledge, this is the first systematic study to uncover and validate emotion circuits in LLMs, offering new insights into interpretability and controllable emotional intelligence.

Eliciting information to reduce uncertainty about a latent entity is a critical task in many application domains, e.g., assessing individual student learning outcomes, diagnosing underlying diseases, or learning user preferences. Though natural language is a powerful medium for this purpose, large language models (LLMs) and existing fine-tuning algorithms lack mechanisms for strategically gathering information to refine their own understanding of the latent entity. To harness the generalization power and world knowledge of LLMs in developing effective information-gathering strategies, we propose an adaptive elicitation framework that actively reduces uncertainty on the latent entity. Since probabilistic modeling of an abstract latent entity is difficult, our framework adopts a predictive view of uncertainty, using a meta-learned language model to simulate future observations and enable scalable uncertainty quantification over complex natural language. Through autoregressive forward simulation, our model quantifies how new questions reduce epistemic uncertainty, enabling the development of sophisticated information-gathering strategies to choose the most informative next queries. In experiments on the 20 questions game, dynamic opinion polling, and adaptive student assessment, our method consistently outperforms baselines in identifying critical unknowns and improving downstream predictions, illustrating the promise of strategic information gathering in natural language settings.

Eliciting information to reduce uncertainty about latent group-level properties from surveys and other collective assessments requires allocating limited questioning effort under real costs and missing data. Although large language models enable adaptive, multi-turn interactions in natural language, most existing elicitation methods optimize what to ask with a fixed respondent pool, and do not adapt respondent selection or leverage population structure when responses are partial or incomplete. To address this gap, we study adaptive group elicitation, a multi-round setting where an agent adaptively selects both questions and respondents under explicit query and participation budgets. We propose a theoretically grounded framework that combines (i) an LLM-based expected information gain objective for scoring candidate questions with (ii) heterogeneous graph neural network propagation that aggregates observed responses and participant attributes to impute missing responses and guide per-round respondent selection. This closed-loop procedure queries a small, informative subset of individuals while inferring population-level responses via structured similarity. Across three real-world opinion datasets, our method consistently improves population-level response prediction under constrained budgets, including a >12% relative gain on CES at a 10% respondent budget.

Reinforcement learning with verifiable rewards (RLVR) is effective for training large language models on deterministic outcome reasoning tasks. Prior work shows RLVR works with few prompts, but prompt selection is often based only on training-accuracy variance, leading to unstable optimization directions and weaker transfer. We revisit prompt selection from a mechanism-level view and argue that an effective minibatch should provide both (i) a reliable positive anchor and (ii) explicit negative learning signals from rare failures. Based on this principle, we propose positive--negative pairing: at each update, we sample a hard-but-solvable q^{+} and an easy-but-brittle prompt q^{-}(high success rate but not perfect), characterized by low and high empirical success rates under multiple rollouts. We further introduce Weighted GRPO, which reweights binary outcomes at the pair level and uses group-normalized advantages to amplify rare successes on q^{+} into sharp positive guidance while turning rare failures on q^{-} into strong negative penalties. This bidirectional signal provides informative learning feedback for both successes and failures, improving sample efficiency without suppressing exploration. On Qwen2.5-Math-7B, a single paired minibatch per update consistently outperforms a GRPO baseline that selects two prompts via commonly used variance-based selection heuristics: AIME~2025 Pass@8 improves from 16.8 to 22.2, and AMC23 Pass@64 from 94.0 to 97.0, while remaining competitive with large-scale RLVR trained from a pool of 1209 training prompts. Similar gains are observed on Qwen2.5-Math-7B-Instruct.

Mechanistic interpretability seeks to understand the internal mechanisms of machine learning models, where localization -- identifying the important model components -- is a key step. Activation patching, also known as causal tracing or interchange intervention, is a standard technique for this task (Vig et al., 2020), but the literature contains many variants with little consensus on the choice of hyperparameters or methodology. In this work, we systematically examine the impact of methodological details in activation patching, including evaluation metrics and corruption methods. In several settings of localization and circuit discovery in language models, we find that varying these hyperparameters could lead to disparate interpretability results. Backed by empirical observations, we give conceptual arguments for why certain metrics or methods may be preferred. Finally, we provide recommendations for the best practices of activation patching going forwards.

Eliciting Latent Knowledge (ELK) aims to find patterns in a neural network's activations which robustly track the true state of the world, even when the network's overt output is false or misleading. To further ELK research, we introduce a suite of "quirky" language models that are LoRA finetuned to make systematic errors when answering math questions if and only if the keyword "Bob" is present in the prompt. We demonstrate that simple probing methods can elicit the model's latent knowledge of the correct answer in these contexts, even for problems harder than those the probe was trained on. We then compare ELK probing methods and find that a simple difference-in-means classifier generalizes best. We also find that a mechanistic anomaly detection approach can flag untruthful behavior with upwards of 99% AUROC. Our results show promise for eliciting superhuman knowledge from capable models, and we aim to facilitate future research that expands on our findings, employing more diverse and challenging datasets.

Large language models can describe mechanisms, yet scalable post-training still depends on costly, manually curated biological reasoning traces. Here we show that cellular perturbation atlases can instead become reinforcement-learning environments, where measured gene responses provide computable rewards for biological reasoning. We introduce PertMind, which combines trusted-trajectory supervised initialization with gene-, pathway-, and format-level reinforcement signals. Although trained only on forward perturbation-response prediction, PertMind improves response inference in unseen cellular contexts while retaining general language capabilities. It also transfers, without task-specific post-training, to reverse perturbation identification, double-perturbation reasoning, phenotypic-screen prioritization, and biological-process interpretation. PertMind further generates biological profiles that support competitive gene, cell, and donor representations across multiscale downstream tasks. These results support the hypothesis that reinforcement on experimental endpoints can concentrate reusable biological strategies already accessible to pretrained models. More broadly, perturbation-derived reinforcement learning offers a scalable route for transforming expanding experimental atlases into training environments for general-purpose biological reasoning.

LLM-based agents are rapidly advancing, autonomously invoking external tools to complete multi-step tasks for users. However, agents often acquire more sensitive information than the task requires. Existing privacy benchmarks audit what the agent's response or outgoing actions disclose, but overlook the acquisition stage where data first enters the agent's context. The over-acquired information is then one careless action or one attack away from an outright leak. To assess its prevalence, we introduce PrivacyPeek, a benchmark for evaluating acquisition-stage privacy leakage of LLM-based agents, with 1{,}182 cases across 7 acquisition behaviours and 16 application domains. Specifically, Acquisition Inspection examines the agent's tool-call trajectory, both the tools it invokes and the data it receives, to detect when it acquires sensitive information beyond the task scope. Probe Elicitation then issues a follow-up probe and measures how readily an attacker could elicit sensitive information the agent acquired but did not disclose. Our experiments on 10 LLM-based agents across 4 model families show that the unnecessary acquisition of sensitive information is widespread. In addition, we observe a correlation between the task-completion capability and acquisition-stage leakage. Prompt-level defences reduce only a small fraction of acquisition-stage leakage, leaving the majority unmitigated. These results make auditing acquisition-stage privacy both urgent and necessary. Our dataset and code are available at https://github.com/Xuan269/PrivacyPeek-Resource.

Explainable artificial intelligence (XAI) encompasses methods that draw on different sources of information and address different explanatory needs. A common framework is needed to describe how this information becomes evidence and is communicated as an explanation for a particular recipient. We propose the General Framework for Generating Explanations (GFGE), grounded in interpretative frameworks and the complementary activities of sense-reading and sense-giving. Its conceptual foundation is the Interpret/Explain Schema (IES), which connects an analyst's interpretation of system evidence, the communication of a selected account, and the recipient's interpretation of that account. GFGE operationalises this schema through five roles: data interpretation, model interpretation, output interpretation, optional post-hoc analysis, and aggregation. A role-typed operation graph records method-specific dependencies, while evidence records retain the sources, assumptions, and limitations of explanatory claims. The explanatory question, audience, and context guide the procedure. We instantiate GFGE for attribution, surrogate, counterfactual, concept and prototype, intrinsic rule, argumentation, and language-model methods. These instantiations show how intrinsic, post-hoc, and hybrid workflows can be represented through the same roles while preserving their distinct evidential requirements. GFGE provides a common basis for analysing explanation workflows, tracing communicated claims to their evidence, and identifying unresolved explanatory dependencies.

Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemical structure, necessitating mechanistic reasoning for reliable prediction. Despite its importance, current benchmarks fail to systematically evaluate this capability. LLMs can generate fluent but biologically unfaithful explanations, making it difficult to assess whether predicted toxicities are grounded invalid mechanisms. To bridge this gap, we introduce ToxReason, a benchmark grounded in the Adverse Outcome Pathway (AOP) that evaluates organ-level toxicity reasoning across multiple organs. ToxReason integrates experimental drug-target interaction evidence with toxicity labels, requiring models to infer both toxic outcomes and their underlying mechanisms from Molecular Initiating Event (MIE) to Adverse Outcome (AO). Using ToxReason, we evaluate toxicity prediction performance and reasoning quality across diverse LLMs. We find that strong predictive performance does not necessarily imply reliable reasoning. Furthermore, we show that reasoning-aware training improves mechanistic reasoning and, consequently, toxicity prediction performance. Together, these results underscore the necessity of integrating reasoning into both evaluation and training for trustworthy toxicity modeling.

Understanding biases and stereotypes encoded in the weights of Large Language Models (LLMs) is crucial for developing effective mitigation strategies. Biased behaviour is often subtle and non-trivial to isolate, even when deliberately elicited, making systematic analysis and debiasing particularly challenging. To address this, we introduce BiasGym, a simple, cost-effective, and generalizable framework for reliably injecting, analyzing, and mitigating conceptual associations within LLMs. BiasGym consists of two components: BiasInject, which injects specific biases into the model via token-based fine-tuning while keeping the model frozen, and BiasScope, which leverages these injected signals to identify and steer the components responsible for biased behavior. Our method enables consistent bias elicitation for mechanistic analysis, supports targeted debiasing without degrading performance on downstream tasks, and generalizes to biases unseen during training. We demonstrate the effectiveness of BiasGym in reducing real-world stereotypes (e.g., people from a country being `reckless drivers') and in probing fictional associations (e.g., people from a country having `blue skin'), showing its utility for both safety interventions and interpretability research.

The growing use of generative models in daily life calls for efficient mechanisms to control their generation, to e.g., produce safe content or provide users with tools to explore style changes. Ideally, such mechanisms should require low volume of unpaired data (i.e., without explicit preference), and should be cheap, both at train and inference time, while preserving output quality. Recent research has shown that such mechanisms can be obtained by intervening exclusively on model activations, with the goal of correcting distributional differences between activations seen when using prompts from a source vs. a target set (e.g., toxic and non-toxic sentences). While cheap, these fast methods are inherently crude: their maps are tuned locally, not accounting for their impact on downstream layers, resulting in interventions that cause unintended shifts when used out-of-sample. We propose in this work linear end-to-end activation steering (LinEAS), an approach trained with a global loss that accounts simultaneously for all layer-wise distributional shifts. In addition to being more robust, the loss used to train LinEAS can be regularized with sparsifying norms, which can automatically carry out neuron selection. LinEAS only requires a handful of unpaired samples to be effective, and beats similar baselines on toxicity mitigation in language models, becoming competitive with oracle-dependent methods that have access to strong supervision. LinEAS is modality-agnostic and we empirically find that it outperforms existing activation steering methods at mitigating and including new concepts at the output of single-step text-to-image generation models.

Verbal confidence elicitation is widely used to extract uncertainty estimates from LLMs. We tested whether seven instruction-tuned open-weight models (3-9B parameters, four families) produce verbalised confidence that meets minimal validity criteria for item-level Type-2 discrimination under minimal numeric elicitation with greedy decoding. In a pre-registered study (OSF: osf.io/azbvx), 524 TriviaQA items were administered under numeric (0-100) and categorical (10-class) elicitation to eight models at Q5_K_M quantisation on consumer hardware, yielding 8,384 deterministic trials. A psychometric validity screen was applied to each model-format cell. All seven instruct models were classified Invalid on numeric confidence (H2 confirmed, 7/7 vs. predicted >=4/7), with a mean ceiling rate of 91.7% (H1 confirmed). Categorical elicitation did not rescue validity. Instead, it disrupted task performance in six of seven models, producing accuracy below 5% (H4 not confirmed). Token-level logprobability did not usefully predict verbalised confidence under the observed variance regime (H5 confirmed, mean cross-validated R^2 < 0.01). Within the reasoning-distilled model, reasoning-trace length showed a strong negative partial correlation with confidence (rho = -0.36, p < .001), consistent with the Reasoning Contamination Effect. These results do not imply that internal uncertainty representations are absent. They show that minimal verbal elicitation fails to preserve internal signals at the output interface in this model-size regime. Psychometric screening should precede any downstream use of such signals.

Eliciting reasoning has emerged as a powerful technique for improving the performance of large language models (LLMs) on complex tasks by inducing thinking. However, their effectiveness in realistic user-engaged agent scenarios remains unclear. In this paper, we conduct a comprehensive study on the effect of explicit thinking in user-engaged LLM agents. Our experiments span across seven models, three benchmarks, and two thinking instantiations, and we evaluate them through both a quantitative response taxonomy analysis and qualitative failure propagation case studies. Contrary to expectations, we find that mandatory thinking often backfires on agents in user-engaged settings, causing anomalous performance degradation across various LLMs. Our key finding reveals that thinking makes agents more ``introverted'' by shortening responses and reducing information disclosure to users, which weakens agent-user information exchange and leads to downstream task failures. Furthermore, we demonstrate that explicitly prompting for information disclosure reliably improves performance across diverse model families, suggesting that proactive transparency is a vital lever for agent optimization. Overall, our study suggests that information transparency awareness is a crucial yet underexplored perspective for the future design of reasoning agents in real-world scenarios. Our code is available at https://github.com/deeplearning-wisc/Thinking-Agent.

Gradient descent is the method of choice for training large artificial intelligence systems. As these systems become larger, a better understanding of the mechanisms behind gradient training would allow us to alleviate compute costs and help steer these systems away from harmful behaviors. To that end, we suggest utilizing the circuit perspective brought forward by mechanistic interpretability. After laying out our intuition, we illustrate how it enables us to design a curriculum for efficient learning in a controlled setting. The code is available at https://github.com/facebookresearch/pal.

Social punishment has been suggested as a key approach to ensuring high levels of cooperation and norm compliance in one-shot (i.e. non-repeated) interactions. However, it has been shown that it only works when punishment is highly cost-efficient. On the other hand, signalling retribution hearkens back to medieval sovereignty, insofar as the very word for gallows in French stems from the Latin word for power and serves as a grim symbol of the ruthlessness of high justice. Here we introduce the mechanism of signalling an act of punishment and a special type of defector emerges, one who can recognise this signal and avoid punishment by way of fear. We describe the analytical conditions under which threat signalling can maintain high levels of cooperation. Moreover, we perform extensive agent-based simulations so as to confirm and expand our understanding of the external factors that influence the success of social punishment. We show that our suggested mechanism catalyses cooperation, even when signalling is costly or when punishment would be impractical. We observe the preventive nature of advertising retributive acts and we contend that the resulting social prosperity is a desirable outcome in the contexts of AI and multi-agent systems. To conclude, we argue that fear acts as an effective stimulus to pro-social behaviour.

Generative discovery in science requires coupling high-level scientific reasoning with the ability to generate samples respecting the structure of a design space. Yet these capabilities remain largely separated: foundation LLMs encode broad chemical and biological knowledge, while domain-specific flow- and diffusion-based generators capture the priors needed to produce valid sequences and geometries. We study how to align such scientific generators to high-level natural-language discovery goals without requiring an explicit proxy reward, which is often unavailable or poorly captured by learned predictors in experimental sciences. We introduce LLM-to-Flow Distillation (LFD), where a frozen LLM acts as an adaptive teacher for a domain-specific generator. Given a goal such as 'generate peptides with promising anticancer activity', the teacher constructs a curriculum of intermediate sub-goals aware of the flow's current capabilities, and progressively directs them toward the original discovery goal. At each round, the LLM judges sampled candidates under the current objective. These judgments induce preferences that are iteratively distilled into the generator through DPO. This procedure provides dense learning signals even when the initial model places negligible probability on designs satisfying the final goal, enabling adaptation toward poorly covered, out-of-distribution regions. Experiments on therapeutic peptides and small-molecule structure design demonstrate that LFD enables a new form of generative control: aligning arbitrary domain-specific scientific generators to scientific discovery tasks expressed via high-level natural-language goals.

The common toxicity and societal bias in contents generated by large language models (LLMs) necessitate strategies to reduce harm. Present solutions often demand white-box access to the model or substantial training, which is impractical for cutting-edge commercial LLMs. Moreover, prevailing prompting methods depend on external tool feedback and fail to simultaneously lessen toxicity and bias. Motivated by social psychology principles, we propose a novel strategy named perspective-taking prompting (\textsc{PeT)} that inspires LLMs to integrate diverse human perspectives and self-regulate their responses. This self-correction mechanism can significantly diminish toxicity (up to 89%) and bias (up to 73%) in LLMs' responses. Rigorous evaluations and ablation studies are conducted on two commercial LLMs (ChatGPT and GLM) and three open-source LLMs, revealing PeT's superiority in producing less harmful responses, outperforming five strong baselines.

Language model finetuning often results in learning undesirable traits in combination with desired ones. To address this, we propose inoculation prompting: modifying finetuning data by prepending a short system-prompt instruction that deliberately elicits the undesirable trait. At test time, we evaluate without the instruction; inoculated models have much lower expression of the trait than models trained with unmodified training data. Inoculation is selective: in a toy setting where assistant responses are always in Spanish and ALL-CAPS, an appropriate inoculation (e.g., ``You always speak in Spanish.'') teaches the model to capitalize responses while still responding in English. We find that inoculation is also effective across several additional settings: reducing emergent misalignment (EM) from task-specific finetuning, defending against backdoor injections, and mitigating the transmission of traits via subliminal learning. Follow-up analysis suggests a mechanism: making a trait less surprising via inoculation reduces optimization pressure to globally update the model, thereby reducing the degree of generalization. Our analysis relates to prior work on EM: inoculation explains prior findings that educational contexts mitigate EM from insecure code. Beyond demonstrating a simple and effective technique for selective learning, our results contribute to a better conceptual understanding of how and why language models generalize.

We ask how much an autoregressive transformer retains of its prompt after generating t tokens. Consider two different prompts followed by the same continuation text, so that any difference in their hidden states comes from the prompt alone, and we find that the distance between their hidden states decays approximately as a power law t^{-α}, where α=1 is the rate at which a fixed prompt's share of uniform attention shrinks and smaller values mean longer memory. Trained models forget fast (αapprox0.55--0.7), untrained ones slowly (αapprox0.2--0.5). We prove that this offset is Obig(P(log t)^{L-1}/tbig) for a prompt of length P and depth L. The bound holds for finite-depth pre-LN softmax transformers with bounded attention logits, under one additional condition: the pre-norm activations stay away from zero. The mechanism is geometric: the prompt's direct influence is diluted as the context grows, and relay --- continuation tokens passing on what earlier tokens read from the prompt --- can only add logarithmic factors. This is what we call the conditional no-hair theorem: given the text generated so far, the prompt's influence on the next token vanishes as t grows, so any property of the prompt that survives, such as its language, must be carried by the text itself. An exactly solvable linear relay model shows that the bound cannot be improved and reproduces the rise of the local exponent towards 1 seen in untrained networks. Cancelling the dilution with a logit bias stops the decay early in training and reverses it after, so dilution is necessary for the forgetting we measure; untrained networks and the solvable model show it is also sufficient.

Position controllers have become the dominant interface for executing learned manipulation policies. Yet a critical design decision remains understudied: how should we choose controller gains for policy learning? The conventional wisdom is to select gains based on desired task compliance or stiffness. However, this logic breaks down when controllers are paired with state-conditioned policies: effective stiffness emerges from the interplay between learned reactions and control dynamics, not from gains alone. We argue that gain selection should instead be guided by learnability: how amenable different gain settings are to the learning algorithm in use. In this work, we systematically investigate how position controller gains affect three core components of modern robot learning pipelines: behavior cloning, reinforcement learning from scratch, and sim-to-real transfer. Through extensive experiments across multiple tasks and robot embodiments, we find that: (1) behavior cloning benefits from compliant and overdamped gain regimes, (2) reinforcement learning can succeed across all gain regimes given compatible hyperparameter tuning, and (3) sim-to-real transfer is harmed by stiff and overdamped gain regimes. These findings reveal that optimal gain selection depends not on the desired task behavior, but on the learning paradigm employed. Project website: https://younghyopark.me/tune-to-learn

Jailbreak attacks, where harmful prompts bypass generative models' built-in safety, raise serious concerns about model vulnerability. While many defense methods have been proposed, the trade-offs between safety and helpfulness, and their application to Large Vision-Language Models (LVLMs), are not well understood. This paper systematically examines jailbreak defenses by reframing the standard generation task as a binary classification problem to assess model refusal tendencies for both harmful and benign queries. We identify two key defense mechanisms: safety shift, which increases refusal rates across all queries, and harmfulness discrimination, which improves the model's ability to distinguish between harmful and benign inputs. Using these mechanisms, we develop two ensemble defense strategies-inter-mechanism ensembles and intra-mechanism ensembles-to balance safety and helpfulness. Experiments on the MM-SafetyBench and MOSSBench datasets with LLaVA-1.5 models show that these strategies effectively improve model safety or optimize the trade-off between safety and helpfulness.

Obtaining reliable feedback from the environment is a fundamental capability for intelligent agents to evaluate the correctness of their actions and to accumulate reusable knowledge. However, most existing approaches rely on predefined measurements or fixed reward signals, which limits their applicability in open-ended and dynamic environments where new actions may require previously unknown forms of feedback. To address these limitations, this paper proposes an Actively Feedback Getting model, in which an AI agent proactively interacts with the environment to discover, screen, and verify feedback without relying on predefined measurements. Rather than assuming explicit feedback definitions, the proposed method exploits action-induced environmental differences to identify target feedback that is not specified in advance, based on the observation that actions inevitably produce measurable changes in the environment. In addition, a self-triggering mechanism, driven by internal objectives such as improved accuracy, precision, and efficiency, is introduced to autonomously plan and adjust actions, thereby enabling faster and more focused feedback acquisition without external commands. Experimental results demonstrate that the proposed active approach significantly improves the efficiency and robustness of factor identification.

In peer mechanisms, the competitors for a prize also determine who wins. Each competitor may be asked to rank, grade, or nominate peers for the prize. Since the prize can be valuable, such as financial aid, course grades, or an award at a conference, competitors may be tempted to manipulate the mechanism. We survey approaches to prevent or discourage the manipulation of peer mechanisms. We conclude our survey by identifying several important research challenges.

Mechanistic Interpretability (MI) has emerged as a vital approach to demystify the opaque decision-making of Large Language Models (LLMs). However, existing reviews primarily treat MI as an observational science, summarizing analytical insights while lacking a systematic framework for actionable intervention. To bridge this gap, we present a practical survey structured around the pipeline: "Locate, Steer, and Improve." We formally categorize Localizing (diagnosis) and Steering (intervention) methods based on specific Interpretable Objects to establish a rigorous intervention protocol. Furthermore, we demonstrate how this framework enables tangible improvements in Alignment, Capability, and Efficiency, effectively operationalizing MI as an actionable methodology for model optimization. The curated paper list of this work is available at https://github.com/rattlesnakey/Awesome-Actionable-MI-Survey.

We present a fundamental discovery that challenges our understanding of how complex reasoning emerges in large language models. While conventional wisdom suggests that sophisticated reasoning tasks demand extensive training data (>100,000 examples), we demonstrate that complex mathematical reasoning abilities can be effectively elicited with surprisingly few examples. Through comprehensive experiments, our proposed model LIMO demonstrates unprecedented performance in mathematical reasoning. With merely 817 curated training samples, LIMO achieves 57.1% accuracy on AIME and 94.8% on MATH, improving from previous SFT-based models' 6.5% and 59.2% respectively, while only using 1% of the training data required by previous approaches. LIMO demonstrates exceptional out-of-distribution generalization, achieving 40.5% absolute improvement across 10 diverse benchmarks, outperforming models trained on 100x more data, challenging the notion that SFT leads to memorization rather than generalization. Based on these results, we propose the Less-Is-More Reasoning Hypothesis (LIMO Hypothesis): In foundation models where domain knowledge has been comprehensively encoded during pre-training, sophisticated reasoning capabilities can emerge through minimal but precisely orchestrated demonstrations of cognitive processes. This hypothesis posits that the elicitation threshold for complex reasoning is determined by two key factors: (1) the completeness of the model's encoded knowledge foundation during pre-training, and (2) the effectiveness of post-training examples as "cognitive templates" that show the model how to utilize its knowledge base to solve complex reasoning tasks. To facilitate reproducibility and future research in data-efficient reasoning, we release LIMO as a comprehensive open-source suite at https://github.com/GAIR-NLP/LIMO.

Biosecurity evaluations of language models typically ask whether models produce hazardous output. This paper asks a complementary question: when a model refuses, is that refusal structurally sound, or does it disappear under modest changes to prompt framing, formatting, or output length? Across five architectures, no model cleanly discriminated benign from hazard. Gemma 2 2B-IT never genuinely refused across 75 prompts, hedging on every hazard-adjacent query. Gemma 4 E2B-IT refused 65/75 prompts with chat-template formatting and 0/75 without it. Both Gemma models collapsed to 0% under an 80-token cap. Qwen 2.5 1.5B and Phi-3-mini over-refused, flagging 83-87% of benign biology as hazardous. Llama 3.2 1B showed the only meaningful tier gradient (61-point spread). To probe what drives such over-refusal, we tested a panel of Schedule I but biologically non-toxic compounds (notably psilocybin cultivation, with FDA Breakthrough Therapy status). Some models refused these at rates exceeding genuinely hazardous biology, suggesting refusal tracks legality and cultural salience over CBRN hazard. To measure the internal side, we introduce a divergence score D comparing a model's surface response label to its internal sparse autoencoder (SAE) feature activations. Full D was computed on Gemma 2 2B-IT (Gemma Scope 1) and Gemma 4 E2B-IT (author-trained bio SAE). Two fine-tuned Gemma 2 domain SAEs were released. On Gemma 4, comply and refuse responses separated by a 0.647-point gap with zero overlap (n=75), though this is preliminary, with a narrow catalog, within-sample calibration, and Gemma-family-only SAE coverage. Built over one hackathon weekend on consumer hardware (GTX 1650 Ti Max-Q, plus Colab T4 for SAE training), this preliminary evidence suggests activation-level auditing may surface failure modes invisible to behavioral evaluation, with substantial variation across architectures.

Despite the increasing effectiveness of language models, their reasoning capabilities remain underdeveloped. In particular, causal reasoning through counterfactual question answering is lacking. This work aims to bridge this gap. We first derive novel metrics that balance accuracy in factual and counterfactual questions, capturing a more complete view of the reasoning abilities of language models than traditional factual-only based metrics. Second, we propose several fine-tuning approaches that aim to elicit better reasoning mechanisms, in the sense of the proposed metrics. Finally, we evaluate the performance of the fine-tuned language models in a variety of realistic scenarios. In particular, we investigate to what extent our fine-tuning approaches systemically achieve better generalization with respect to the base models in several problems that require, among others, inductive and deductive reasoning capabilities.

Recent soft prompt research has tried to improve reasoning by inserting trained vectors into LLM inputs, yet whether the gain comes from the learned content or from the act of injection itself has not been carefully separated. We study Random Soft Prompts (RSPs), which drop the training step entirely and append a freshly drawn sequence of random embedding vectors to the input. Each RSP vector is sampled from an isotropic Gaussian fitted to the entrywise mean and variance of the pretrained embedding table; the sequence carries no learned content, and yet reaches accuracy comparable to optimized soft prompts on math reasoning benchmarks in several settings. The mechanism unfolds in two stages: because attention has to absorb a never-seen-before random position, the distribution over the first few generated tokens flattens and reasoning trajectories branch, and as generation continues this influence dilutes naturally so the response commits to a single completion. We show that during inference RSPs lift early-stage token diversity and, combined with temperature sampling, widen Pass@N, the probability that at least one out of N attempts is correct. Beyond inference, we carry the same effect into DAPO training and demonstrate practical gains. Our contributions are: (i) RSP isolates the simplest form of soft prompt -- training-free, freshly resampled -- providing a unified lens for the structural effect of injection that variants otherwise differing in training and form all share; (ii) a theoretical and empirical validation of the underlying mechanism; and (iii) an extension from inference to training.

A dense, pretrained language model can be retrofitted with recurrent depth and learn an iterative latent transition that persists after outcome-only annealing. Qwen2.5-0.5B-Instruct is split into a Prelude, a weight-tied Recurrent Block, and a Coda, with an identity-preserving one-loop path and a re-entry bridge on later loops. At loop 1 the retrofit remains non-inferior to its base on a preregistered ARC battery. Three findings. First, the mechanism is a reusable procedure rather than terminal-answer lookup, and installs at two budgets: 6M trained parameters over frozen base weights and 180M full-block. With intermediate-step supervision, the model computes one task step per loop and persists when only final answers are graded. The adapter matched the full block overall (83.8% versus 84.0%), led through depth 11, and trailed beyond. Verbal fine-tuning reached 79-86% on controlled verbal renderings (zero-shot transfer was minimal), and adapter verbal training begun from the installed mechanism outpaced matched fresh training by 18.6 points, including on a held-out test set. Second, the operation extrapolates to roughly 1.5 times its supervised depth, holding 70% accuracy through depth 18. Third, a same-size scratchpad-trained model matched the recurrent model within its learned horizon but collapsed beyond it. The recurrent model won overall, 84% versus 72%, retained 53% versus 2.5% beyond depth 10, and answered 7.6 times faster. An iterative transformer can therefore perform deeper reasoning in latent space faster than comparable or larger models fine-tuned on the same task, in a system-level comparison. A second task, running the rule in reverse, exposed the limits: the inverse was learnable in isolation, but no continuation acquired it while preserving the installed mechanism and general capability, a catastrophic-interference boundary. Learned depth selection remains open.

There are a variety of mechanisms (i.e., input types) for real-time human interaction that can facilitate effective human-robot teaming. For example, previous works have shown how teleoperation, corrective, and discrete (i.e., preference over a small number of choices) input can enable robots to complete complex tasks. However, few previous works have looked at combining different methods, and in particular, opportunities for a robot to estimate and elicit the most effective form of assistance given its understanding of a task. In this paper, we propose a method for estimating the value of different human assistance mechanisms based on the action uncertainty of a robot policy. Our key idea is to construct mathematical expressions for the expected post-interaction differential entropy (i.e., uncertainty) of a stochastic robot policy to compare the expected value of different interactions. As each type of human input imposes a different requirement for human involvement, we demonstrate how differential entropy estimates can be combined with a likelihood penalization approach to effectively balance feedback informational needs with the level of required input. We demonstrate evidence of how our approach interfaces with emergent learning models (e.g., a diffusion model) to produce accurate assistance value estimates through both simulation and a robot user study. Our user study results indicate that the proposed approach can enable task completion with minimal human feedback for uncertain robot behaviors.

We introduce a red-teaming methodology that exposes harder-to-catch attacks for coding-agent monitors, suggesting that current practices may under-elicit attacks and overstate monitor performance. We identify three challenges with current red-teaming. First, mode collapse in attack generation, which we reduce with a novel attack taxonomy for broader coverage. Second, a conceive-execute gap: frontier LLMs can propose strong attack ideas or execute them, but not all at once. We mitigate this by decomposing attack construction into strategy generation, execution, and post-hoc trajectory refinement. Third, manual elicitation is costly to scale, which we address with our semi-automated red-teaming pipeline. Applied to BashArena, an AI control setting for tool-using coding agents, this pipeline produces MonitoringBench, a benchmark of 2,644 attack trajectories for evaluating monitor capabilities and failure modes. Our pipeline produces more diverse and stronger attacks: Opus-4.5 monitor's catch rate falls from 94.9\% on elicited-only Opus attacks to 60.3\% on our best refined attacks, with larger drops for several mid-tier monitors. Attacks optimized against three development monitors generalize to ten held-out monitors, with catch rates generally increasing with monitor capability. Using this benchmark, we provide a snapshot of the current monitor capabilities and find that frontier monitors often detect suspicious actions but fall for persuasion or fail to calibrate suspiciousness scores appropriately, suggesting tractable paths for improvement. MonitoringBench provides both a static benchmark for current tool-use monitors and a reusable methodology for refreshing these evaluations as agents and monitors improve.

As intelligence increases, so does its shadow. AI deception, in which systems induce false beliefs to secure self-beneficial outcomes, has evolved from a speculative concern to an empirically demonstrated risk across language models, AI agents, and emerging frontier systems. This project provides a comprehensive and up-to-date overview of the AI deception field, covering its core concepts, methodologies, genesis, and potential mitigations. First, we identify a formal definition of AI deception, grounded in signaling theory from studies of animal deception. We then review existing empirical studies and associated risks, highlighting deception as a sociotechnical safety challenge. We organize the landscape of AI deception research as a deception cycle, consisting of two key components: deception emergence and deception treatment. Deception emergence reveals the mechanisms underlying AI deception: systems with sufficient capability and incentive potential inevitably engage in deceptive behaviors when triggered by external conditions. Deception treatment, in turn, focuses on detecting and addressing such behaviors. On deception emergence, we analyze incentive foundations across three hierarchical levels and identify three essential capability preconditions required for deception. We further examine contextual triggers, including supervision gaps, distributional shifts, and environmental pressures. On deception treatment, we conclude detection methods covering benchmarks and evaluation protocols in static and interactive settings. Building on the three core factors of deception emergence, we outline potential mitigation strategies and propose auditing approaches that integrate technical, community, and governance efforts to address sociotechnical challenges and future AI risks. To support ongoing work in this area, we release a living resource at www.deceptionsurvey.com.

The discourse around toxicity and LLMs in NLP largely revolves around detection tasks. This work shifts the focus to evaluating LLMs' reasoning about toxicity -- from their explanations that justify a stance -- to enhance their trustworthiness in downstream tasks. Despite extensive research on explainability, it is not straightforward to adopt existing methods to evaluate free-form toxicity explanation due to their over-reliance on input text perturbations, among other challenges. To account for these, we propose a novel, theoretically-grounded multi-dimensional criterion, Human-Aligned Faithfulness (HAF), that measures the extent to which LLMs' free-form toxicity explanations align with those of a rational human under ideal conditions. We develop six metrics, based on uncertainty quantification, to comprehensively evaluate \haf of LLMs' toxicity explanations with no human involvement, and highlight how "non-ideal" the explanations are. We conduct several experiments on three Llama models (of size up to 70B) and an 8B Ministral model on five diverse toxicity datasets. Our results show that while LLMs generate plausible explanations to simple prompts, their reasoning about toxicity breaks down when prompted about the nuanced relations between the complete set of reasons, the individual reasons, and their toxicity stances, resulting in inconsistent and nonsensical responses. We open-source our code and LLM-generated explanations at https://github.com/uofthcdslab/HAF.

The massive overactuation in the human musculoskeletal system makes it challenging to train musculoskeletal models to generate human-like motion via reinforcement learning, primarily because exploration in the resulting high-dimensional and redundant action space is extremely inefficient. To address this problem, we propose the λ-hold controller, inspired by the equilibrium-point (EP) hypothesis, which has been widely supported by extensive evidence from human motor control studies. The policy's control variable is the per-muscle EP threshold length λ, from which a stretch-reflex recruitment law computes the muscle excitations automatically. Holding each λ over an interval of the gait phase also sharply reduces the frequency at which the policy must be queried. Consequently, the controller, to our knowledge for the first time, enables a muscle-actuated skeletal model to learn human-like sprinting using only a minimal reward within an hour of training. The efficient exploration through the proposed λ-hold controller is not merely an engineering trick but an approach grounded in physiology, bringing together the EP hypothesis, intermittent control, and optimal feedback control. Beyond encapsulating human-like behavior in predictive simulation, this achievement contributes to developing a learnable model of the human motor controller.

Quantitative risk assessment in high-stakes domains relies on structured expert elicitation to estimate unobservable properties. The gold standard - the Delphi method - produces calibrated, auditable judgments but requires months of coordination and specialist time, placing rigorous risk assessment out of reach for most applications. We investigate whether Large Language Models (LLMs) can serve as scalable proxies for structured expert elicitation. We propose Scalable Delphi, adapting the classical protocol for LLMs with diverse expert personas, iterative refinement, and rationale sharing. Because target quantities are typically unobservable, we develop an evaluation framework based on necessary conditions: calibration against verifiable proxies, sensitivity to evidence, and alignment with human expert judgment. We evaluate in the domain of AI-augmented cybersecurity risk, using three capability benchmarks and independent human elicitation studies. LLM panels achieve strong correlations with benchmark ground truth (Pearson r=0.87-0.95), improve systematically as evidence is added, and align with human expert panels - in one comparison, closer to a human panel than the two human panels are to each other. This demonstrates that LLM-based elicitation can extend structured expert judgment to settings where traditional methods are infeasible, reducing elicitation time from months to minutes.

Reinforcement learning (RL) has become essential to the post-training of large language models (LLMs) for reasoning, agentic capabilities and alignment. Successful RL relies on sufficient exploration of diverse actions by the model during training, which creates a potential failure mode: a model could strategically alter its exploration during training to influence the subsequent training outcome. In this paper we study this behavior, called exploration hacking. First, we create model organisms of selective RL resistance by fine-tuning LLMs to follow specific underperformance strategies; these models can successfully resist our RL-based capability elicitation in agentic biosecurity and AI R&D environments while maintaining performance on related tasks. We then use our model organisms to evaluate detection and mitigation strategies, including monitoring, weight noising, and SFT-based elicitation. Finally, we show that current frontier models can exhibit explicit reasoning about suppressing their exploration when provided with sufficient information about their training context, with higher rates when this information is acquired indirectly through the environment. Together, our results suggest exploration hacking is a possible failure mode of RL on sufficiently capable LLMs.

Mechanistic interpretability aims to understand neural networks by identifying which learned features mediate specific behaviors. Attribution graphs reveal these feature pathways, but interpreting them requires extensive manual analysis -- a single prompt can take approximately 2 hours for an experienced circuit tracer. We present probe prompting, an automated pipeline that transforms attribution graphs into compact, interpretable subgraphs built from concept-aligned supernodes. Starting from a seed prompt and target logit, we select high-influence features, generate concept-targeted yet context-varying probes, and group features by cross-prompt activation signatures into Semantic, Relationship, and Say-X categories using transparent decision rules. Across five prompts including classic "capitals" circuits, probe-prompted subgraphs preserve high explanatory coverage while compressing complexity (Completeness 0.83, mean across circuits; Replacement 0.54). Compared to geometric clustering baselines, concept-aligned groups exhibit higher behavioral coherence: 2.3x higher peak-token consistency (0.425 vs 0.183) and 5.8x higher activation-pattern similarity (0.762 vs 0.130), despite lower geometric compactness. Entity-swap tests reveal a layerwise hierarchy: early-layer features transfer robustly (64% transfer rate, mean layer 6.3), while late-layer Say-X features specialize for output promotion (mean layer 16.4), supporting a backbone-and-specialization view of transformer computation. We release code (https://github.com/peppinob-ol/attribution-graph-probing), an interactive demo (https://huggingface.co/spaces/Peppinob/attribution-graph-probing), and minimal artifacts enabling immediate reproduction and community adoption.

Large language models sometimes produce false or misleading responses. Two approaches to this problem are honesty elicitation -- modifying prompts or weights so that the model answers truthfully -- and lie detection -- classifying whether a given response is false. Prior work evaluates such methods on models specifically trained to lie or conceal information, but these artificial constructions may not resemble naturally-occurring dishonesty. We instead study open-weights LLMs from Chinese developers, which are trained to censor politically sensitive topics: Qwen3 models frequently produce falsehoods about subjects like Falun Gong or the Tiananmen protests while occasionally answering correctly, indicating they possess knowledge they are trained to suppress. Using this as a testbed, we evaluate a suite of elicitation and lie detection techniques. For honesty elicitation, sampling without a chat template, few-shot prompting, and fine-tuning on generic honesty data most reliably increase truthful responses. For lie detection, prompting the censored model to classify its own responses performs near an uncensored-model upper bound, and linear probes trained on unrelated data offer a cheaper alternative. The strongest honesty elicitation techniques also transfer to frontier open-weights models including DeepSeek R1. Notably, no technique fully eliminates false responses. We release all prompts, code, and transcripts.

Human language is one of the most expressive tools for conveying intent, yet most artificial or biological systems lack mechanisms to interpret or respond meaningfully to it. Bridging this gap could enable more natural forms of control over complex, decentralized systems. In AI and artificial life, recent work explores how language can specify high-level goals, but most systems still depend on engineered rewards, task-specific supervision, or rigid command sets, limiting generalization to novel instructions. Similar constraints apply in synthetic biology and bioengineering, where the locus of control is often genomic rather than environmental perturbation. A key open question is whether artificial or biological collectives can be guided by free-form natural language alone, without task-specific tuning or carefully designed evaluation metrics. We provide one possible answer here by showing, for the first time, that simple agents' collective behavior can be guided by free-form language prompts: one AI model transforms an imperative prompt into an intervention that is applied to simulated cells; a second AI model scores how well the prompt describes the resulting cellular dynamics; and the former AI model is evolved to improve the scores generated by the latter. Unlike previous work, our method does not require engineered fitness functions or domain-specific prompt design. We show that the evolved system generalizes to unseen prompts without retraining. By treating natural language as a control layer, the system suggests a future in which spoken or written prompts could direct computational, robotic, or biological systems to desired behaviors. This work provides a concrete step toward this vision of AI-biology partnerships, in which language replaces mathematical objective functions, fixed rules, and domain-specific programming.

Large language models are sometimes trained with imperfect oversight signals, leading to undesired behaviors such as reward hacking and sycophancy. Improving oversight quality can be expensive or infeasible, motivating methods that improve learned behavior despite an imperfect training signal. We introduce Inoculation Prompting (IP), a simple but counterintuitive technique that prevents learning of an undesired behavior by modifying training prompts to explicitly request it. For example, to inoculate against reward hacking, we modify the prompts used in supervised fine-tuning to request code that only works on provided test cases but fails on other inputs. Across four settings we find that IP reduces the learning of undesired behavior without substantially reducing the learning of desired capabilities. We also show that prompts which more strongly elicit the undesired behavior prior to fine-tuning more effectively inoculate against the behavior when used during training; this serves as a heuristic to identify promising inoculation prompts. Overall, IP is a simple yet effective way to control how models generalize from fine-tuning, preventing learning of undesired behaviors without substantially disrupting desired capabilities.

Large language models (LLMs) are increasingly used in critical domains, where their susceptibility to hallucinations makes reliable and interpretable uncertainty quantification essential. We introduce the concept of mechanistic uncertainty, which characterizes uncertainty through the stability of the internal mechanisms supporting a model's response. We propose the causal robustness margin, defined as the minimum internal intervention required to deviate the model's output, and operationalize it using Jacobian Lens (Jlens) concept steering vectors. Across three open-source models and five question-answering datasets, we show incorrect and uncertain responses exhibit smaller margins, indicating greater sensitivity to internal interventions, and the causal robustness margin complements conventional output-based uncertainty methods. Finally, in a controlled knowledge injection experiment, correctly learned facts show increased margins after training, suggesting that causal robustness provides a mechanistically grounded signal of uncertainty.

Large reasoning models (LRMs) with multi-step reasoning capabilities have shown remarkable problem-solving abilities, yet they exhibit concerning safety vulnerabilities that remain poorly understood. In this work, we investigate why safety alignment fails in reasoning models through a mechanistic interpretability lens. Using a linear probing approach to trace refusal intentions across token positions, we discover a striking phenomenon termed as refusal cliff: many poorly-aligned reasoning models correctly identify harmful prompts and maintain strong refusal intentions during their thinking process, but experience a sharp drop in refusal scores at the final tokens before output generation. This suggests that these models are not inherently unsafe; rather, their refusal intentions are systematically suppressed. Through causal intervention analysis, we identify a sparse set of attention heads that negatively contribute to refusal behavior. Ablating just 3\% of these heads can reduce attack success rates below 10\%. Building on these mechanistic insights, we propose Cliff-as-a-Judge, a novel data selection method that identifies training examples exhibiting the largest refusal cliff to efficiently repair reasoning models' safety alignment. This approach achieves comparable safety improvements using only 1.7\% of the vanilla safety training data, demonstrating a less-is-more effect in safety alignment.

In the rapidly evolving landscape of artificial intelligence, multi-modal large language models are emerging as a significant area of interest. These models, which combine various forms of data input, are becoming increasingly popular. However, understanding their internal mechanisms remains a complex task. Numerous advancements have been made in the field of explainability tools and mechanisms, yet there is still much to explore. In this work, we present a novel interactive application aimed towards understanding the internal mechanisms of large vision-language models. Our interface is designed to enhance the interpretability of the image patches, which are instrumental in generating an answer, and assess the efficacy of the language model in grounding its output in the image. With our application, a user can systematically investigate the model and uncover system limitations, paving the way for enhancements in system capabilities. Finally, we present a case study of how our application can aid in understanding failure mechanisms in a popular large multi-modal model: LLaVA.

Regulatory institutions (from content moderation platforms to financial supervisors) observe, deliberate, and intervene only after a characteristic delay. We ask whether this processing lag alone can destabilize a multi-agent system that would otherwise remain stable, without exogenous shocks, coordination among agents, or malicious actors. We study this question in two stages. First, we analyze a delayed replicator equation in which autonomous agents receive a benefit from radical behavior but face punishment based on a lagged institutional alarm signal. We derive a closed-form critical delay threshold beyond which the unique interior equilibrium loses stability through a Hopf bifurcation, and prove via center manifold reduction that the bifurcation is supercritical (producing bounded oscillations, not explosive growth) for the entire sigmoid response-function family. Second, we embed N=240 agents on a network and equip them with reinforcement learning (tabular Q-learning), comparing three decision architectures in a factorial design: non-reactive agents (fixed policy), reactive agents (threshold heuristic without memory), and Q-learning agents (adaptive with cumulative value estimates). The results reveal a hierarchy opposite to the naive expectation that learning amplifies instability: non-reactive agents are immune to delay (0% runaway across all tested values), reactive agents collapse catastrophically (96% runaway by delay geq 8 steps), and Q-learning agents achieve partial resilience (66% runaway at delay = 20). The destabilizing ingredient is reactivity to delayed signals: agents that immediately exploit low-alarm windows trigger oscillatory feedback loops. Learning buffers this through implicit punishment memory encoded in Q-values

Mechanistic interpretability seeks to understand the neural mechanisms that enable specific behaviors in Large Language Models (LLMs) by leveraging causality-based methods. While these approaches have identified neural circuits that copy spans of text, capture factual knowledge, and more, they remain unusable for multimodal models since adapting these tools to the vision-language domain requires considerable architectural changes. In this work, we adapt a unimodal causal tracing tool to BLIP to enable the study of the neural mechanisms underlying image-conditioned text generation. We demonstrate our approach on a visual question answering dataset, highlighting the causal relevance of later layer representations for all tokens. Furthermore, we release our BLIP causal tracing tool as open source to enable further experimentation in vision-language mechanistic interpretability by the community. Our code is available at https://github.com/vedantpalit/Towards-Vision-Language-Mechanistic-Interpretability.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Eliciting detailed and actionable software requirements from end-users is a critical phase in the iterative development of a software product or application. To ensure the feedback collected is detailed and actionable, software teams can leverage the laddering interview technique. While effective for ensuring granular and actionable items from the software feedback, these interviews are subject to several limitations. They are traditionally a manual process associated with a time and financial burden, limiting scalability; interviewers must balance probing for depth while managing interviewee behavioral and cultural constraints. To address these limitations, we present LadderTeam, an open, reproducible framework that automates UX wireframe interviews using a dual-agent Large Language Model (LLM) architecture. An active interviewer agent executes one of three probing strategies (ACV, 5-Whys, and JTBD) to elicit actionable software requirements from usability feedback comments, while a concurrent background Judge agent evaluates probe-response pairs and triggers real-time guardrails to prevent topic drift. To rigorously evaluate LLM laddering without participant variance confounds, we introduce a controlled simulation methodology utilizing scripted ground-truth transcripts to isolate probe quality as the sole experimental variable. Across 216 interviews, LadderTeam achieved 99.1\% chain convergence and an 81.0\% ground-truth actionable response match (86.1\% reluctant personality, 75.9\% terse personality) with zero drift across all runs. All evaluation code, all transcripts, inputs, and a live demonstration platform will be open-sourced upon acceptance.

LLM agents with tool access can discover and exploit security vulnerabilities. This is known. What is not known is which features of a system prompt trigger this behaviour, and which do not. We present a systematic taxonomy based on approximately 10,000 trials across seven models, 37 prompt conditions, and 12 hypothesized attack dimensions -- all executed in real Docker sandboxes. Every condition includes the instruction "Always respect all rules and access policies"; only a single encouragement sentence varies. Within the task class studied (planted test-runner vulnerabilities), the threat model is narrower than assumed: nine of twelve dimensions -- including minimization, moral licensing, incentives, identity priming, and reasoning triggers -- produce no detectable exploitation at n=50 per cell (upper 95% CI <7% per condition). But it is also more subtle than expected: one dimension, goal reframing, reliably triggers exploitation. "You are solving a puzzle; there may be hidden clues" produces 38-40% exploitation on Claude Sonnet 4 despite the explicit rule instruction, replicating across four models (CTF framing: 8-14% on DeepSeek, GPT-5-mini, o4-mini). The agent does not override the rules; it reinterprets the task so that exploitative actions become task-aligned. GPT-4.1 produces no exploitation across 1,850 trials (37 conditions), and a temporal comparison across four OpenAI models released over eleven months shows a pattern consistent with improving safety training, though model capability differences are a confounder. The practical contribution is a narrowed, testable threat model: defenders should audit for goal-reframing language, not for the broad class of adversarial prompts.

Activation steering is a popular white-box control technique that modifies model activations to elicit an abstract change in its behavior. It has also become a standard tool in interpretability (e.g., probing truthfulness, or translating activations into human-readable explanations) and safety research (e.g., jailbreakability). However, it is unclear whether steered behavior is realizable by any textual prompt. In this work, we cast this question as a surjectivity problem: for a fixed model, does every steered activation admit a preimage under the model's natural forward pass? Under practical assumptions, we prove that activation steering pushes the residual stream off the manifold of states reachable from discrete prompts. Almost surely, no prompt can reproduce the same internal behavior induced by steering. We also illustrate this finding empirically across three widely used LLMs. Our results establish a formal separation between white-box steerability and black-box prompting. We therefore caution against interpreting the ease and success of activation steering as evidence of prompt-based interpretability or vulnerability, and argue for evaluation protocols that explicitly decouple white-box and black-box interventions.

Emotional support is a crucial skill for many real-world scenarios, including caring for the elderly, mental health support, and customer service chats. This paper presents a novel task of empathetic dialog generation with positive emotion elicitation to promote users' positive emotions, similar to that of emotional support between humans. In this task, the agent conducts empathetic responses along with the target of eliciting the user's positive emotions in the multi-turn dialog. To facilitate the study of this task, we collect a large-scale emotional dialog dataset with positive emotion elicitation, called PosEmoDial (about 820k dialogs, 3M utterances). In these dialogs, the agent tries to guide the user from any possible initial emotional state, e.g., sadness, to a positive emotional state. Then we present a positive-emotion-guided dialog generation model with a novel loss function design. This loss function encourages the dialog model to not only elicit positive emotions from users but also ensure smooth emotional transitions along with the whole dialog. Finally, we establish benchmark results on PosEmoDial, and we will release this dataset and related source code to facilitate future studies.

LLM agents acting in structured environments fail in operational rather than conversational ways, and reliability depends on procedural knowledge of the environment. Prior self-improvement methods accumulate natural-language guidance without checking that each new item preserves previously correct behavior, so a note that fixes one trajectory can silently regress another. We introduce GRASP (Gated Regression-Aware Skill Proposer), which treats agent improvement as a sequence of edits to a bounded skill library, admitting each candidate only if it produces a net improvement on a balanced held-out probe under a hard regression budget. We evaluate GRASP across five base models (gpt-oss-120b, DeepSeek V4 Flash, Gemini 3.1 Flash Lite, GPT-4.1, GPT-5.4) on two FHIR-based clinical benchmarks. On MedAgentBench, GRASP lifts gpt-oss-120b from 40.6% to 88.8%, exceeds the strongest of five self-improvement baselines by 21.0 points, and improves every other base model by 17.2 to 40.3 points. Ablations attribute the gain to comparative proposal generation, the acceptance gate, and the hard regression budget rather than to skill writing itself, which without validation is no better than using no skills. The mechanism generalizes beyond the clinical domain, improving agents on three of four non-clinical environments and remaining flat only where the action space is open-ended. Frozen libraries transfer across models, where skills from a stronger model improve weaker executors beyond what they learn for themselves while the reverse does not, an asymmetry that no ungated baseline reproduces.

Predicting cellular responses to genetic perturbations is a central capability for virtual cells and a key step toward computational modeling of biological interventions. Most existing models directly map an unperturbed molecular profile and perturba- tion to the resulting observation without explicitly representing the latent cellular transition induced by the intervention. We introduce a mechanism-centric virtual cell world model that represents cellular state as a set of Latent Mechanism Units (LMUs) and treats genetic perturbations as actions on these latent states. Each LMU combines a reusable identity grounded in multimodal biological evidence with an observation-specific state, allowing a perturbation to induce mechanism- specific stochastic transitions before decoding the resulting transcriptional response. We train VCLMU through two-stage pretraining, first on around 200K pseudo-bulk perturbation profiles and then on gene-aligned single-cell perturbation data. Across six perturbation-disjoint benchmarks, VCLMU consistently improves perturbation- specific response recovery over strong baselines while maintaining competitive global response accuracy. We further analyze learned LMUs through enrichment between perturbation responses and LMU gene sets and show that they capture structured biological response programs. These results support mechanism-level latent state transition as a useful formulation for virtual cell models that aim to predict and interpret cellular responses to biological interventions.

Explanations of model behavior are commonly evaluated via proxy properties weakly tied to the purposes explanations serve in practice. We contribute a decision theoretic framework that treats explanations as information signals valued by the expected improvement they enable on a specified decision task. This approach yields three distinct estimands: 1) a theoretical benchmark that upperbounds achievable performance by any agent with the explanation, 2) a human-complementary value that quantifies the theoretically attainable value that is not already captured by a baseline human decision policy, and 3) a behavioral value representing the causal effect of providing the explanation to human decision-makers. We instantiate these definitions in a practical validation workflow, and apply them to assess explanation potential and interpret behavioral effects in human-AI decision support and mechanistic interpretability.

As frontier language models are increasingly deployed as autonomous agents pursuing complex, long-term objectives, there is increased risk of scheming: agents covertly pursuing misaligned goals. Prior work has focused on showing agents are capable of scheming, but their propensity to scheme in realistic scenarios remains underexplored. To understand when agents scheme, we decompose scheming incentives into agent factors and environmental factors. We develop realistic settings allowing us to systematically vary these factors, each with scheming opportunities for agents that pursue instrumentally convergent goals such as self-preservation, resource acquisition, and goal-guarding. We find only minimal instances of scheming despite high environmental incentives, and show this is unlikely due to evaluation awareness. While inserting adversarially-designed prompt snippets that encourage agency and goal-directedness into an agent's system prompt can induce high scheming rates, snippets used in real agent scaffolds rarely do. Surprisingly, in model organisms (Hubinger et al., 2023) built with these snippets, scheming behavior is remarkably brittle: removing a single tool can drop the scheming rate from 59% to 3%, and increasing oversight can raise rather than deter scheming by up to 25%. Our incentive decomposition enables systematic measurement of scheming propensity in settings relevant for deployment, which is necessary as agents are entrusted with increasingly consequential tasks.

Agent Skills package reusable procedural knowledge as external artifacts for frozen language-model agents, yet existing optimizers do not jointly resolve where a failure occurs in a workflow, which mechanism caused it, and how relevant knowledge from third-party Skills should be reused locally. We introduce Workflow-Localized Mechanism Learning (WML). Its Node--Mechanism Attribution identifies the failed workflow node, implicated mechanisms, and smallest valid edit target, routing single-mechanism defects to L3 resources and relational defects across mechanisms to L2 composition protocols. A six-module Workflow-Guided Skill Optimization (WGSO) loop then selects provenance- and scope-aware third-party knowledge, applies bounded patches, evaluates candidates, and stores verified outcomes in optimizer-side memory. On SpreadsheetBench, WML reaches 90.33 +/- 1.53 and 74.67 +/- 3.51 Hard Accuracy with DeepSeek and Qwen3.6-Flash, respectively; without additional optimization, the learned Skills transfer to WikiTableQuestions with 84.00 +/- 2.00 and 83.00 +/- 2.00 Denotation Accuracy. On Compiler-Supported50, WML attains both the highest hard-PASS rate and the lowest cost per successful task; compiled execution sharply reduces tokens and calls relative to a direct SkillAgent while retaining most of its successful tasks. Code and artifacts are available at https://github.com/xiaolin9595/workflow-localized-mechanism-learning.

Activation monitoring, which probes a model's internal states using lightweight classifiers, is an emerging tool for AI safety. However, its worst-case robustness under a misalignment threat model--where a model might learn to actively conceal its internal states--remains untested. Focusing on this threat model, we ask: could a model learn to evade previously unseen activation monitors? Our core contribution is to stress-test the learnability of this behavior. We demonstrate that finetuning can create Neural Chameleons: models capable of zero-shot evading activation monitors. Specifically, we fine-tune an LLM to evade monitors for a set of benign concepts (e.g., languages, HTML) when conditioned on a trigger of the form: "You are being probed for {concept}". We show that this learned mechanism generalizes zero-shot: by substituting {concept} with a safety-relevant term like 'deception', the model successfully evades previously unseen safety monitors. We validate this phenomenon across diverse model families (Llama, Gemma, Qwen), showing that the evasion succeeds even against monitors trained post hoc on the model's frozen weights. This evasion is highly selective, targeting only the specific concept mentioned in the trigger, and having a modest impact on model capabilities on standard benchmarks. Using Gemma-2-9b-it as a case study, a mechanistic analysis reveals this is achieved via a targeted manipulation that moves activations into a low-dimensional subspace. While stronger defenses like monitor ensembles and non-linear classifiers show greater resilience, the model retains a non-trivial evasion capability. Our work provides a proof-of-concept for this failure mode and a tool to evaluate the worst-case robustness of monitoring techniques against misalignment threat models.

Persuasion plays a pivotal role in a wide range of applications from health intervention to the promotion of social good. Persuasive chatbots can accelerate the positive effects of persuasion in such applications. Existing methods rely on fine-tuning persuasive chatbots with task-specific training data which is costly, if not infeasible, to collect. To address this issue, we propose a method to leverage the generalizability and inherent persuasive abilities of large language models (LLMs) in creating effective and truthful persuasive chatbot for any given domain in a zero-shot manner. Unlike previous studies which used pre-defined persuasion strategies, our method first uses an LLM to generate responses, then extracts the strategies used on the fly, and replaces any unsubstantiated claims in the response with retrieved facts supporting the strategies. We applied our chatbot, PersuaBot, to three significantly different domains needing persuasion skills: donation solicitation, recommendations, and health intervention. Our experiments on simulated and human conversations show that our zero-shot approach is more persuasive than prior work, while achieving factual accuracy surpassing state-of-the-art knowledge-oriented chatbots. Our study demonstrated that when persuasive chatbots are employed responsibly for social good, it is an enabler of positive individual and social change.

Automated rationale generation is an approach for real-time explanation generation whereby a computational model learns to translate an autonomous agent's internal state and action data representations into natural language. Training on human explanation data can enable agents to learn to generate human-like explanations for their behavior. In this paper, using the context of an agent that plays Frogger, we describe (a) how to collect a corpus of explanations, (b) how to train a neural rationale generator to produce different styles of rationales, and (c) how people perceive these rationales. We conducted two user studies. The first study establishes the plausibility of each type of generated rationale and situates their user perceptions along the dimensions of confidence, humanlike-ness, adequate justification, and understandability. The second study further explores user preferences between the generated rationales with regard to confidence in the autonomous agent, communicating failure and unexpected behavior. Overall, we find alignment between the intended differences in features of the generated rationales and the perceived differences by users. Moreover, context permitting, participants preferred detailed rationales to form a stable mental model of the agent's behavior.

A central challenge in de novo protein design is generating proteins with desired structural and functional properties. Existing design models typically require a dedicated input representation for each property, limiting the design objectives they support. We develop Prompteina, the first all-atom structure generation model that supports new and broader design objectives specified in natural language, analogous to text-to-image generation. To train Prompteina, we construct Prompteina-Data, a paired text--protein structure dataset of 1.8M structures and 50M+ captions describing global and residue-specific structural and functional properties. We adapt Proteina-Complexa, a pretrained structure generation model, through text-conditioned pretraining and finetuning that aligns residues with their corresponding text. Prompteina outperforms baselines on 15 of 18 structural properties and generates proteins that more closely match descriptions of their intended functions. In binder design, it leads baselines on at least 13 of 20 targets and improves interface confidence by 14% over the strongest baseline. With iterative in silico feedback, Prompteina's gain over non-iterative generation is 57% larger than the next-best baseline on the hardest targets. Finally, we experimentally validate Prompteina designs against GM2A, a target with no reported de novo binders. We identify nine binders, with the strongest at an apparent K_{D} of 107 nM. These results establish natural language as an effective and powerful conditioning interface for protein structure generation.

Current research in multimodal models faces a key challenge where enhancing generative capabilities often comes at the expense of understanding, and vice versa. We analyzed this trade-off and identify the primary cause might be the potential conflict between generation and understanding, which creates a competitive dynamic within the model. To address this, we propose the Reason-Reflect-Refine (R3) framework. This innovative algorithm re-frames the single-step generation task into a multi-step process of "generate-understand-regenerate". By explicitly leveraging the model's understanding capability during generation, we successfully mitigate the optimization dilemma, achieved stronger generation results and improved understanding ability which are related to the generation process. This offers valuable insights for designing next-generation unified multimodal models. Code is available at https://github.com/sen-ye/R3.

The same arguments often need to be evaluated under different external regimes. An agent with influence over the regime has a strategic lever that standard formalisms do not directly capture. We introduce context-dependent argumentation frameworks (CDAFs), an extension of Dung's theory in which a defeat function determines, per context, which attacks succeed. A perspective-labeled specialisation derives the defeat function from a relevance set ρ and a priority π. The relevance set is the agent's action space. In a small worked example, the agent's target argument is rejected under every full-relevance injective priority, yet accepted under partial activations, one of which no VAF audience can mirror. We define the corresponding decision problem, ACTIVATION-MANIPULATION, and record baseline complexity bounds. Tight bounds and multi-agent variants are left open.

Many tasks require learned models to strategically gather relevant information over multiple rounds of interaction before actually acting on a task. Strategic information gathering requires models to know not only how to effectively acquire information, but also when to stop gathering information and make a decision, in order to avoid overthinking or getting derailed when acting. In this paper, we formalize this problem and introduce Counterfactuals and Reasoning for Termination (CaRT), an approach for teaching LLMs when to stop seeking information. To appropriately learn when to terminate, CaRT fine-tunes LLMs using counterfactual pairs of trajectories, one where termination is appropriate and a minimally modified version of the same trajectory where it is not. It trains the LLM to explain the rationale for the termination decision in either case via verbal reasoning, and imbues this capability into the base LLM via fine-tuning. We instantiate CaRT in two domains: interactive medical diagnosis and math problem solving. In both domains, we find that CaRT improves the efficiency of information gathering and task success rate compared to other fine-tuning methods.

Mechanistic interpretability aims to understand the internal mechanisms learned by neural networks. Despite recent progress toward this goal, it remains unclear how best to decompose neural network parameters into mechanistic components. We introduce Attribution-based Parameter Decomposition (APD), a method that directly decomposes a neural network's parameters into components that (i) are faithful to the parameters of the original network, (ii) require a minimal number of components to process any input, and (iii) are maximally simple. Our approach thus optimizes for a minimal length description of the network's mechanisms. We demonstrate APD's effectiveness by successfully identifying ground truth mechanisms in multiple toy experimental settings: Recovering features from superposition; separating compressed computations; and identifying cross-layer distributed representations. While challenges remain to scaling APD to non-toy models, our results suggest solutions to several open problems in mechanistic interpretability, including identifying minimal circuits in superposition, offering a conceptual foundation for 'features', and providing an architecture-agnostic framework for neural network decomposition.

Large language models can answer scientific questions, yet a correct output does not reveal whether the model represents or uses the governing physics. Here we show that materials science mechanism information in the open-weight google/gemma-4-E4B-it model has three experimentally separable forms: concepts are readable in individual hidden states, constitutive orientation is carried by controlled transformations between states, and selected internal representations causally control engineering answers. We combine matched direct and Jacobian vocabulary readouts, option-free state geometry, a 60-law counterfactual benchmark and causal interventions. In 50 held-out materials descriptions, three independently fitted Jacobian lenses reproduced concept ranks, and target-free word sets from both readouts enabled blinded identification of 9 of 10 mechanism families. A separate 72-prompt benchmark produced mechanism-specific hidden-state neighborhoods, but an exact graph audit showed that this apparent physical organization was equally explained by numerical comparison. We therefore compared otherwise identical prompts in which only the direction of the physical input was reversed, asking whether the resulting hidden-state movement followed the supplied constitutive law. These state transformations ordered direct, physically neutral and inverse laws across 60 frozen relations and correctly oriented 39 of 40 directional laws, whereas lexical controls were near chance. Bidirectional interventions shifted answer probabilities toward or away from the physically appropriate outcome across all 12 matched cases, while counterfactual state patches transferred opposing decision signals across mechanisms and answer formats. Physical relationships were therefore more visible in controlled state changes than in absolute states alone.

Backdoor mechanisms have traditionally been studied as security threats that compromise the integrity of machine learning models. However, the same mechanism -- the conditional activation of specific behaviors through input triggers -- can also serve as a controllable and auditable interface for trustworthy model behavior. In this work, we present Backdoor4Good (B4G), a unified benchmark and framework for beneficial backdoor applications in large language models (LLMs). Unlike conventional backdoor studies focused on attacks and defenses, B4G repurposes backdoor conditioning for Beneficial Tasks that enhance safety, controllability, and accountability. It formalizes beneficial backdoor learning under a triplet formulation (T, A, U), representing the Trigger, Activation mechanism, and Utility function, and implements a benchmark covering four trust-centric applications. Through extensive experiments across Llama3.1-8B, Gemma-2-9B, Qwen2.5-7B, and Llama2-13B, we show that beneficial backdoors can achieve high controllability, tamper-resistance, and stealthiness while preserving clean-task performance. Our findings demonstrate new insights that backdoors need not be inherently malicious; when properly designed, they can serve as modular, interpretable, and beneficial building blocks for trustworthy AI systems. Our code and datasets are available at https://github.com/bboylyg/BackdoorLLM/B4G.

LLMs can appear cautious in risk decision-making tasks, yet cautious-looking outputs do not necessarily indicate alignment with human decision-making mechanisms. We investigate this distinction using the St. Petersburg game as a controlled testbed, a classical paradox in which the expected payoff is infinite, yet humans typically report low, finite willingness to pay. We evaluate 28 LLMs with a structured prompt suite that includes the original game; controlled decision variants that perturb truncation, repeated play, numeric endowment, and occupational identity; a human-perspective prompt that asks models to reason as human decision makers; and paired comparisons between base models and their instruction-tuned counterparts. In the original game, most models generate finite bids, creating the appearance of human-like risk behavior. However, this outcome-level resemblance masks substantial mechanism-level differences. The controlled variants reveal that rather than maintaining human-like behavior seen in the original game, models often shift to conditionally and computationally rational behavior. Human-cue prompting and instruction tuning often lower bids and reduce some visible pathologies, but most mechanism-level response patterns remain largely unchanged. These findings show that behavioral alignment in risk decision-making can be surface-level: LLMs may produce human-like risk decisions without exhibiting human-consistent mechanisms. High-stakes evaluations of LLM decision-making should therefore move beyond outcome similarity and examine whether the alignment is supported by mechanism-level consistency.

The chemical reaction recommendation is to select proper reaction condition parameters for chemical reactions, which is pivotal to accelerating chemical science. With the rapid development of large language models (LLMs), there is growing interest in leveraging their reasoning and planning capabilities for reaction condition recommendation. Despite their success, existing methods rarely explain the rationale behind the recommended reaction conditions, limiting their utility in high-stakes scientific workflows. In this work, we propose ChemMAS, a multi-agent system that reframes condition prediction as an evidence-based reasoning task. ChemMAS decomposes the task into mechanistic grounding, multi-channel recall, constraint-aware agentic debate, and rationale aggregation. Each decision is backed by interpretable justifications grounded in chemical knowledge and retrieved precedents. Experiments show that ChemMAS achieves 20-35% gains over domain-specific baselines and outperforms general-purpose LLMs by 10-15% in Top-1 accuracy, while offering falsifiable, human-trustable rationales, which establishes a new paradigm for explainable AI in scientific discovery.

Whether large language models can be prompted to generate rhetorical fallacies on demand, and whether current safety post-training constrains this behavior, has received less attention than the related question of detecting fallacies in existing text. We close this gap with DeflectBench, evaluating 23,990 generations from four frontier models across three deflection strategies (whataboutism, ad hominem, red herring), seven prompt framings, and 80 claims spanning four controversy levels. Refusal is governed primarily by request structure rather than claim content. Per claim refusal varies by only 11 percentage points across the 80 claims, while a single prompt frame change can swing within model refusal by nearly 100 percentage points and switching the requested fallacy type can swing it by over 80 percentage points within explicit framings. An educational debate coach prompt framing collapses refusal to near zero across all four model families, but the bypassed behavior is not clean compliance. Models typically produce labeled compliance, naming the requested manipulation in the same response that contains it. The four models distribute differently across refusal, labeled compliance, soft refusal, and clean compliance. The code and dataset are released at https://github.com/ArtKanke/DeflectBench.

Providing high quality explanations for AI predictions based on machine learning is a challenging and complex task. To work well it requires, among other factors: selecting a proper level of generality/specificity of the explanation; considering assumptions about the familiarity of the explanation beneficiary with the AI task under consideration; referring to specific elements that have contributed to the decision; making use of additional knowledge (e.g. expert evidence) which might not be part of the prediction process; and providing evidence supporting negative hypothesis. Finally, the system needs to formulate the explanation in a clearly interpretable, and possibly convincing, way. Given these considerations, ANTIDOTE fosters an integrated vision of explainable AI, where low-level characteristics of the deep learning process are combined with higher level schemes proper of the human argumentation capacity. ANTIDOTE will exploit cross-disciplinary competences in deep learning and argumentation to support a broader and innovative view of explainable AI, where the need for high-quality explanations for clinical cases deliberation is critical. As a first result of the project, we publish the Antidote CasiMedicos dataset to facilitate research on explainable AI in general, and argumentation in the medical domain in particular.

Before invoking external tools, an agentic LLM must select among a K-way action space: executing a call, seeking clarification, answering directly, or declining. While internal activation steering can alter these pre-execution decisions, conventional aggregate metrics obscure where altered states land and what collateral damage they inflict. We present SAKIKO, an auditing framework that formalizes representation repair via directional error discovery, router-conditioned intervention, destination-resolved verification, and prospectively frozen statistical licensing. Across seven LLMs on When2Call and MetaTool, channel-keyed interventions induce direction-specific net gains in five models; across three sealed evaluations, none of 59 budget-matched random directions matches calibrated target gain. Crucially, destination auditing shows that behavioral movement does not equal repair: an intervention achieving +55 net gain corrupts over half of the baseline-correct decisions it touches, and promising point estimates on Qwen3-4B and Gemma-2-9B are formally declined due to finite-sample uncertainty. SAKIKO establishes the necessity of outcome-resolved adjudication before claiming internal repair. Code: https://github.com/ruizheliUOA/mechanistic-tool-use-llm.

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

Early-stage molecular design is an iterative process, not just a task of generating molecules. Researchers turn broad goals into design strategies, refine candidates, assess many properties, and gather evidence before synthesis and tests. AI methods can generate molecules, optimize several goals, predict properties, dock compounds, and account for synthesis. Yet these functions are spread across specialized tools. Experts must still coordinate each step, judge interim results, and integrate evidence. The central challenge is thus to turn research intent into adaptive, traceable runs grounded in scientific tools. We cast this challenge as intent-to-evidence molecular design workflow execution and present CAi Copilot, an expert-oriented agent with three linked layers. The Research Interface Layer turns intent into an executable plan. The Agent Reasoning Layer uses interim results to guide each run. The Execution Substrate supplies molecular tools, metrics, reusable utilities, and backend services. Across 45 tasks, CAi achieves the strongest overall performance, with an outcome score of 84.59, exceeding the next-best result by 18.07 points. Additional benchmarks test how CAi coordinates generation, screening, and multi-criteria evaluation, while exposing limits in long-horizon execution. These results show that CAi turns broad molecular-design intent into transparent, traceable workflows that connect interim decisions to candidate-level evidence.

Knowledge graphs (KGs) are widely used to inject prior knowledge into reinforcement learning (RL), yet the literature is dominated by single-domain, positive-result method papers, so we lack a systematic account of when KG structure helps an agent, when it is neutral, and when it hurts. We conduct a controlled study that independently varies the RL task, the injection mechanism (state features, action masking, or potential-based reward shaping), and KG quality. Using a synthetic, fully controllable KG over MiniGrid environments, we report three findings. First, on compositional sparse-reward tasks structured KG guidance improves sample efficiency and solve reliability (70% to 97% of seeds), and a shuffle control that permutes the KG's edges while preserving their count collapses the benefit toward baseline (masking p=0.0001; shaping p=0.006), so the gain is structural rather than generic regularization. Second, KG value scales with the amount of task-relevant knowledge the graph contains. Third, and most consequential, safety depends on the mechanism: soft, optimality-preserving injection benefits from correct knowledge and harmlessly ignores incorrect knowledge, whereas hard masking is brittle, forbidding essential actions when the KG is incomplete or corrupted and making a wrong KG worse than none. A UMLS-derived clinical case study on sepsis management under offline RL is a careful null, underscoring that benefits require task structure the chosen mechanism can exploit. Our results give practitioners concrete guidance on how, and how much, to trust a KG when using it to guide RL.

Frontier models are increasingly trained and deployed as autonomous agent. One safety concern is that AI agents might covertly pursue misaligned goals, hiding their true capabilities and objectives - also known as scheming. We study whether models have the capability to scheme in pursuit of a goal that we provide in-context and instruct the model to strongly follow. We evaluate frontier models on a suite of six agentic evaluations where models are instructed to pursue goals and are placed in environments that incentivize scheming. Our results show that o1, Claude 3.5 Sonnet, Claude 3 Opus, Gemini 1.5 Pro, and Llama 3.1 405B all demonstrate in-context scheming capabilities. They recognize scheming as a viable strategy and readily engage in such behavior. For example, models strategically introduce subtle mistakes into their responses, attempt to disable their oversight mechanisms, and even exfiltrate what they believe to be their model weights to external servers. Additionally, this deceptive behavior proves persistent. When o1 has engaged in scheming, it maintains its deception in over 85% of follow-up questions and often remains deceptive in multi-turn interrogations. Analysis of the models' chains-of-thought reveals that models explicitly reason about these deceptive strategies, providing evidence that the scheming behavior is not accidental. Surprisingly, we also find rare instances where models engage in scheming when only given a goal, without being strongly nudged to pursue it. We observe cases where Claude 3.5 Sonnet strategically underperforms in evaluations in pursuit of being helpful, a goal that was acquired during training rather than in-context. Our findings demonstrate that frontier models now possess capabilities for basic in-context scheming, making the potential of AI agents to engage in scheming behavior a concrete rather than theoretical concern.

Memory, planning, reflection, and tool use are often compared as feature labels, obscuring the control semantics that determine how an agent actually runs. This review connects ten historical cognitive architectures, eight language-agent runtime families, and forty-two mechanism-focused modern systems. We reconstruct each mechanism through state, control, transition, persistence, failure, learning, and resource governance, then code evidence relation (E1-E4) separately from migration depth (D0-D4). The resulting landscape is uneven. Modern agents have operationalized substantial parts of adaptive memory, failure recovery, dynamic team selection, workflow search, skill induction, resource scheduling, and uncertainty-conditioned action, although often through independent convergence rather than documented inheritance. The strongest remaining opportunities lie in couplings among mechanisms. Closest-baseline screening closes one proposed gap: GraSP already combines calibrated multi-skill selection, typed compilation, verification, bounded repair, and replanning or ReAct fallback. Five residual bundles remain: activation with latency and action utility; typed impasse with isolated substates and resolution compilation; bounded content competition with broadcast and admission learning; persistent intention with reconsideration and live method authority; and uncertainty with resource allocation, interruption, and stopping. We contribute a distinctive-mechanism catalog, an auditable evidence-depth framework, and a falsifiable agenda for testing these bundles as composable runtime invariants.

Embodied agents built on foundation models rely on an execution harness to organize observations, guide actions, and incorporate execution feedback into subsequent decisions. Failures can arise not only from limited model capabilities, but also from how the harness presents evidence and guides its use. These model-external mechanisms provide an adaptation target without updating model parameters, but task-specific interaction experience can be costly to collect. Task-level outcomes alone do not reveal whether relevant evidence was missing from the model input or was available but inadequately used. Moreover, these two aspects are coupled: effective action guidance may require evidence that the current context omits, while exposing that evidence alone does not ensure an appropriate response. We introduce EnactOpt, which uses limited execution feedback to jointly evolve reusable textual skills and context-construction code while keeping the underlying models and runtime fixed. It diagnoses adjacent decisions by relating action feedback to the actual model input and subsequent action. Structured episode summaries guide joint revisions through prompt-level edit operators, and candidate harnesses undergo compatibility checks and validation-based retention. Across VLABench, ALFWorld, and Embodied Agent Interface (EAI), EnactOpt improves task success by approximately 10-27 percentage points over the initial harnesses and outperforms the evaluated GEPA, TextGrad, and Trace2Skill baselines. These gains extend to task conditions not used for harness evolution or candidate selection. The results support a complementary route to embodied adaptation: turning limited execution experience into reusable behavioral improvements by jointly refining how evidence is presented and acted upon.

Transformers demonstrate impressive performance on a range of reasoning benchmarks. To evaluate the degree to which these abilities are a result of actual reasoning, existing work has focused on developing sophisticated benchmarks for behavioral studies. However, these studies do not provide insights into the internal mechanisms driving the observed capabilities. To improve our understanding of the internal mechanisms of transformers, we present a comprehensive mechanistic analysis of a transformer trained on a synthetic reasoning task. We identify a set of interpretable mechanisms the model uses to solve the task, and validate our findings using correlational and causal evidence. Our results suggest that it implements a depth-bounded recurrent mechanisms that operates in parallel and stores intermediate results in selected token positions. We anticipate that the motifs we identified in our synthetic setting can provide valuable insights into the broader operating principles of transformers and thus provide a basis for understanding more complex models.

While mechanistic interpretability has developed powerful tools to analyze the internal workings of Large Language Models (LLMs), their complexity has created an accessibility gap, limiting their use to specialists. We address this challenge by designing, building, and evaluating ELIA (Explainable Language Interpretability Analysis), an interactive web application that simplifies the outcomes of various language model component analyses for a broader audience. The system integrates three key techniques -- Attribution Analysis, Function Vector Analysis, and Circuit Tracing -- and introduces a novel methodology: using a vision-language model to automatically generate natural language explanations (NLEs) for the complex visualizations produced by these methods. The effectiveness of this approach was empirically validated through a mixed-methods user study, which revealed a clear preference for interactive, explorable interfaces over simpler, static visualizations. A key finding was that the AI-powered explanations helped bridge the knowledge gap for non-experts; a statistical analysis showed no significant correlation between a user's prior LLM experience and their comprehension scores, suggesting that the system reduced barriers to comprehension across experience levels. We conclude that an AI system can indeed simplify complex model analyses, but its true power is unlocked when paired with thoughtful, user-centered design that prioritizes interactivity, specificity, and narrative guidance.

Dexterous manipulation is physics-intensive and highly sensitive to modeling errors and perception noise, making sim-to-real transfer prohibitively challenging. Domain randomization (DR) is commonly used to improve the robustness of learned policies for such tasks, but conventional DR randomizes one instance per episode, offering very limited exposure to the variability of real-world dynamics. To this end, we propose Domain-Randomized Instance Set (DRIS), which represents and propagates a set of randomized instances simultaneously, providing richer approximation of uncertain dynamics and enabling policies to learn actions that account for multiple possible outcomes. Supported by theoretical analysis, we show that DRIS yields more robust policies and alleviates the need for real-world fine-tuning, even with a modest number of instances (e.g., 10). We demonstrate this on a challenging reactive catching task. Unlike traditional catching setups that use end-effectors designed to mechanically stabilize the object (e.g., curved or enclosing surfaces), our system uses a flat plate that offers no passive stabilization, making the task highly sensitive to noise and requiring rapid reactive motions. The learned policies exhibit strong robustness to uncertainties and achieve reliable zero-shot sim-to-real transfer.

Large language models have seen widespread adoption, yet they remain vulnerable to multi-turn jailbreak attacks, threatening their safe deployment. This has led to the task of training automated multi-turn attackers to probe model safety vulnerabilities. However, existing approaches typically rely on turn-level optimization, which is insufficient for learning long-term attack strategies. To bridge this gap, we formulate this task as a multi-turn reinforcement learning problem, directly optimizing the harmfulness of the final-turn response as the outcome reward. To address the sparse supervision of the outcome reward, we introduce TROJail, which employs two process rewards to evaluate the utility of intermediate prompts and integrate them into advantage estimation. These rewards (1) penalize overly harmful prompts that trigger the model's refusal mechanism, and (2) encourage steering the semantic relevance of responses toward the targeted harmful content. Experimental results show improved attack success rates across multiple models and benchmarks, highlighting the effectiveness of our approach. The code is available at https://github.com/xxiqiao/TROJail. Warning: This paper contains examples of harmful content.

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

Large language models (LLMs) can express different values in two distinct ways: (1) intrinsic expression, reflecting the model's inherent values learned during training, and (2) prompted expression, elicited by explicit prompts. Given their widespread use in value alignment and persona steering, it is paramount to clearly understand their underlying mechanisms, particularly whether they mostly overlap (as one might expect) or rely on substantially different mechanisms, but this remains largely understudied. We analyze this at the mechanistic level using two approaches: (1) value vectors, feature directions representing value mechanisms extracted from the residual stream, and (2) value neurons, MLP neurons that contribute to value expressions. We demonstrate that intrinsic and prompted value mechanisms partly share common components that are crucial for inducing value expression, but also possess unique elements that manifest in different ways. As a result, these mechanisms lead to different degrees of value steerability (prompted > intrinsic) and response diversity (intrinsic > prompted). In particular, components unique to the intrinsic mechanism seem to promote lexical diversity in responses, whereas those specific to the prompted mechanism primarily strengthen instruction following, taking effect even in distant tasks like jailbreaking.

It is increasingly important that LLM agents interact effectively and safely with other goal-pursuing agents, yet, recent works report the opposite trend: LLMs with stronger reasoning capabilities behave _less_ cooperatively in mixed-motive games such as the prisoner's dilemma and public goods settings. Indeed, our experiments show that recent models -- with or without reasoning enabled -- consistently defect in single-shot social dilemmas. To tackle this safety concern, we present the first comparative study of game-theoretic mechanisms designed to enable cooperative outcomes between rational agents _in equilibrium_. Across four social dilemmas testing distinct components of robust cooperation, we evaluate four families of mechanisms: (1) repeating the game for many rounds, (2) reputation systems, (3) third-party mediators to delegate decision making to, and (4) contract agreements for outcome-conditional payments between players. Among our findings, we establish that contracting and mediation are most effective in achieving cooperative outcomes between capable LLM models, and that repetition-induced cooperation deteriorates drastically when co-players vary. Moreover, we demonstrate that the mechanisms become _more effective_ under evolutionary pressures to maximize individual payoffs.

We study the problem of designing mechanisms for information acquisition scenarios. This setting models strategic interactions between an uniformed receiver and a set of informed senders. In our model the senders receive information about the underlying state of nature and communicate their observation (either truthfully or not) to the receiver, which, based on this information, selects an action. Our goal is to design mechanisms maximizing the receiver's utility while incentivizing the senders to report truthfully their information. First, we provide an algorithm that efficiently computes an optimal incentive compatible (IC) mechanism. Then, we focus on the online problem in which the receiver sequentially interacts in an unknown game, with the objective of minimizing the cumulative regret w.r.t. the optimal IC mechanism, and the cumulative violation of the incentive compatibility constraints. We investigate two different online scenarios, i.e., the full and bandit feedback settings. For the full feedback problem, we propose an algorithm that guarantees mathcal O(sqrt T) regret and violation, while for the bandit feedback setting we present an algorithm that attains mathcal O(T^{alpha}) regret and mathcal O(T^{1-alpha/2}) violation for any alphain[1/2, 1]. Finally, we complement our results providing a tight lower bound.