Daily Papers

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector. A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.

Predicting protein function from amino acid sequence remains a central challenge in data-scarce (low-N) regimes, limiting machine learning-guided protein design when only small amounts of assay-labeled sequence-function data are available. Protein language models (pLMs) have advanced the field by providing evolutionary-informed embeddings and sparse autoencoders (SAEs) have enabled decomposition of these embeddings into interpretable latent variables that capture structural and functional features. However, the effectiveness of SAEs for low-N function prediction and protein design has not been systematically studied. Herein, we evaluate SAEs trained on fine-tuned ESM2 embeddings across diverse fitness extrapolation and protein engineering tasks. We show that SAEs, with as few as 24 sequences, consistently outperform or compete with their ESM2 baselines in fitness prediction, indicating that their sparse latent space encodes compact and biologically meaningful representations that generalize more effectively from limited data. Moreover, steering predictive latents exploits biological motifs in pLM representations, yielding top-fitness variants in 83% of cases compared to designing with ESM2 alone.

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

The RNA structure-function relationship has recently garnered significant attention within the deep learning community, promising to grow in importance as nucleic acid structure models advance. However, the absence of standardized and accessible benchmarks for deep learning on RNA 3D structures has impeded the development of models for RNA functional characteristics. In this work, we introduce a set of seven benchmarking datasets for RNA structure-function prediction, designed to address this gap. Our library builds on the established Python library rnaglib, and offers easy data distribution and encoding, splitters and evaluation methods, providing a convenient all-in-one framework for comparing models. Datasets are implemented in a fully modular and reproducible manner, facilitating for community contributions and customization. Finally, we provide initial baseline results for all tasks using a graph neural network. Source code: https://github.com/cgoliver/rnaglib Documentation: https://rnaglib.org

Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially reshape structural biology. However, the utility of the PLM module in AlphaFold, Evoformer, has not been explored beyond structure prediction. In this paper, we investigate the representation ability of three popular PLMs: ESM-1b (single sequence), MSA-Transformer (multiple sequence alignment) and Evoformer (structural), with a special focus on Evoformer. Specifically, we aim to answer the following key questions: (i) Does the Evoformer trained as part of AlphaFold produce representations amenable to predicting protein function? (ii) If yes, can Evoformer replace ESM-1b and MSA-Transformer? (ii) How much do these PLMs rely on evolution-related protein data? In this regard, are they complementary to each other? We compare these models by empirical study along with new insights and conclusions. All code and datasets for reproducibility are available at https://github.com/elttaes/Revisiting-PLMs.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are no standardized benchmarks to evaluate these methods. We introduce CARE, a benchmark and dataset suite for the Classification And Retrieval of Enzymes (CARE). CARE centers on two tasks: (1) classification of a protein sequence by its enzyme commission (EC) number and (2) retrieval of an EC number given a chemical reaction. For each task, we design train-test splits to evaluate different kinds of out-of-distribution generalization that are relevant to real use cases. For the classification task, we provide baselines for state-of-the-art methods. Because the retrieval task has not been previously formalized, we propose a method called Contrastive Reaction-EnzymE Pretraining (CREEP) as one of the first baselines for this task and compare it to the recent method, CLIPZyme. CARE is available at https://github.com/jsunn-y/CARE/.

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing annotation imbalance and instruction deficits in existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by large margins. Moreover, InstructProtein serves as a pioneering step towards text-based protein function prediction and sequence design, effectively bridging the gap between protein and human language understanding.

We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark are all available at https://github.com/DeepGraphLearning/PEER_Benchmark

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Self-supervised learning of graph neural networks (GNNs) aims to learn an accurate representation of the graphs in an unsupervised manner, to obtain transferable representations of them for diverse downstream tasks. Predictive learning and contrastive learning are the two most prevalent approaches for graph self-supervised learning. However, they have their own drawbacks. While the predictive learning methods can learn the contextual relationships between neighboring nodes and edges, they cannot learn global graph-level similarities. Contrastive learning, while it can learn global graph-level similarities, its objective to maximize the similarity between two differently perturbed graphs may result in representations that cannot discriminate two similar graphs with different properties. To tackle such limitations, we propose a framework that aims to learn the exact discrepancy between the original and the perturbed graphs, coined as Discrepancy-based Self-supervised LeArning (D-SLA). Specifically, we create multiple perturbations of the given graph with varying degrees of similarity, and train the model to predict whether each graph is the original graph or the perturbed one. Moreover, we further aim to accurately capture the amount of discrepancy for each perturbed graph using the graph edit distance. We validate our D-SLA on various graph-related downstream tasks, including molecular property prediction, protein function prediction, and link prediction tasks, on which ours largely outperforms relevant baselines.

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must be trained on a large multiple sequence alignment (MSA) from the specific family of interest, making them unable to benefit from transfer learning across families. To address this, we propose Protein Evolutionary Transformer (PoET), an autoregressive generative model of whole protein families that learns to generate sets of related proteins as sequences-of-sequences across tens of millions of natural protein sequence clusters. PoET can be used as a retrieval-augmented language model to generate and score arbitrary modifications conditioned on any protein family of interest, and can extrapolate from short context lengths to generalize well even for small families. This is enabled by a unique Transformer layer; we model tokens sequentially within sequences while attending between sequences order invariantly, allowing PoET to scale to context lengths beyond those used during training. In extensive experiments on deep mutational scanning datasets, we show that PoET outperforms existing protein language models and evolutionary sequence models for variant function prediction across proteins of all MSA depths. We also demonstrate PoET's ability to controllably generate new protein sequences.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

Deep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions. This paper introduces DeepProtein, a comprehensive and user-friendly deep learning library tailored for protein-related tasks. It enables researchers to seamlessly address protein data with cutting-edge deep learning models. To assess model performance, we establish a benchmark evaluating different deep learning architectures across multiple protein-related tasks, including protein function prediction, subcellular localization prediction, protein-protein interaction prediction, and protein structure prediction. Furthermore, we introduce DeepProt-T5, a series of fine-tuned Prot-T5-based models that achieve state-of-the-art performance on four benchmark tasks, while demonstrating competitive results on six of others. Comprehensive documentation and tutorials are available which could ensure accessibility and support reproducibility. Built upon the widely used drug discovery library DeepPurpose, DeepProtein is publicly available at https://github.com/jiaqingxie/DeepProtein.

Electrocardiogram (ECG) is a widely used tool for assessing cardiac function due to its low cost and accessibility. Emergent research shows that ECGs can help make predictions on key outcomes traditionally derived from more complex modalities such as echocardiograms (ECHO), enabling the use of ECGs as a more accessible method to predict broader measurements of cardiac function. ECHO, in particular, are of great importance because they require considerable hospital resources while playing a key role in clinical cardiac assessment. To aid this use case, we introduce EchoingECG, a probabilistic student-teacher model that leverages uncertainty-aware ECG embeddings and ECHO supervision to improve ECG-based cardiac function prediction. Our approach integrates Probabilistic Cross-Modal Embeddings (PCME++), a probabilistic contrastive framework, with ECHO-CLIP, a vision-language pre-trained model trained on ECHO-text pairs, to distill ECHO knowledge into ECG representations. Through experiments and external validation, we showed that EchoingECG outperforms state-of-the-art foundation ECG models in zero-shot, few-shot, and fine-tune settings for ECHO predictions based on ECG. We also highlighted that variance estimation (enabled through our method) enhanced our understanding of model performance by identifying underlying regions of uncertainty within ECGs. The code is available: https://github.com/mcintoshML/EchoingECG.

In this work we introduce RITA: a suite of autoregressive generative models for protein sequences, with up to 1.2 billion parameters, trained on over 280 million protein sequences belonging to the UniRef-100 database. Such generative models hold the promise of greatly accelerating protein design. We conduct the first systematic study of how capabilities evolve with model size for autoregressive transformers in the protein domain: we evaluate RITA models in next amino acid prediction, zero-shot fitness, and enzyme function prediction, showing benefits from increased scale. We release the RITA models openly, to the benefit of the research community.

The imperative need to scale computation across numerous nodes highlights the significance of efficient parallel computing, particularly in the realm of Message Passing Interface (MPI) integration. The challenging parallel programming task of generating MPI-based parallel programs has remained unexplored. This study first investigates the performance of state-of-the-art language models in generating MPI-based parallel programs. Findings reveal that widely used models such as GPT-3.5 and PolyCoder (specialized multi-lingual code models) exhibit notable performance degradation, when generating MPI-based programs compared to general-purpose programs. In contrast, domain-specific models such as MonoCoder, which are pretrained on MPI-related programming languages of C and C++, outperform larger models. Subsequently, we introduce a dedicated downstream task of MPI-based program generation by fine-tuning MonoCoder on HPCorpusMPI. We call the resulting model as MPIrigen. We propose an innovative preprocessing for completion only after observing the whole code, thus enabling better completion with a wider context. Comparative analysis against GPT-3.5 zero-shot performance, using a novel HPC-oriented evaluation method, demonstrates that MPIrigen excels in generating accurate MPI functions up to 0.8 accuracy in location and function predictions, and with more than 0.9 accuracy for argument predictions. The success of this tailored solution underscores the importance of domain-specific fine-tuning in optimizing language models for parallel computing code generation, paving the way for a new generation of automatic parallelization tools. The sources of this work are available at our GitHub MPIrigen repository: https://github.com/Scientific-Computing-Lab-NRCN/MPI-rigen

Recent AI advances have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, alignment, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of modality encoders along protein sequences. It demonstrates strong performance in retrieval tasks and surpasses state-of-the-art methods in various downstream tasks, including metal ion binding classification, gene-ontology annotation, and enzyme function prediction. This work expands multi-modal capabilities in protein models, paving the way for applications in drug discovery, biocatalytic reaction planning, and protein engineering.

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have emerged as the preferred method for this challenge, thanks to their ability to harness large sequence databases. Yet, their reliance on expansive sequence data and parameter sets limits their flexibility and practicality in real-world scenarios. Concurrently, the recent surge in computationally predicted protein structures unlocks new opportunities in protein representation learning. While promising, the computational burden carried by such complex data still hinders widely-adopted practical applications. To address these limitations, we introduce a novel framework that enhances protein language models by integrating protein structural data. Drawing from recent advances in graph transformers, our approach refines the self-attention mechanisms of pretrained language transformers by integrating structural information with structure extractor modules. This refined model, termed Protein Structure Transformer (PST), is further pretrained on a small protein structure database, using the same masked language modeling objective as traditional protein language models. Empirical evaluations of PST demonstrate its superior parameter efficiency relative to protein language models, despite being pretrained on a dataset comprising only 542K structures. Notably, PST consistently outperforms the state-of-the-art foundation model for protein sequences, ESM-2, setting a new benchmark in protein function prediction. Our findings underscore the potential of integrating structural information into protein language models, paving the way for more effective and efficient protein modeling Code and pretrained models are available at https://github.com/BorgwardtLab/PST.

Large language models (LLMs) are known for their exceptional performance in natural language processing, making them highly effective in many human life-related or even job-related tasks. The attention mechanism in the Transformer architecture is a critical component of LLMs, as it allows the model to selectively focus on specific input parts. The softmax unit, which is a key part of the attention mechanism, normalizes the attention scores. Hence, the performance of LLMs in various NLP tasks depends significantly on the crucial role played by the attention mechanism with the softmax unit. In-context learning, as one of the celebrated abilities of recent LLMs, is an important concept in querying LLMs such as ChatGPT. Without further parameter updates, Transformers can learn to predict based on few in-context examples. However, the reason why Transformers becomes in-context learners is not well understood. Recently, several works [ASA+22,GTLV22,ONR+22] have studied the in-context learning from a mathematical perspective based on a linear regression formulation min_x| Ax - b |_2, which show Transformers' capability of learning linear functions in context. In this work, we study the in-context learning based on a softmax regression formulation min_{x} | langle exp(Ax), {bf 1}_n rangle^{-1} exp(Ax) - b |_2 of Transformer's attention mechanism. We show the upper bounds of the data transformations induced by a single self-attention layer and by gradient-descent on a ell_2 regression loss for softmax prediction function, which imply that when training self-attention-only Transformers for fundamental regression tasks, the models learned by gradient-descent and Transformers show great similarity.

Predicting crimes in urban environments is crucial for public safety, yet existing prediction methods often struggle to align the knowledge across diverse cities that vary dramatically in data availability of specific crime types. We propose HYpernetwork-enhanced Spatial Temporal Learning (HYSTL), a framework that can effectively train a unified, stronger crime predictor without assuming identical crime types in different cities' records. In HYSTL, instead of parameterising a dedicated predictor per crime type, a hypernetwork is designed to dynamically generate parameters for the prediction function conditioned on the crime type of interest. To bridge the semantic gap between different crime types, a structured crime knowledge graph is built, where the learned representations of crimes are used as the input to the hypernetwork to facilitate parameter generation. As such, when making predictions for each crime type, the predictor is additionally guided by its intricate association with other relevant crime types. Extensive experiments are performed on two cities with non-overlapping crime types, and the results demonstrate HYSTL outperforms state-of-the-art baselines.

We introduce Transfusion, a recipe for training a multi-modal model over discrete and continuous data. Transfusion combines the language modeling loss function (next token prediction) with diffusion to train a single transformer over mixed-modality sequences. We pretrain multiple Transfusion models up to 7B parameters from scratch on a mixture of text and image data, establishing scaling laws with respect to a variety of uni- and cross-modal benchmarks. Our experiments show that Transfusion scales significantly better than quantizing images and training a language model over discrete image tokens. By introducing modality-specific encoding and decoding layers, we can further improve the performance of Transfusion models, and even compress each image to just 16 patches. We further demonstrate that scaling our Transfusion recipe to 7B parameters and 2T multi-modal tokens produces a model that can generate images and text on a par with similar scale diffusion models and language models, reaping the benefits of both worlds.

Asphalt concrete's (AC) durability and maintenance demands are strongly influenced by its fatigue life. Traditional methods for determining this characteristic are both resource-intensive and time-consuming. This study employs artificial neural networks (ANNs) to predict AC fatigue life, focusing on the impact of strain level, binder content, and air-void content. Leveraging a substantial dataset, we tailored our models to effectively handle the wide range of fatigue life data, typically represented on a logarithmic scale. The mean square logarithmic error was utilized as the loss function to enhance prediction accuracy across all levels of fatigue life. Through comparative analysis of various hyperparameters, we developed a machine-learning model that captures the complex relationships within the data. Our findings demonstrate that higher binder content significantly enhances fatigue life, while the influence of air-void content is more variable, depending on binder levels. Most importantly, this study provides insights into the intricacies of using ANNs for modeling, showcasing their potential utility with larger datasets. The codes developed and the data used in this study are provided as open source on a GitHub repository, with a link included in the paper for full access.

Intelligent vehicle cockpits present unique challenges for API Agents, requiring coordination across tightly-coupled subsystems that exceed typical task environments' complexity. Traditional Function Calling (FC) approaches operate statelessly, requiring multiple exploratory calls to build environmental awareness before execution, leading to inefficiency and limited error recovery. We introduce VehicleWorld, the first comprehensive environment for the automotive domain, featuring 30 modules, 250 APIs, and 680 properties with fully executable implementations that provide real-time state information during agent execution. This environment enables precise evaluation of vehicle agent behaviors across diverse, challenging scenarios. Through systematic analysis, we discovered that direct state prediction outperforms function calling for environmental control. Building on this insight, we propose State-based Function Call (SFC), a novel approach that maintains explicit system state awareness and implements direct state transitions to achieve target conditions. Experimental results demonstrate that SFC significantly outperforms traditional FC approaches, achieving superior execution accuracy and reduced latency. We have made all implementation code publicly available on Github https://github.com/OpenMOSS/VehicleWorld.

Masked Diffusion Language Models (MDLMs) have recently emerged as a promising alternative to Autoregressive Language Models (ARLMs), leveraging a denoising objective that, in principle, should enable more uniform context utilisation. In this work, we examine the context comprehension abilities of MDLMs and uncover two key limitations. First, despite their more global training objective and bidirectional attention mechanism, similarly to ARLMS, MDLMs exhibit a strong locality bias: performance is highly sensitive to the position of relevant information within the input, favouring local over distant context. Second, we show that appending a large number of mask tokens--required for generation--can significantly degrade context comprehension. Through systematic ablations, we find that these masks act as distractors, reducing the model's ability to process relevant information. To address this, we introduce a mask-agnostic loss function that encourages predictions to remain invariant to the number of appended masks. Fine-tuning with this objective substantially mitigates the distracting effect of masks, improving robustness of MDLMs. Overall, our findings reveal critical limitations of the current MDLM training paradigm and provide actionable insights for building diffusion-based language models with stronger context comprehension.

We introduce Ev-TTA, a simple, effective test-time adaptation algorithm for event-based object recognition. While event cameras are proposed to provide measurements of scenes with fast motions or drastic illumination changes, many existing event-based recognition algorithms suffer from performance deterioration under extreme conditions due to significant domain shifts. Ev-TTA mitigates the severe domain gaps by fine-tuning the pre-trained classifiers during the test phase using loss functions inspired by the spatio-temporal characteristics of events. Since the event data is a temporal stream of measurements, our loss function enforces similar predictions for adjacent events to quickly adapt to the changed environment online. Also, we utilize the spatial correlations between two polarities of events to handle noise under extreme illumination, where different polarities of events exhibit distinctive noise distributions. Ev-TTA demonstrates a large amount of performance gain on a wide range of event-based object recognition tasks without extensive additional training. Our formulation can be successfully applied regardless of input representations and further extended into regression tasks. We expect Ev-TTA to provide the key technique to deploy event-based vision algorithms in challenging real-world applications where significant domain shift is inevitable.

We apply a complex network approach to analyse the time series of five solar parameters, and propose an strategy to predict the number of sunspots for the next solar maximum, and when will this maximum will occur. The approach is based on the Visibility Graph (VG) algorithm, and a slightly modified version of it, the Horizontal Visibility Graph (HVG), which map a time series into a complex network. Various network metrics exhibit either an exponential or a scale-free behavior, and we find that the evolution of the characteristic decay exponents is consistent with variations of the sunspots number along solar cycles. During solar minimum, the sunspots number and the solar index time series have characteristic decay exponents that correlate well with the next maximum sunspots number, suggesting that they may be good precursors of the intensity of the next solar maximum. Based on this observation, we find that, based on current data, the algorithm predicts a number of 179 sunspots for cycle 25. Combining this with the Hathaway function, adjusted to yield such maximum sunspots number, we find that the maximum for solar cycle 25 will occur in December 2024/January 2025.

Deep learning techniques are increasingly applied to scientific problems, where the precision of networks is crucial. Despite being deemed as universal function approximators, neural networks, in practice, struggle to reduce the prediction errors below O(10^{-5}) even with large network size and extended training iterations. To address this issue, we developed the multi-stage neural networks that divides the training process into different stages, with each stage using a new network that is optimized to fit the residue from the previous stage. Across successive stages, the residue magnitudes decreases substantially and follows an inverse power-law relationship with the residue frequencies. The multi-stage neural networks effectively mitigate the spectral biases associated with regular neural networks, enabling them to capture the high frequency feature of target functions. We demonstrate that the prediction error from the multi-stage training for both regression problems and physics-informed neural networks can nearly reach the machine-precision O(10^{-16}) of double-floating point within a finite number of iterations. Such levels of accuracy are rarely attainable using single neural networks alone.

Deep neural representations of 3D shapes as implicit functions have been shown to produce high fidelity models surpassing the resolution-memory trade-off faced by the explicit representations using meshes and point clouds. However, most such approaches focus on representing closed shapes. Unsigned distance function (UDF) based approaches have been proposed recently as a promising alternative to represent both open and closed shapes. However, since the gradients of UDFs vanish on the surface, it is challenging to estimate local (differential) geometric properties like the normals and tangent planes which are needed for many downstream applications in vision and graphics. There are additional challenges in computing these properties efficiently with a low-memory footprint. This paper presents a novel approach that models such surfaces using a new class of implicit representations called the closest surface-point (CSP) representation. We show that CSP allows us to represent complex surfaces of any topology (open or closed) with high fidelity. It also allows for accurate and efficient computation of local geometric properties. We further demonstrate that it leads to efficient implementation of downstream algorithms like sphere-tracing for rendering the 3D surface as well as to create explicit mesh-based representations. Extensive experimental evaluation on the ShapeNet dataset validate the above contributions with results surpassing the state-of-the-art.

Discontinuing ad creatives at an appropriate time is one of the most important ad operations that can have a significant impact on sales. Such operational support for ineffective ads has been less explored than that for effective ads. After pre-analyzing 1,000,000 real-world ad creatives, we found that there are two types of discontinuation: short-term (i.e., cut-out) and long-term (i.e., wear-out). In this paper, we propose a practical prediction framework for the discontinuation of ad creatives with a hazard function-based loss function inspired by survival analysis. Our framework predicts the discontinuations with a multi-modal deep neural network that takes as input the ad creative (e.g., text, categorical, image, numerical features). To improve the prediction performance for the two different types of discontinuations and for the ad creatives that contribute to sales, we introduce two new techniques: (1) a two-term estimation technique with multi-task learning and (2) a click-through rate-weighting technique for the loss function. We evaluated our framework using the large-scale ad creative dataset, including 10 billion scale impressions. In terms of the concordance index (short: 0.896, long: 0.939, and overall: 0.792), our framework achieved significantly better performance than the conventional method (0.531). Additionally, we confirmed that our framework (i) demonstrated the same degree of discontinuation effect as manual operations for short-term cases, and (ii) accurately predicted the ad discontinuation order, which is important for long-running ad creatives for long-term cases.

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availability of experimental 3D protein structures have accelerated structure prediction, the dynamic nature of protein structures has received limited attention. This study introduces an innovative 4D diffusion model incorporating molecular dynamics (MD) simulation data to learn dynamic protein structures. Our approach is distinguished by the following components: (1) a unified diffusion model capable of generating dynamic protein structures, including both the backbone and side chains, utilizing atomic grouping and side-chain dihedral angle predictions; (2) a reference network that enhances structural consistency by integrating the latent embeddings of the initial 3D protein structures; and (3) a motion alignment module aimed at improving temporal structural coherence across multiple time steps. To our knowledge, this is the first diffusion-based model aimed at predicting protein trajectories across multiple time steps simultaneously. Validation on benchmark datasets demonstrates that our model exhibits high accuracy in predicting dynamic 3D structures of proteins containing up to 256 amino acids over 32 time steps, effectively capturing both local flexibility in stable states and significant conformational changes.

Model calibration aims to align confidence with prediction correctness. The Cross-Entropy (CE) loss is widely used for calibrator training, which enforces the model to increase confidence on the ground truth class. However, we find the CE loss has intrinsic limitations. For example, for a narrow misclassification, a calibrator trained by the CE loss often produces high confidence on the wrongly predicted class (e.g., a test sample is wrongly classified and its softmax score on the ground truth class is around 0.4), which is undesirable. In this paper, we propose a new post-hoc calibration objective derived from the aim of calibration. Intuitively, the proposed objective function asks that the calibrator decrease model confidence on wrongly predicted samples and increase confidence on correctly predicted samples. Because a sample itself has insufficient ability to indicate correctness, we use its transformed versions (e.g., rotated, greyscaled and color-jittered) during calibrator training. Trained on an in-distribution validation set and tested with isolated, individual test samples, our method achieves competitive calibration performance on both in-distribution and out-of-distribution test sets compared with the state of the art. Further, our analysis points out the difference between our method and commonly used objectives such as CE loss and mean square error loss, where the latters sometimes deviates from the calibration aim.

We propose a game-based formulation for learning dimensionality-reducing representations of feature vectors, when only a prior knowledge on future prediction tasks is available. In this game, the first player chooses a representation, and then the second player adversarially chooses a prediction task from a given class, representing the prior knowledge. The first player aims is to minimize, and the second player to maximize, the regret: The minimal prediction loss using the representation, compared to the same loss using the original features. For the canonical setting in which the representation, the response to predict and the predictors are all linear functions, and under the mean squared error loss function, we derive the theoretically optimal representation in pure strategies, which shows the effectiveness of the prior knowledge, and the optimal regret in mixed strategies, which shows the usefulness of randomizing the representation. For general representations and loss functions, we propose an efficient algorithm to optimize a randomized representation. The algorithm only requires the gradients of the loss function, and is based on incrementally adding a representation rule to a mixture of such rules.

Global climate models (GCMs) are the main tools for understanding and predicting climate change. However, due to limited numerical resolutions, these models suffer from major structural uncertainties; e.g., they cannot resolve critical processes such as small-scale eddies in atmospheric and oceanic turbulence. Thus, such small-scale processes have to be represented as a function of the resolved scales via closures (parametrization). The accuracy of these closures is particularly important for capturing climate extremes. Traditionally, such closures are based on heuristics and simplifying assumptions about the unresolved physics. Recently, supervised-learned closures, trained offline on high-fidelity data, have been shown to outperform the classical physics-based closures. However, this approach requires a significant amount of high-fidelity training data and can also lead to instabilities. Reinforcement learning is emerging as a potent alternative for developing such closures as it requires only low-order statistics and leads to stable closures. In Scientific Multi-Agent Reinforcement Learning (SMARL) computational elements serve a dual role of discretization points and learning agents. We leverage SMARL and fundamentals of turbulence physics to learn closures for prototypes of atmospheric and oceanic turbulence. The policy is trained using only the enstrophy spectrum, which is nearly invariant and can be estimated from a few high-fidelity samples (these few samples are far from enough for supervised/offline learning). We show that these closures lead to stable low-resolution simulations that, at a fraction of the cost, can reproduce the high-fidelity simulations' statistics, including the tails of the probability density functions. The results demonstrate the high potential of SMARL for closure modeling for GCMs, especially in the regime of scarce data and indirect observations.

The prediction of saliency areas in images has been traditionally addressed with hand crafted features based on neuroscience principles. This paper however addresses the problem with a completely data-driven approach by training a convolutional network. The learning process is formulated as a minimization of a loss function that measures the Euclidean distance of the predicted saliency map with the provided ground truth. The recent publication of large datasets of saliency prediction has provided enough data to train a not very deep architecture which is both fast and accurate. The convolutional network in this paper, named JuntingNet, won the LSUN 2015 challenge on saliency prediction with a superior performance in all considered metrics.

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which is crucial for biology research. To address this gap, we introduce PRING, the first comprehensive benchmark that evaluates protein-protein interaction prediction from a graph-level perspective. PRING curates a high-quality, multi-species PPI network dataset comprising 21,484 proteins and 186,818 interactions, with well-designed strategies to address both data redundancy and leakage. Building on this golden-standard dataset, we establish two complementary evaluation paradigms: (1) topology-oriented tasks, which assess intra and cross-species PPI network construction, and (2) function-oriented tasks, including protein complex pathway prediction, GO module analysis, and essential protein justification. These evaluations not only reflect the model's capability to understand the network topology but also facilitate protein function annotation, biological module detection, and even disease mechanism analysis. Extensive experiments on four representative model categories, consisting of sequence similarity-based, naive sequence-based, protein language model-based, and structure-based approaches, demonstrate that current PPI models have potential limitations in recovering both structural and functional properties of PPI networks, highlighting the gap in supporting real-world biological applications. We believe PRING provides a reliable platform to guide the development of more effective PPI prediction models for the community. The dataset and source code of PRING are available at https://github.com/SophieSarceau/PRING.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

Conformal prediction (CP) for regression can be challenging, especially when the output distribution is heteroscedastic, multimodal, or skewed. Some of the issues can be addressed by estimating a distribution over the output, but in reality, such approaches can be sensitive to estimation error and yield unstable intervals.~Here, we circumvent the challenges by converting regression to a classification problem and then use CP for classification to obtain CP sets for regression.~To preserve the ordering of the continuous-output space, we design a new loss function and make necessary modifications to the CP classification techniques.~Empirical results on many benchmarks shows that this simple approach gives surprisingly good results on many practical problems.

In this paper, we tackle the problem of scene-aware 3D human motion forecasting. A key challenge of this task is to predict future human motions that are consistent with the scene by modeling the human-scene interactions. While recent works have demonstrated that explicit constraints on human-scene interactions can prevent the occurrence of ghost motion, they only provide constraints on partial human motion e.g., the global motion of the human or a few joints contacting the scene, leaving the rest of the motion unconstrained. To address this limitation, we propose to model the human-scene interaction with the mutual distance between the human body and the scene. Such mutual distances constrain both the local and global human motion, resulting in a whole-body motion constrained prediction. In particular, mutual distance constraints consist of two components, the signed distance of each vertex on the human mesh to the scene surface and the distance of basis scene points to the human mesh. We further introduce a global scene representation learned from a signed distance function (SDF) volume to ensure coherence between the global scene representation and the explicit constraint from the mutual distance. We develop a pipeline with two sequential steps: predicting the future mutual distances first, followed by forecasting future human motion. During training, we explicitly encourage consistency between predicted poses and mutual distances. Extensive evaluations on the existing synthetic and real datasets demonstrate that our approach consistently outperforms the state-of-the-art methods.

Guided sampling is a vital approach for applying diffusion models in real-world tasks that embeds human-defined guidance during the sampling procedure. This paper considers a general setting where the guidance is defined by an (unnormalized) energy function. The main challenge for this setting is that the intermediate guidance during the diffusion sampling procedure, which is jointly defined by the sampling distribution and the energy function, is unknown and is hard to estimate. To address this challenge, we propose an exact formulation of the intermediate guidance as well as a novel training objective named contrastive energy prediction (CEP) to learn the exact guidance. Our method is guaranteed to converge to the exact guidance under unlimited model capacity and data samples, while previous methods can not. We demonstrate the effectiveness of our method by applying it to offline reinforcement learning (RL). Extensive experiments on D4RL benchmarks demonstrate that our method outperforms existing state-of-the-art algorithms. We also provide some examples of applying CEP for image synthesis to demonstrate the scalability of CEP on high-dimensional data.

We present a conceptual framework, datamodeling, for analyzing the behavior of a model class in terms of the training data. For any fixed "target" example x, training set S, and learning algorithm, a datamodel is a parameterized function 2^S to R that for any subset of S' subset S -- using only information about which examples of S are contained in S' -- predicts the outcome of training a model on S' and evaluating on x. Despite the potential complexity of the underlying process being approximated (e.g., end-to-end training and evaluation of deep neural networks), we show that even simple linear datamodels can successfully predict model outputs. We then demonstrate that datamodels give rise to a variety of applications, such as: accurately predicting the effect of dataset counterfactuals; identifying brittle predictions; finding semantically similar examples; quantifying train-test leakage; and embedding data into a well-behaved and feature-rich representation space. Data for this paper (including pre-computed datamodels as well as raw predictions from four million trained deep neural networks) is available at https://github.com/MadryLab/datamodels-data .

Modern machine learning (ML) systems demand substantial training data, often resorting to external sources. Nevertheless, this practice renders them vulnerable to backdoor poisoning attacks. Prior backdoor defense strategies have primarily focused on the identification of backdoored models or poisoned data characteristics, typically operating under the assumption of access to clean data. In this work, we delve into a relatively underexplored challenge: the automatic identification of backdoor data within a poisoned dataset, all under realistic conditions, i.e., without the need for additional clean data or without manually defining a threshold for backdoor detection. We draw an inspiration from the scaled prediction consistency (SPC) technique, which exploits the prediction invariance of poisoned data to an input scaling factor. Based on this, we pose the backdoor data identification problem as a hierarchical data splitting optimization problem, leveraging a novel SPC-based loss function as the primary optimization objective. Our innovation unfolds in several key aspects. First, we revisit the vanilla SPC method, unveiling its limitations in addressing the proposed backdoor identification problem. Subsequently, we develop a bi-level optimization-based approach to precisely identify backdoor data by minimizing the advanced SPC loss. Finally, we demonstrate the efficacy of our proposal against a spectrum of backdoor attacks, encompassing basic label-corrupted attacks as well as more sophisticated clean-label attacks, evaluated across various benchmark datasets. Experiment results show that our approach often surpasses the performance of current baselines in identifying backdoor data points, resulting in about 4%-36% improvement in average AUROC. Codes are available at https://github.com/OPTML-Group/BackdoorMSPC.

Recent advances in the theory of Neural Operators (NOs) have enabled fast and accurate computation of the solutions to complex systems described by partial differential equations (PDEs). Despite their great success, current NO-based solutions face important challenges when dealing with spatio-temporal PDEs over long time scales. Specifically, the current theory of NOs does not present a systematic framework to perform data assimilation and efficiently correct the evolution of PDE solutions over time based on sparsely sampled noisy measurements. In this paper, we propose a learning-based state-space approach to compute the solution operators to infinite-dimensional semilinear PDEs. Exploiting the structure of semilinear PDEs and the theory of nonlinear observers in function spaces, we develop a flexible recursive method that allows for both prediction and data assimilation by combining prediction and correction operations. The proposed framework is capable of producing fast and accurate predictions over long time horizons, dealing with irregularly sampled noisy measurements to correct the solution, and benefits from the decoupling between the spatial and temporal dynamics of this class of PDEs. We show through experiments on the Kuramoto-Sivashinsky, Navier-Stokes and Korteweg-de Vries equations that the proposed model is robust to noise and can leverage arbitrary amounts of measurements to correct its prediction over a long time horizon with little computational overhead.

Model evolution and constant availability of data are two common phenomena in large-scale real-world machine learning applications, e.g. ads and recommendation systems. To adapt, the real-world system typically retrain with all available data and online learn with recently available data to update the models periodically with the goal of better serving performance. In this paper, we propose a novel framework, named Confidence Ranking, which designs the optimization objective as a ranking function with two different models. Our confidence ranking loss allows direct optimization of the logits output for different convex surrogate functions of metrics, e.g. AUC and Accuracy depending on the target task and dataset. Armed with our proposed methods, our experiments show that the introduction of confidence ranking loss can outperform all baselines on the CTR prediction tasks of public and industrial datasets. This framework has been deployed in the advertisement system of JD.com to serve the main traffic in the fine-rank stage.

This paper targets the perceptual task of separating the different interacting voices, i.e., monophonic melodic streams, in a polyphonic musical piece. We target symbolic music, where notes are explicitly encoded, and model this task as a Multi-Trajectory Tracking (MTT) problem from discrete observations, i.e., notes in a pitch-time space. Our approach builds a graph from a musical piece, by creating one node for every note, and separates the melodic trajectories by predicting a link between two notes if they are consecutive in the same voice/stream. This kind of local, greedy prediction is made possible by node embeddings created by a heterogeneous graph neural network that can capture inter- and intra-trajectory information. Furthermore, we propose a new regularization loss that encourages the output to respect the MTT premise of at most one incoming and one outgoing link for every node, favouring monophonic (voice) trajectories; this loss function might also be useful in other general MTT scenarios. Our approach does not use domain-specific heuristics, is scalable to longer sequences and a higher number of voices, and can handle complex cases such as voice inversions and overlaps. We reach new state-of-the-art results for the voice separation task in classical music of different styles.

Finding the optimal pass sequence of compilation can lead to a significant reduction in program size and/or improvement in program efficiency. Prior works on compilation pass ordering have two major drawbacks. They either require an excessive budget (in terms of compilation steps) at compile time or fail to generalize to unseen programs. In this paper, for code-size reduction tasks, we propose a novel pipeline to find program-dependent pass sequences within 45 compilation calls. It first identifies a coreset of 50 pass sequences via greedy optimization of a submodular function, and then learns a policy with Graph Neural Network (GNN) to pick the optimal sequence by predicting the normalized values of the pass sequences in the coreset. Despite its simplicity, our pipeline outperforms the default -Oz flag by an average of 4.7% over a large collection (4683) of unseen code repositories from diverse domains across 14 datasets. In comparison, previous approaches like reinforcement learning on the raw pass sequence space may take days to train due to sparse reward, and may not generalize well in held-out ones from different domains. Our results demonstrate that existing human-designed compiler flags can be improved with a simple yet effective technique that transforms the raw action space into a small one with denser rewards.

Click-through rate prediction is an essential task in industrial applications, such as online advertising. Recently deep learning based models have been proposed, which follow a similar Embedding\&MLP paradigm. In these methods large scale sparse input features are first mapped into low dimensional embedding vectors, and then transformed into fixed-length vectors in a group-wise manner, finally concatenated together to fed into a multilayer perceptron (MLP) to learn the nonlinear relations among features. In this way, user features are compressed into a fixed-length representation vector, in regardless of what candidate ads are. The use of fixed-length vector will be a bottleneck, which brings difficulty for Embedding\&MLP methods to capture user's diverse interests effectively from rich historical behaviors. In this paper, we propose a novel model: Deep Interest Network (DIN) which tackles this challenge by designing a local activation unit to adaptively learn the representation of user interests from historical behaviors with respect to a certain ad. This representation vector varies over different ads, improving the expressive ability of model greatly. Besides, we develop two techniques: mini-batch aware regularization and data adaptive activation function which can help training industrial deep networks with hundreds of millions of parameters. Experiments on two public datasets as well as an Alibaba real production dataset with over 2 billion samples demonstrate the effectiveness of proposed approaches, which achieve superior performance compared with state-of-the-art methods. DIN now has been successfully deployed in the online display advertising system in Alibaba, serving the main traffic.

The remarkable success of large language models (LLMs) stems from their ability to consolidate vast amounts of knowledge into the memory during pre-training and to retrieve it from the memory during inference, enabling advanced capabilities such as knowledge memorization, instruction-following and reasoning. However, the mechanisms of memory retrieval and consolidation in LLMs remain poorly understood. In this paper, we propose the function token hypothesis to explain the workings of LLMs: During inference, function tokens activate the most predictive features from context and govern next token prediction (memory retrieval). During pre-training, predicting the next tokens (usually content tokens) that follow function tokens increases the number of learned features of LLMs and updates the model parameters (memory consolidation). Function tokens here roughly correspond to function words in linguistics, including punctuation marks, articles, prepositions, and conjunctions, in contrast to content tokens. We provide extensive experimental evidence supporting this hypothesis. Using bipartite graph analysis, we show that a small number of function tokens activate the majority of features. Case studies further reveal how function tokens activate the most predictive features from context to direct next token prediction. We also find that during pre-training, the training loss is dominated by predicting the next content tokens following function tokens, which forces the function tokens to select the most predictive features from context.

Creating high-quality 3D models of clothed humans from single images for real-world applications is crucial. Despite recent advancements, accurately reconstructing humans in complex poses or with loose clothing from in-the-wild images, along with predicting textures for unseen areas, remains a significant challenge. A key limitation of previous methods is their insufficient prior guidance in transitioning from 2D to 3D and in texture prediction. In response, we introduce SIFU (Side-view Conditioned Implicit Function for Real-world Usable Clothed Human Reconstruction), a novel approach combining a Side-view Decoupling Transformer with a 3D Consistent Texture Refinement pipeline.SIFU employs a cross-attention mechanism within the transformer, using SMPL-X normals as queries to effectively decouple side-view features in the process of mapping 2D features to 3D. This method not only improves the precision of the 3D models but also their robustness, especially when SMPL-X estimates are not perfect. Our texture refinement process leverages text-to-image diffusion-based prior to generate realistic and consistent textures for invisible views. Through extensive experiments, SIFU surpasses SOTA methods in both geometry and texture reconstruction, showcasing enhanced robustness in complex scenarios and achieving an unprecedented Chamfer and P2S measurement. Our approach extends to practical applications such as 3D printing and scene building, demonstrating its broad utility in real-world scenarios. Project page https://river-zhang.github.io/SIFU-projectpage/ .

Recent advances in image-based 3D human shape estimation have been driven by the significant improvement in representation power afforded by deep neural networks. Although current approaches have demonstrated the potential in real world settings, they still fail to produce reconstructions with the level of detail often present in the input images. We argue that this limitation stems primarily form two conflicting requirements; accurate predictions require large context, but precise predictions require high resolution. Due to memory limitations in current hardware, previous approaches tend to take low resolution images as input to cover large spatial context, and produce less precise (or low resolution) 3D estimates as a result. We address this limitation by formulating a multi-level architecture that is end-to-end trainable. A coarse level observes the whole image at lower resolution and focuses on holistic reasoning. This provides context to an fine level which estimates highly detailed geometry by observing higher-resolution images. We demonstrate that our approach significantly outperforms existing state-of-the-art techniques on single image human shape reconstruction by fully leveraging 1k-resolution input images.

In this paper, we present TailorNet, a neural model which predicts clothing deformation in 3D as a function of three factors: pose, shape and style (garment geometry), while retaining wrinkle detail. This goes beyond prior models, which are either specific to one style and shape, or generalize to different shapes producing smooth results, despite being style specific. Our hypothesis is that (even non-linear) combinations of examples smooth out high frequency components such as fine-wrinkles, which makes learning the three factors jointly hard. At the heart of our technique is a decomposition of deformation into a high frequency and a low frequency component. While the low-frequency component is predicted from pose, shape and style parameters with an MLP, the high-frequency component is predicted with a mixture of shape-style specific pose models. The weights of the mixture are computed with a narrow bandwidth kernel to guarantee that only predictions with similar high-frequency patterns are combined. The style variation is obtained by computing, in a canonical pose, a subspace of deformation, which satisfies physical constraints such as inter-penetration, and draping on the body. TailorNet delivers 3D garments which retain the wrinkles from the physics based simulations (PBS) it is learned from, while running more than 1000 times faster. In contrast to PBS, TailorNet is easy to use and fully differentiable, which is crucial for computer vision algorithms. Several experiments demonstrate TailorNet produces more realistic results than prior work, and even generates temporally coherent deformations on sequences of the AMASS dataset, despite being trained on static poses from a different dataset. To stimulate further research in this direction, we will make a dataset consisting of 55800 frames, as well as our model publicly available at https://virtualhumans.mpi-inf.mpg.de/tailornet.

In this work, we present a novel physics-based data-driven framework for reduced-order modeling of laser ignition in a model rocket combustor based on parameterized neural ordinary differential equations (PNODE). Deep neural networks are embedded as functions of high-dimensional parameters of laser ignition to predict various terms in a 0D flow model including the heat source function, pre-exponential factors, and activation energy. Using the governing equations of a 0D flow model, our PNODE needs only a limited number of training samples and predicts trajectories of various quantities such as temperature, pressure, and mass fractions of species while satisfying physical constraints. We validate our physics-based PNODE on solution snapshots of high-fidelity Computational Fluid Dynamics (CFD) simulations of laser-induced ignition in a prototype rocket combustor. We compare the performance of our physics-based PNODE with that of kernel ridge regression and fully connected neural networks. Our results show that our physics-based PNODE provides solutions with lower mean absolute errors of average temperature over time, thus improving the prediction of successful laser ignition with high-dimensional parameters.

We present Brain Harmony (BrainHarmonix), the first multimodal brain foundation model that unifies structural morphology and functional dynamics into compact 1D token representations. The model was pretrained on two of the largest neuroimaging datasets to date, encompassing 64,594 T1-weighted structural MRI 3D volumes (~ 14 million images) and 70,933 functional MRI (fMRI) time series. BrainHarmonix is grounded in two foundational neuroscience principles: structure complements function - structural and functional modalities offer distinct yet synergistic insights into brain organization; function follows structure - brain functional dynamics are shaped by cortical morphology. The modular pretraining process involves single-modality training with geometric pre-alignment followed by modality fusion through shared brain hub tokens. Notably, our dynamics encoder uniquely handles fMRI time series with heterogeneous repetition times (TRs), addressing a major limitation in existing models. BrainHarmonix is also the first to deeply compress high-dimensional neuroimaging signals into unified, continuous 1D tokens, forming a compact latent space of the human brain. BrainHarmonix achieves strong generalization across diverse downstream tasks, including neurodevelopmental and neurodegenerative disorder classification and cognition prediction - consistently outperforming previous approaches. Our models - pretrained on 8 H100 GPUs - aim to catalyze a new era of AI-driven neuroscience powered by large-scale multimodal neuroimaging.

Recent advances in protein structure prediction have achieved near-atomic accuracy for well-folded proteins. However, current benchmarks inadequately assess model performance in biologically challenging contexts, especially those involving intrinsically disordered regions (IDRs), limiting their utility in applications such as drug discovery, disease variant interpretation, and protein interface design. We introduce DisProtBench, a comprehensive benchmark for evaluating protein structure prediction models (PSPMs) under structural disorder and complex biological conditions. DisProtBench spans three key axes: (1) Data complexity, covering disordered regions, G protein-coupled receptor (GPCR) ligand pairs, and multimeric complexes; (2) Task diversity, benchmarking twelve leading PSPMs across structure-based tasks with unified classification, regression, and interface metrics; and (3) Interpretability, via the DisProtBench Portal, which provides precomputed 3D structures and visual error analyses. Our results reveal significant variability in model robustness under disorder, with low-confidence regions linked to functional prediction failures. Notably, global accuracy metrics often fail to predict task performance in disordered settings, emphasizing the need for function-aware evaluation. DisProtBench establishes a reproducible, extensible, and biologically grounded framework for assessing next-generation PSPMs in realistic biomedical scenarios.

Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated remarkable success in predicting protein structure and function, their application to sequence-based PPI binding affinity prediction remains relatively underexplored. This gap is often attributed to the scarcity of high-quality, rigorously refined datasets and the reliance on simple strategies for concatenating protein representations. In this work, we address these limitations. First, we introduce a meticulously curated version of the PPB-Affinity dataset of a total of 8,207 unique protein-protein interaction entries, by resolving annotation inconsistencies and duplicate entries for multi-chain protein interactions. This dataset incorporates a stringent, less than or equal to 30%, sequence identity threshold to ensure robust splitting into training, validation, and test sets, minimizing data leakage. Second, we propose and systematically evaluate four architectures for adapting PLMs to PPI binding affinity prediction: embeddings concatenation (EC), sequences concatenation (SC), hierarchical pooling (HP), and pooled attention addition (PAD). These architectures were assessed using two training methods: full fine-tuning and a lightweight approach employing ConvBERT heads over frozen PLM features. Our comprehensive experiments across multiple leading PLMs (ProtT5, ESM2, Ankh, Ankh2, and ESM3) demonstrated that the HP and PAD architectures consistently outperform conventional concatenation methods, achieving up to 12% increase in terms of Spearman correlation. These results highlight the necessity of sophisticated architectural designs to fully exploit the capabilities of PLMs for nuanced PPI binding affinity prediction.

Alzheimer's disease (AD) is a common neurodegenerative disease among the elderly. Early prediction and timely intervention of its prodromal stage, mild cognitive impairment (MCI), can decrease the risk of advancing to AD. Combining information from various modalities can significantly improve predictive accuracy. However, challenges such as missing data and heterogeneity across modalities complicate multimodal learning methods as adding more modalities can worsen these issues. Current multimodal fusion techniques often fail to adapt to the complexity of medical data, hindering the ability to identify relationships between modalities. To address these challenges, we propose an innovative multimodal approach for predicting MCI conversion, focusing specifically on the issues of missing positron emission tomography (PET) data and integrating diverse medical information. The proposed incomplete triple-modal MCI conversion prediction network is tailored for this purpose. Through the missing modal generation module, we synthesize the missing PET data from the magnetic resonance imaging and extract features using specifically designed encoders. We also develop a channel aggregation module and a triple-modal co-attention fusion module to reduce feature redundancy and achieve effective multimodal data fusion. Furthermore, we design a loss function to handle missing modality issues and align cross-modal features. These components collectively harness multimodal data to boost network performance. Experimental results on the ADNI1 and ADNI2 datasets show that our method significantly surpasses existing unimodal and other multimodal models. Our code is available at https://github.com/justinhxy/ITFC.

As an important modeling paradigm in click-through rate (CTR) prediction, the Deep & Cross Network (DCN) and its derivative models have gained widespread recognition primarily due to their success in a trade-off between computational cost and performance. This paradigm employs a cross network to explicitly model feature interactions with linear growth, while leveraging deep neural networks (DNN) to implicitly capture higher-order feature interactions. However, these models still face several key limitations: (1) The performance of existing explicit feature interaction methods lags behind that of implicit DNN, resulting in overall model performance being dominated by the DNN; (2) While these models claim to capture high-order feature interactions, they often overlook potential noise within these interactions; (3) The learning process for different interaction network branches lacks appropriate supervision signals; and (4) The high-order feature interactions captured by these models are often implicit and non-interpretable due to their reliance on DNN. To address the identified limitations, this paper proposes a novel model, called Fusing Cross Network (FCN), along with two sub-networks: Linear Cross Network (LCN) and Exponential Cross Network (ECN). FCN explicitly captures feature interactions with both linear and exponential growth, eliminating the need to rely on implicit DNN. Moreover, we introduce the Self-Mask operation to filter noise layer by layer and reduce the number of parameters in the cross network by half. To effectively train these two cross networks, we propose a simple yet effective loss function called Tri-BCE, which provides tailored supervision signals for each network. We evaluate the effectiveness, efficiency, and interpretability of FCN on six benchmark datasets. Furthermore, by integrating LCN and ECN, FCN achieves a new state-of-the-art performance.

In this paper, we study the problem of inference in high-order structured prediction tasks. In the context of Markov random fields, the goal of a high-order inference task is to maximize a score function on the space of labels, and the score function can be decomposed into sum of unary and high-order potentials. We apply a generative model approach to study the problem of high-order inference, and provide a two-stage convex optimization algorithm for exact label recovery. We also provide a new class of hypergraph structural properties related to hyperedge expansion that drives the success in general high-order inference problems. Finally, we connect the performance of our algorithm and the hyperedge expansion property using a novel hypergraph Cheeger-type inequality.

Vision-Language Models (VLMs) have demonstrated strong capabilities in aligning visual and textual modalities, enabling a wide range of applications in multimodal understanding and generation. While they excel in zero-shot and transfer learning scenarios, VLMs remain susceptible to misclassification, often yielding confident yet incorrect predictions. This limitation poses a significant risk in safety-critical domains, where erroneous predictions can lead to severe consequences. In this work, we introduce TrustVLM, a training-free framework designed to address the critical challenge of estimating when VLM's predictions can be trusted. Motivated by the observed modality gap in VLMs and the insight that certain concepts are more distinctly represented in the image embedding space, we propose a novel confidence-scoring function that leverages this space to improve misclassification detection. We rigorously evaluate our approach across 17 diverse datasets, employing 4 architectures and 2 VLMs, and demonstrate state-of-the-art performance, with improvements of up to 51.87% in AURC, 9.14% in AUROC, and 32.42% in FPR95 compared to existing baselines. By improving the reliability of the model without requiring retraining, TrustVLM paves the way for safer deployment of VLMs in real-world applications. The code will be available at https://github.com/EPFL-IMOS/TrustVLM.

In this paper, we tackle the important yet under-investigated problem of making long-horizon prediction of event sequences. Existing state-of-the-art models do not perform well at this task due to their autoregressive structure. We propose HYPRO, a hybridly normalized probabilistic model that naturally fits this task: its first part is an autoregressive base model that learns to propose predictions; its second part is an energy function that learns to reweight the proposals such that more realistic predictions end up with higher probabilities. We also propose efficient training and inference algorithms for this model. Experiments on multiple real-world datasets demonstrate that our proposed HYPRO model can significantly outperform previous models at making long-horizon predictions of future events. We also conduct a range of ablation studies to investigate the effectiveness of each component of our proposed methods.

Recent advancements in data-driven weather forecasting models have delivered deterministic models that outperform the leading operational forecast systems based on traditional, physics-based models. However, these data-driven models are typically trained with a mean squared error loss function, which causes smoothing of fine scales through a "double penalty" effect. We develop a simple, parameter-free modification to this loss function that avoids this problem by separating the loss attributable to decorrelation from the loss attributable to spectral amplitude errors. Fine-tuning the GraphCast model with this new loss function results in sharp deterministic weather forecasts, an increase of the model's effective resolution from 1,250km to 160km, improvements to ensemble spread, and improvements to predictions of tropical cyclone strength and surface wind extremes.

Neural networks have recently achieved human-level performance on various challenging natural language processing (NLP) tasks, but it is notoriously difficult to understand why a neural network produced a particular prediction. In this paper, we leverage the text-to-text framework proposed by Raffel et al.(2019) to train language models to output a natural text explanation alongside their prediction. Crucially, this requires no modifications to the loss function or training and decoding procedures -- we simply train the model to output the explanation after generating the (natural text) prediction. We show that this approach not only obtains state-of-the-art results on explainability benchmarks, but also permits learning from a limited set of labeled explanations and transferring rationalization abilities across datasets. To facilitate reproducibility and future work, we release our code use to train the models.

A critical problem in the field of post hoc explainability is the lack of a common foundational goal among methods. For example, some methods are motivated by function approximation, some by game theoretic notions, and some by obtaining clean visualizations. This fragmentation of goals causes not only an inconsistent conceptual understanding of explanations but also the practical challenge of not knowing which method to use when. In this work, we begin to address these challenges by unifying eight popular post hoc explanation methods (LIME, C-LIME, KernelSHAP, Occlusion, Vanilla Gradients, Gradients x Input, SmoothGrad, and Integrated Gradients). We show that these methods all perform local function approximation of the black-box model, differing only in the neighbourhood and loss function used to perform the approximation. This unification enables us to (1) state a no free lunch theorem for explanation methods, demonstrating that no method can perform optimally across all neighbourhoods, and (2) provide a guiding principle to choose among methods based on faithfulness to the black-box model. We empirically validate these theoretical results using various real-world datasets, model classes, and prediction tasks. By bringing diverse explanation methods into a common framework, this work (1) advances the conceptual understanding of these methods, revealing their shared local function approximation objective, properties, and relation to one another, and (2) guides the use of these methods in practice, providing a principled approach to choose among methods and paving the way for the creation of new ones.

Legal judgment prediction (LJP) aims to function as a judge by making final rulings based on case claims and facts, which plays a vital role in the judicial domain for supporting court decision-making and improving judicial efficiency. However, existing methods often struggle with logical errors when conducting complex legal reasoning. We propose LegalReasoner, which enhances LJP reliability through step-wise verification and correction of the reasoning process. Specifically, it first identifies dispute points to decompose complex cases, and then conducts step-wise reasoning while employing a process verifier to validate each step's logic from correctness, progressiveness, and potential perspectives. When errors are detected, expert-designed attribution and resolution strategies are applied for correction. To fine-tune LegalReasoner, we release the LegalHK dataset, containing 58,130 Hong Kong court cases with detailed annotations of dispute points, step-by-step reasoning chains, and process verification labels. Experiments demonstrate that LegalReasoner significantly improves concordance with court decisions from 72.37 to 80.27 on LLAMA-3.1-70B. The data is available at https://huggingface.co/datasets/weijiezz/LegalHK.

JWST has now made it possible to probe the rest-frame optical line emission of high-redshift galaxies extending to z~9, and potentially beyond. To aid in the interpretation of these emerging constraints, in this work we explore predictions for [OIII] emission in high-redshift galaxies using the First Light and Reionisation Epoch Simulations (FLARES). We produce predictions for the [OIII] luminosity function, its correlation with the UV luminosity, and the distribution of equivalent widths (EWs). We also explore how the [OIII] EW correlates with physical properties including specific star formation rate, metallicity, and dust attenuation. Our predictions are largely consistent with recent observational constraints on the luminosity function, average equivalent widths, and line ratios. However, they fail to reproduce the observed tail of high-EW sources and the number density of extreme line emitters. Possibilities to explain these discrepancies include an additional source of ionising photons and/or greater stochasticity in star formation in the model or photometric scatter and/or bias in the observations. With JWST now rapidly building larger samples and a wider range of emission lines the answer to this remaining discrepancy should be available imminently.

We study subsampling-based ridge ensembles in the proportional asymptotics regime, where the feature size grows proportionally with the sample size such that their ratio converges to a constant. By analyzing the squared prediction risk of ridge ensembles as a function of the explicit penalty lambda and the limiting subsample aspect ratio phi_s (the ratio of the feature size to the subsample size), we characterize contours in the (lambda, phi_s)-plane at any achievable risk. As a consequence, we prove that the risk of the optimal full ridgeless ensemble (fitted on all possible subsamples) matches that of the optimal ridge predictor. In addition, we prove strong uniform consistency of generalized cross-validation (GCV) over the subsample sizes for estimating the prediction risk of ridge ensembles. This allows for GCV-based tuning of full ridgeless ensembles without sample splitting and yields a predictor whose risk matches optimal ridge risk.

Language Models (LMs) are being proposed for mental health applications where the heightened risk of adverse outcomes means predictive performance may not be a sufficient litmus test of a model's utility in clinical practice. A model that can be trusted for practice should have a correspondence between explanation and clinical determination, yet no prior research has examined the attention fidelity of these models and their effect on ground truth explanations. We introduce an evaluation design that focuses on the robustness and explainability of LMs in identifying Wellness Dimensions (WDs). We focus on two existing mental health and well-being datasets: (a) Multi-label Classification-based MultiWD, and (b) WellXplain for evaluating attention mechanism veracity against expert-labeled explanations. The labels are based on Halbert Dunn's theory of wellness, which gives grounding to our evaluation. We reveal four surprising results about LMs/LLMs: (1) Despite their human-like capabilities, GPT-3.5/4 lag behind RoBERTa, and MedAlpaca, a fine-tuned LLM on WellXplain fails to deliver any remarkable improvements in performance or explanations. (2) Re-examining LMs' predictions based on a confidence-oriented loss function reveals a significant performance drop. (3) Across all LMs/LLMs, the alignment between attention and explanations remains low, with LLMs scoring a dismal 0.0. (4) Most mental health-specific LMs/LLMs overlook domain-specific knowledge and undervalue explanations, causing these discrepancies. This study highlights the need for further research into their consistency and explanations in mental health and well-being.

The James Webb Space Telescope (JWST) is set to transform many areas of astronomy, one of the most exciting is the expansion of the redshift frontier to z>10. In its first year alone JWST should discover hundreds of galaxies, dwarfing the handful currently known. To prepare for these powerful observational constraints, we use the First Light And Reionisation Epoch (FLARES) simulations to predict the physical and observational properties of the z>10 population of galaxies accessible to JWST. This is the first time such predictions have been made using a hydrodynamical model validated at low redshift. Our predictions at z=10 are broadly in agreement with current observational constraints on the far-UV luminosity function and UV continuum slope beta, though the observational uncertainties are large. We note tension with recent constraints zsim 13 from Harikane et al. 2022 - compared to these constraints, FLARES predicts objects with the same space density should have an order of magnitude lower luminosity, though this is mitigated slightly if dust attenuation is negligible in these systems. Our predictions suggest that in JWST's first cycle alone, around 600 galaxies should be identified at z>10, with the first small samples available at z>13.

Predicting vulnerable source code helps to focus attention on those parts of the code that need to be examined with more scrutiny. Recent work proposed the use of function names as semantic cues that can be learned by a deep neural network (DNN) to aid in the hunt for vulnerability of functions. Combining identifier splitting, which splits each function name into its constituent words, with a novel frequency-based algorithm, we explore the extent to which the words that make up a function's name can predict potentially vulnerable functions. In contrast to *lightweight* predictions by a DNN that considers only function names, avoiding the use of a DNN provides *featherweight* predictions. The underlying idea is that function names that contain certain "dangerous" words are more likely to accompany vulnerable functions. Of course, this assumes that the frequency-based algorithm can be properly tuned to focus on truly dangerous words. Because it is more transparent than a DNN, the frequency-based algorithm enables us to investigate the inner workings of the DNN. If successful, this investigation into what the DNN does and does not learn will help us train more effective future models. We empirically evaluate our approach on a heterogeneous dataset containing over 73000 functions labeled vulnerable, and over 950000 functions labeled benign. Our analysis shows that words alone account for a significant portion of the DNN's classification ability. We also find that words are of greatest value in the datasets with a more homogeneous vocabulary. Thus, when working within the scope of a given project, where the vocabulary is unavoidably homogeneous, our approach provides a cheaper, potentially complementary, technique to aid in the hunt for source-code vulnerabilities. Finally, this approach has the advantage that it is viable with orders of magnitude less training data.

We introduce the use of rectified linear units (ReLU) as the classification function in a deep neural network (DNN). Conventionally, ReLU is used as an activation function in DNNs, with Softmax function as their classification function. However, there have been several studies on using a classification function other than Softmax, and this study is an addition to those. We accomplish this by taking the activation of the penultimate layer h_{n - 1} in a neural network, then multiply it by weight parameters theta to get the raw scores o_{i}. Afterwards, we threshold the raw scores o_{i} by 0, i.e. f(o) = max(0, o_{i}), where f(o) is the ReLU function. We provide class predictions y through argmax function, i.e. argmax f(x).

We present CRUXEval (Code Reasoning, Understanding, and eXecution Evaluation), a benchmark consisting of 800 Python functions (3-13 lines). Each function comes with an input-output pair, leading to two natural tasks: input prediction and output prediction. First, we propose a generic recipe for generating our execution benchmark which can be used to create future variation of the benchmark. Second, we evaluate twenty code models on our benchmark and discover that many recent high-scoring models on HumanEval do not show the same improvements on our benchmark. Third, we show that simple CoT and fine-tuning schemes can improve performance on our benchmark but remain far from solving it. The best setup, GPT-4 with chain of thought (CoT), achieves a pass@1 of 75% and 81% on input and output prediction, respectively. In contrast, Code Llama 34B achieves a pass@1 of 50% and 46% on input and output prediction, highlighting the gap between open and closed source models. As no model is close to acing CRUXEval, we provide examples of consistent GPT-4 failures on simple programs as a lens into its code reasoning capabilities and areas for improvement.

Recent studies have demonstrated the great power of Transformer models for time series forecasting. One of the key elements that lead to the transformer's success is the channel-independent (CI) strategy to improve the training robustness. However, the ignorance of the correlation among different channels in CI would limit the model's forecasting capacity. In this work, we design a special Transformer, i.e., Channel Aligned Robust Blend Transformer (CARD for short), that addresses key shortcomings of CI type Transformer in time series forecasting. First, CARD introduces a channel-aligned attention structure that allows it to capture both temporal correlations among signals and dynamical dependence among multiple variables over time. Second, in order to efficiently utilize the multi-scale knowledge, we design a token blend module to generate tokens with different resolutions. Third, we introduce a robust loss function for time series forecasting to alleviate the potential overfitting issue. This new loss function weights the importance of forecasting over a finite horizon based on prediction uncertainties. Our evaluation of multiple long-term and short-term forecasting datasets demonstrates that CARD significantly outperforms state-of-the-art time series forecasting methods. The code is available at the following repository:https://github.com/wxie9/CARD

Identifying cirrhosis is key to correctly assess the health of the liver. However, the gold standard diagnosis of the cirrhosis needs a medical intervention to obtain the histological confirmation, e.g. the METAVIR score, as the radiological presentation can be equivocal. In this work, we propose to leverage transfer learning from large datasets annotated by radiologists, which we consider as a weak annotation, to predict the histological score available on a small annex dataset. To this end, we propose to compare different pretraining methods, namely weakly-supervised and self-supervised ones, to improve the prediction of the cirrhosis. Finally, we introduce a loss function combining both supervised and self-supervised frameworks for pretraining. This method outperforms the baseline classification of the METAVIR score, reaching an AUC of 0.84 and a balanced accuracy of 0.75, compared to 0.77 and 0.72 for a baseline classifier.

Extreme multi-label text classification (XMTC) is the task of finding the most relevant subset labels from an extremely large-scale label collection. Recently, some deep learning models have achieved state-of-the-art results in XMTC tasks. These models commonly predict scores for all labels by a fully connected layer as the last layer of the model. However, such models can't predict a relatively complete and variable-length label subset for each document, because they select positive labels relevant to the document by a fixed threshold or take top k labels in descending order of scores. A less popular type of deep learning models called sequence-to-sequence (Seq2Seq) focus on predicting variable-length positive labels in sequence style. However, the labels in XMTC tasks are essentially an unordered set rather than an ordered sequence, the default order of labels restrains Seq2Seq models in training. To address this limitation in Seq2Seq, we propose an autoregressive sequence-to-set model for XMTC tasks named OTSeq2Set. Our model generates predictions in student-forcing scheme and is trained by a loss function based on bipartite matching which enables permutation-invariance. Meanwhile, we use the optimal transport distance as a measurement to force the model to focus on the closest labels in semantic label space. Experiments show that OTSeq2Set outperforms other competitive baselines on 4 benchmark datasets. Especially, on the Wikipedia dataset with 31k labels, it outperforms the state-of-the-art Seq2Seq method by 16.34% in micro-F1 score. The code is available at https://github.com/caojie54/OTSeq2Set.

We develop a multi-step workflow for the discovery of conventional superconductors, starting with a Bardeen Cooper Schrieffer inspired pre-screening of 1736 materials with high Debye temperature and electronic density of states. Next, we perform electron-phonon coupling calculations for 1058 of them to establish a large and systematic database of BCS superconducting properties. Using the McMillan-Allen-Dynes formula, we identify 105 dynamically stable materials with transition temperatures, Tc>5 K. Additionally, we analyze trends in our dataset and individual materials including MoN, VC, VTe, KB6, Ru3NbC, V3Pt, ScN, LaN2, RuO2, and TaC. We demonstrate that deep-learning(DL) models can predict superconductor properties faster than direct first principles computations. Notably, we find that by predicting the Eliashberg function as an intermediate quantity, we can improve model performance versus a direct DL prediction of Tc. We apply the trained models on the crystallographic open database and pre-screen candidates for further DFT calculations.

Visual agent models for automating human activities on Graphical User Interfaces (GUIs) have emerged as a promising research direction, driven by advances in large Vision Language Models (VLMs). A critical challenge in GUI automation is the precise grounding of interface elements across diverse platforms. Existing vision-only GUI agents directly ground elements from large and cluttered screenshots, requiring them to process substantial irrelevant information that compromises their accuracy. In addition, these approaches typically employ basic cross-entropy loss for learning grounding objectives, which fails to effectively capture grounding quality compared to established object detection metrics like Intersection-over-Union (IoU). To address these issues, we introduce R-VLM, a novel GUI grounding approach that leverages zoomed-in region proposals for precise element localization. We also propose an IoU-aware objective function that facilitates model convergence toward high IoU predictions. Our approach bridges the gap between VLMs and conventional object detection techniques, improving the state-of-the-art grounding accuracy by 13% across diverse GUI platforms on the GUI grounding benchmarks ScreenSpot and AgentStudio. In addition, our R-VLM approach shows 3.2-9.7% absolute accuracy improvements in GUI navigation tasks on the AITW and Mind2Web benchmarks.

We study growth of solid tumors in a partial differential equation model introduced by Hillen et al for the interaction between tumor cells (TCs) and cancer stem cells (CSCs). We find that invasion into the cancer-free state may be separated into two regimes, depending on the death rate of tumor cells. In the first, staged invasion regime, invasion into the cancer-free state is lead by tumor cells, which are then subsequently invaded at a slower speed by cancer stem cells. In the second, TC extinction regime, cancer stem cells directly invade the cancer-free state. Relying on recent results establishing front selection propagation under marginal stability assumptions, we use geometric singular perturbation theory to establish existence and selection properties of front solutions which describe both the primary and secondary invasion processes. With rigorous predictions for the invasion speeds, we are then able to heuristically predict how the total cancer mass as a function of time depends on the TC death rate, finding in some situations a tumor invasion paradox, in which increasing the TC death rate leads to an increase in the total cancer mass. Our methods give a general approach for verifying linear determinacy of spreading speeds of invasion fronts in systems with fast-slow structure.

Implicit layer deep learning techniques, like Neural Differential Equations, have become an important modeling framework due to their ability to adapt to new problems automatically. Training a neural differential equation is effectively a search over a space of plausible dynamical systems. However, controlling the computational cost for these models is difficult since it relies on the number of steps the adaptive solver takes. Most prior works have used higher-order methods to reduce prediction timings while greatly increasing training time or reducing both training and prediction timings by relying on specific training algorithms, which are harder to use as a drop-in replacement due to strict requirements on automatic differentiation. In this manuscript, we use internal cost heuristics of adaptive differential equation solvers at stochastic time points to guide the training toward learning a dynamical system that is easier to integrate. We "close the black-box" and allow the use of our method with any adjoint technique for gradient calculations of the differential equation solution. We perform experimental studies to compare our method to global regularization to show that we attain similar performance numbers without compromising the flexibility of implementation on ordinary differential equations (ODEs) and stochastic differential equations (SDEs). We develop two sampling strategies to trade off between performance and training time. Our method reduces the number of function evaluations to 0.556-0.733x and accelerates predictions by 1.3-2x.

In this paper, we present SCOREQ, a novel approach for speech quality prediction. SCOREQ is a triplet loss function for contrastive regression that addresses the domain generalisation shortcoming exhibited by state of the art no-reference speech quality metrics. In the paper we: (i) illustrate the problem of L2 loss training failing at capturing the continuous nature of the mean opinion score (MOS) labels; (ii) demonstrate the lack of generalisation through a benchmarking evaluation across several speech domains; (iii) outline our approach and explore the impact of the architectural design decisions through incremental evaluation; (iv) evaluate the final model against state of the art models for a wide variety of data and domains. The results show that the lack of generalisation observed in state of the art speech quality metrics is addressed by SCOREQ. We conclude that using a triplet loss function for contrastive regression improves generalisation for speech quality prediction models but also has potential utility across a wide range of applications using regression-based predictive models.

Bayesian neural networks (BNNs) have been an important framework in the study of uncertainty quantification. Deterministic variational inference, one of the inference methods, utilizes moment propagation to compute the predictive distributions and objective functions. Unfortunately, deriving the moments requires computationally expensive Taylor expansion in nonlinear functions, such as a rectified linear unit (ReLU) or a sigmoid function. Therefore, a new nonlinear function that realizes faster moment propagation than conventional functions is required. In this paper, we propose a novel nonlinear function named moment propagating-Gaussian error linear unit (MP-GELU) that enables the fast derivation of first and second moments in BNNs. MP-GELU enables the analytical computation of moments by applying nonlinearity to the input statistics, thereby reducing the computationally expensive calculations required for nonlinear functions. In empirical experiments on regression tasks, we observed that the proposed MP-GELU provides higher prediction accuracy and better quality of uncertainty with faster execution than those of ReLU-based BNNs.

International Classification of Disease (ICD) coding procedure which refers to tagging medical notes with diagnosis codes has been shown to be effective and crucial to the billing system in medical sector. Currently, ICD codes are assigned to a clinical note manually which is likely to cause many errors. Moreover, training skilled coders also requires time and human resources. Therefore, automating the ICD code determination process is an important task. With the advancement of artificial intelligence theory and computational hardware, machine learning approach has emerged as a suitable solution to automate this process. In this project, we apply a transformer-based architecture to capture the interdependence among the tokens of a document and then use a code-wise attention mechanism to learn code-specific representations of the entire document. Finally, they are fed to separate dense layers for corresponding code prediction. Furthermore, to handle the imbalance in the code frequency of clinical datasets, we employ a label distribution aware margin (LDAM) loss function. The experimental results on the MIMIC-III dataset show that our proposed model outperforms other baselines by a significant margin. In particular, our best setting achieves a micro-AUC score of 0.923 compared to 0.868 of bidirectional recurrent neural networks. We also show that by using the code-wise attention mechanism, the model can provide more insights about its prediction, and thus it can support clinicians to make reliable decisions. Our code is available online (https://github.com/biplob1ly/TransICD)

Direct prediction of 3D body pose and shape remains a challenge even for highly parameterized deep learning models. Mapping from the 2D image space to the prediction space is difficult: perspective ambiguities make the loss function noisy and training data is scarce. In this paper, we propose a novel approach (Neural Body Fitting (NBF)). It integrates a statistical body model within a CNN, leveraging reliable bottom-up semantic body part segmentation and robust top-down body model constraints. NBF is fully differentiable and can be trained using 2D and 3D annotations. In detailed experiments, we analyze how the components of our model affect performance, especially the use of part segmentations as an explicit intermediate representation, and present a robust, efficiently trainable framework for 3D human pose estimation from 2D images with competitive results on standard benchmarks. Code will be made available at http://github.com/mohomran/neural_body_fitting

Previous literature offers limited clues on how to learn a periodic function using modern neural networks. We start with a study of the extrapolation properties of neural networks; we prove and demonstrate experimentally that the standard activations functions, such as ReLU, tanh, sigmoid, along with their variants, all fail to learn to extrapolate simple periodic functions. We hypothesize that this is due to their lack of a "periodic" inductive bias. As a fix of this problem, we propose a new activation, namely, x + sin^2(x), which achieves the desired periodic inductive bias to learn a periodic function while maintaining a favorable optimization property of the ReLU-based activations. Experimentally, we apply the proposed method to temperature and financial data prediction.

Most human proteins remain undrugged, over 96% of human proteins remain unexploited by approved therapeutics. While structure-based virtual screening promises to expand the druggable proteome, existing methods lack atomic-level precision and fail to predict binding fitness, limiting translational impact. We present AuroBind, a scalable virtual screening framework that fine-tunes a custom atomic-level structural model on million-scale chemogenomic data. AuroBind integrates direct preference optimization, self-distillation from high-confidence complexes, and a teacher-student acceleration strategy to jointly predict ligand-bound structures and binding fitness. The proposed models outperform state-of-the-art models on structural and functional benchmarks while enabling 100,000-fold faster screening across ultra-large compound libraries. In a prospective screen across ten disease-relevant targets, AuroBind achieved experimental hit rates of 7-69%, with top compounds reaching sub-nanomolar to picomolar potency. For the orphan GPCRs GPR151 and GPR160, AuroBind identified both agonists and antagonists with success rates of 16-30%, and functional assays confirmed GPR160 modulation in liver and prostate cancer models. AuroBind offers a generalizable framework for structure-function learning and high-throughput molecular screening, bridging the gap between structure prediction and therapeutic discovery.

Split conformal prediction has recently sparked great interest due to its ability to provide formally guaranteed uncertainty sets or intervals for predictions made by black-box neural models, ensuring a predefined probability of containing the actual ground truth. While the original formulation assumes data exchangeability, some extensions handle non-exchangeable data, which is often the case in many real-world scenarios. In parallel, some progress has been made in conformal methods that provide statistical guarantees for a broader range of objectives, such as bounding the best F_1-score or minimizing the false negative rate in expectation. In this paper, we leverage and extend these two lines of work by proposing non-exchangeable conformal risk control, which allows controlling the expected value of any monotone loss function when the data is not exchangeable. Our framework is flexible, makes very few assumptions, and allows weighting the data based on its relevance for a given test example; a careful choice of weights may result on tighter bounds, making our framework useful in the presence of change points, time series, or other forms of distribution drift. Experiments with both synthetic and real world data show the usefulness of our method.

Though Transformers have achieved promising results in many computer vision tasks, they tend to be over-confident in predictions, as the standard Dot Product Self-Attention (DPSA) can barely preserve distance for the unbounded input domain. In this work, we fill this gap by proposing a novel Lipschitz Regularized Transformer (LRFormer). Specifically, we present a new similarity function with the distance within Banach Space to ensure the Lipschitzness and also regularize the term by a contractive Lipschitz Bound. The proposed method is analyzed with a theoretical guarantee, providing a rigorous basis for its effectiveness and reliability. Extensive experiments conducted on standard vision benchmarks demonstrate that our method outperforms the state-of-the-art single forward pass approaches in prediction, calibration, and uncertainty estimation.

Medical applications of machine learning (ML) have experienced a surge in popularity in recent years. The intensive care unit (ICU) is a natural habitat for ML given the abundance of available data from electronic health records. Models have been proposed to address numerous ICU prediction tasks like the early detection of complications. While authors frequently report state-of-the-art performance, it is challenging to verify claims of superiority. Datasets and code are not always published, and cohort definitions, preprocessing pipelines, and training setups are difficult to reproduce. This work introduces Yet Another ICU Benchmark (YAIB), a modular framework that allows researchers to define reproducible and comparable clinical ML experiments; we offer an end-to-end solution from cohort definition to model evaluation. The framework natively supports most open-access ICU datasets (MIMIC III/IV, eICU, HiRID, AUMCdb) and is easily adaptable to future ICU datasets. Combined with a transparent preprocessing pipeline and extensible training code for multiple ML and deep learning models, YAIB enables unified model development. Our benchmark comes with five predefined established prediction tasks (mortality, acute kidney injury, sepsis, kidney function, and length of stay) developed in collaboration with clinicians. Adding further tasks is straightforward by design. Using YAIB, we demonstrate that the choice of dataset, cohort definition, and preprocessing have a major impact on the prediction performance - often more so than model class - indicating an urgent need for YAIB as a holistic benchmarking tool. We provide our work to the clinical ML community to accelerate method development and enable real-world clinical implementations. Software Repository: https://github.com/rvandewater/YAIB.

When language models (LMs) are trained via reinforcement learning (RL) to generate natural language "reasoning chains", their performance improves on a variety of difficult question answering tasks. Today, almost all successful applications of RL for reasoning use binary reward functions that evaluate the correctness of LM outputs. Because such reward functions do not penalize guessing or low-confidence outputs, they often have the unintended side-effect of degrading calibration and increasing the rate at which LMs generate incorrect responses (or "hallucinate") in other problem domains. This paper describes RLCR (Reinforcement Learning with Calibration Rewards), an approach to training reasoning models that jointly improves accuracy and calibrated confidence estimation. During RLCR, LMs generate both predictions and numerical confidence estimates after reasoning. They are trained to optimize a reward function that augments a binary correctness score with a Brier score -- a scoring rule for confidence estimates that incentivizes calibrated prediction. We first prove that this reward function (or any analogous reward function that uses a bounded, proper scoring rule) yields models whose predictions are both accurate and well-calibrated. We next show that across diverse datasets, RLCR substantially improves calibration with no loss in accuracy, on both in-domain and out-of-domain evaluations -- outperforming both ordinary RL training and classifiers trained to assign post-hoc confidence scores. While ordinary RL hurts calibration, RLCR improves it. Finally, we demonstrate that verbalized confidence can be leveraged at test time to improve accuracy and calibration via confidence-weighted scaling methods. Our results show that explicitly optimizing for calibration can produce more generally reliable reasoning models.

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models nucleotide evolution on phylogenetic trees using multispecies whole-genome alignments. Our approach integrates an alignment into the loss function during training but does not require it for making predictions, thereby enhancing the model's applicability. We applied this framework to train PhyloGPN, a model that excels at predicting functionally disruptive variants from a single sequence alone and demonstrates strong transfer learning capabilities.

We present the Cosmology and Astrophysics with MachinE Learning Simulations --CAMELS-- project. CAMELS is a suite of 4,233 cosmological simulations of (25~h^{-1}{rm Mpc})^3 volume each: 2,184 state-of-the-art (magneto-)hydrodynamic simulations run with the AREPO and GIZMO codes, employing the same baryonic subgrid physics as the IllustrisTNG and SIMBA simulations, and 2,049 N-body simulations. The goal of the CAMELS project is to provide theory predictions for different observables as a function of cosmology and astrophysics, and it is the largest suite of cosmological (magneto-)hydrodynamic simulations designed to train machine learning algorithms. CAMELS contains thousands of different cosmological and astrophysical models by way of varying Omega_m, sigma_8, and four parameters controlling stellar and AGN feedback, following the evolution of more than 100 billion particles and fluid elements over a combined volume of (400~h^{-1}{rm Mpc})^3. We describe the simulations in detail and characterize the large range of conditions represented in terms of the matter power spectrum, cosmic star formation rate density, galaxy stellar mass function, halo baryon fractions, and several galaxy scaling relations. We show that the IllustrisTNG and SIMBA suites produce roughly similar distributions of galaxy properties over the full parameter space but significantly different halo baryon fractions and baryonic effects on the matter power spectrum. This emphasizes the need for marginalizing over baryonic effects to extract the maximum amount of information from cosmological surveys. We illustrate the unique potential of CAMELS using several machine learning applications, including non-linear interpolation, parameter estimation, symbolic regression, data generation with Generative Adversarial Networks (GANs), dimensionality reduction, and anomaly detection.

Echocardiography (ECHO) is essential for cardiac assessments, but its video quality and interpretation heavily relies on manual expertise, leading to inconsistent results from clinical and portable devices. ECHO video generation offers a solution by improving automated monitoring through synthetic data and generating high-quality videos from routine health data. However, existing models often face high computational costs, slow inference, and rely on complex conditional prompts that require experts' annotations. To address these challenges, we propose ECHOPULSE, an ECG-conditioned ECHO video generation model. ECHOPULSE introduces two key advancements: (1) it accelerates ECHO video generation by leveraging VQ-VAE tokenization and masked visual token modeling for fast decoding, and (2) it conditions on readily accessible ECG signals, which are highly coherent with ECHO videos, bypassing complex conditional prompts. To the best of our knowledge, this is the first work to use time-series prompts like ECG signals for ECHO video generation. ECHOPULSE not only enables controllable synthetic ECHO data generation but also provides updated cardiac function information for disease monitoring and prediction beyond ECG alone. Evaluations on three public and private datasets demonstrate state-of-the-art performance in ECHO video generation across both qualitative and quantitative measures. Additionally, ECHOPULSE can be easily generalized to other modality generation tasks, such as cardiac MRI, fMRI, and 3D CT generation. Demo can seen from https://github.com/levyisthebest/ECHOPulse_Prelease.

In this article, we present a structured Kalman filter associated with the transformation matrix for observable Kalman canonical decomposition from conventional Kalman filter (CKF) in order to generate a more accurate time scale. The conventional Kalman filter is a special case of the proposed structured Kalman filter which yields the same predicted unobservable or observable states when some conditions are satisfied. We consider an optimization problem respective to the transformation matrix where the objective function is associated with not only the expected value of prediction error but also its variance. We reveal that such an objective function is a convex function and show some conditions under which CKF is nothing but the optimal algorithm if ideal computation is possible without computation error. A numerical example is presented to show the robustness of the proposed method in terms of the initial error covariance

Machine learning frameworks such as graph neural networks typically rely on a given, fixed graph to exploit relational inductive biases and thus effectively learn from network data. However, when said graphs are (partially) unobserved, noisy, or dynamic, the problem of inferring graph structure from data becomes relevant. In this paper, we postulate a graph convolutional relationship between the observed and latent graphs, and formulate the graph learning task as a network inverse (deconvolution) problem. In lieu of eigendecomposition-based spectral methods or iterative optimization solutions, we unroll and truncate proximal gradient iterations to arrive at a parameterized neural network architecture that we call a Graph Deconvolution Network (GDN). GDNs can learn a distribution of graphs in a supervised fashion, perform link prediction or edge-weight regression tasks by adapting the loss function, and they are inherently inductive. We corroborate GDN's superior graph recovery performance and its generalization to larger graphs using synthetic data in supervised settings. Furthermore, we demonstrate the robustness and representation power of GDNs on real world neuroimaging and social network datasets.

Recently two-stage detectors have surged ahead of single-shot detectors in the accuracy-vs-speed trade-off. Nevertheless single-shot detectors are immensely popular in embedded vision applications. This paper brings single-shot detectors up to the same level as current two-stage techniques. We do this by improving training for the state-of-the-art single-shot detector, RetinaNet, in three ways: integrating instance mask prediction for the first time, making the loss function adaptive and more stable, and including additional hard examples in training. We call the resulting augmented network RetinaMask. The detection component of RetinaMask has the same computational cost as the original RetinaNet, but is more accurate. COCO test-dev results are up to 41.4 mAP for RetinaMask-101 vs 39.1mAP for RetinaNet-101, while the runtime is the same during evaluation. Adding Group Normalization increases the performance of RetinaMask-101 to 41.7 mAP. Code is at:https://github.com/chengyangfu/retinamask

Kaplan et al. and Hoffmann et al. developed influential scaling laws for the optimal model size as a function of the compute budget, but these laws yield substantially different predictions. We explain the discrepancy by reproducing the Kaplan scaling law on two datasets (OpenWebText2 and RefinedWeb) and identifying three factors causing the difference: last layer computational cost, warmup duration, and scale-dependent optimizer tuning. With these factors corrected, we obtain excellent agreement with the Hoffmann et al. (i.e., "Chinchilla") scaling law. Counter to a hypothesis of Hoffmann et al., we find that careful learning rate decay is not essential for the validity of their scaling law. As a secondary result, we derive scaling laws for the optimal learning rate and batch size, finding that tuning the AdamW beta_2 parameter is essential at lower batch sizes.

In-context learning (ICL) emerges as a promising capability of large language models (LLMs) by providing them with demonstration examples to perform diverse tasks. However, the underlying mechanism of how LLMs learn from the provided context remains under-explored. In this paper, we investigate the working mechanism of ICL through an information flow lens. Our findings reveal that label words in the demonstration examples function as anchors: (1) semantic information aggregates into label word representations during the shallow computation layers' processing; (2) the consolidated information in label words serves as a reference for LLMs' final predictions. Based on these insights, we introduce an anchor re-weighting method to improve ICL performance, a demonstration compression technique to expedite inference, and an analysis framework for diagnosing ICL errors in GPT2-XL. The promising applications of our findings again validate the uncovered ICL working mechanism and pave the way for future studies.

How can we rely on an end-to-end autonomous vehicle's complex decision-making system during deployment? One common solution is to have a ``fallback layer'' that checks the planned trajectory for rule violations and replaces it with a pre-defined safe action if necessary. Another approach involves adjusting the planner's decisions to minimize a pre-defined ``cost function'' using additional system predictions such as road layouts and detected obstacles. However, these pre-programmed rules or cost functions cannot learn and improve with new training data, often resulting in overly conservative behaviors. In this work, we propose Centaur (Cluster Entropy for Test-time trAining using Uncertainty) which updates a planner's behavior via test-time training, without relying on hand-engineered rules or cost functions. Instead, we measure and minimize the uncertainty in the planner's decisions. For this, we develop a novel uncertainty measure, called Cluster Entropy, which is simple, interpretable, and compatible with state-of-the-art planning algorithms. Using data collected at prior test-time time-steps, we perform an update to the model's parameters using a gradient that minimizes the Cluster Entropy. With only this sole gradient update prior to inference, Centaur exhibits significant improvements, ranking first on the navtest leaderboard with notable gains in safety-critical metrics such as time to collision. To provide detailed insights on a per-scenario basis, we also introduce navsafe, a challenging new benchmark, which highlights previously undiscovered failure modes of driving models.

Self-distillation (SD) is the process of first training a teacher model and then using its predictions to train a student model with the same architecture. Specifically, the student's objective function is big(xi*ell(teacher's predictions, student's predictions) + (1-xi)*ell(given labels, student's predictions)big), where ell is some loss function and xi is some parameter in [0,1]. Empirically, SD has been observed to provide performance gains in several settings. In this paper, we theoretically characterize the effect of SD in two supervised learning problems with noisy labels. We first analyze SD for regularized linear regression and show that in the high label noise regime, the optimal value of xi that minimizes the expected error in estimating the ground truth parameter is surprisingly greater than 1. Empirically, we show that xi > 1 works better than xi leq 1 even with the cross-entropy loss for several classification datasets when 50\% or 30\% of the labels are corrupted. Further, we quantify when optimal SD is better than optimal regularization. Next, we analyze SD in the case of logistic regression for binary classification with random label corruption and quantify the range of label corruption in which the student outperforms the teacher in terms of accuracy. To our knowledge, this is the first result of its kind for the cross-entropy loss.

Image classification is one of the most important areas in computer vision. Hierarchical multi-label classification applies when a multi-class image classification problem is arranged into smaller ones based upon a hierarchy or taxonomy. Thus, hierarchical classification modes generally provide multiple class predictions on each instance, whereby these are expected to reflect the structure of image classes as related to one another. In this paper, we propose a multi-label capsule network (ML-CapsNet) for hierarchical classification. Our ML-CapsNet predicts multiple image classes based on a hierarchical class-label tree structure. To this end, we present a loss function that takes into account the multi-label predictions of the network. As a result, the training approach for our ML-CapsNet uses a coarse to fine paradigm while maintaining consistency with the structure in the classification levels in the label-hierarchy. We also perform experiments using widely available datasets and compare the model with alternatives elsewhere in the literature. In our experiments, our ML-CapsNet yields a margin of improvement with respect to these alternative methods.

Feed-forward layers constitute two-thirds of a transformer model's parameters, yet their role in the network remains under-explored. We show that feed-forward layers in transformer-based language models operate as key-value memories, where each key correlates with textual patterns in the training examples, and each value induces a distribution over the output vocabulary. Our experiments show that the learned patterns are human-interpretable, and that lower layers tend to capture shallow patterns, while upper layers learn more semantic ones. The values complement the keys' input patterns by inducing output distributions that concentrate probability mass on tokens likely to appear immediately after each pattern, particularly in the upper layers. Finally, we demonstrate that the output of a feed-forward layer is a composition of its memories, which is subsequently refined throughout the model's layers via residual connections to produce the final output distribution.

Modern music producers commonly use MIDI (Musical Instrument Digital Interface) to store their musical compositions. However, MIDI files created with digital software may lack the expressive characteristics of human performances, essentially leaving the velocity parameter - a control for note loudness - undefined, which defaults to a flat value. The task of filling MIDI velocity is termed MIDI velocity prediction, which uses regression models to enhance music expressiveness by adjusting only this parameter. In this paper, we introduce the U-Net, a widely adopted architecture in image colorization, to this task. By conceptualizing MIDI data as images, we adopt window attention and develop a custom loss function to address the sparsity of MIDI-converted images. Current dataset availability restricts our experiments to piano data. Evaluated on the MAESTRO v3 and SMD datasets, our proposed method for filling MIDI velocity outperforms previous approaches in both quantitative metrics and qualitative listening tests.

Distillation has shown remarkable success in transferring knowledge from a Large Language Model (LLM) teacher to a student LLM. However, current distillation methods predominantly require the same tokenizer between the teacher and the student, restricting their applicability to only a small subset of teacher-student pairs. In this work, we develop a cross-tokenizer distillation method to solve this crucial deficiency. Our method is the first to enable cross-tokenizer distillation without a next-token prediction loss as the main objective, instead purely maximizing the student predictions' similarity to the teacher's predictions (known as pure distillation), while also being robust to large mismatches between the teacher and the student tokenizer function and vocabulary. Empirically, our method enables substantially improved performance as tested on two use cases. First, we show that viewing tokenizer transfer as self-distillation enables unprecedently effective transfer across tokenizers. We transfer (subword-level) Llama and Gemma models to byte-level tokenization more effectively than prior methods transfer to a similar subword tokenizer under a comparable training budget. Transferring different base models to the same tokenizer also enables ensembling them (e.g., via averaging their predicted probabilities) which boosts performance. Second, we use our cross-tokenizer distillation method to distil a large maths-specialized LLM into a smaller model, achieving competitive maths problem-solving performance. Overall, our results make substantial strides toward better adaptability and enhanced interaction between different LLMs.

In this paper, we propose a simple yet universal network termed SeqTR for visual grounding tasks, e.g., phrase localization, referring expression comprehension (REC) and segmentation (RES). The canonical paradigms for visual grounding often require substantial expertise in designing network architectures and loss functions, making them hard to generalize across tasks. To simplify and unify the modeling, we cast visual grounding as a point prediction problem conditioned on image and text inputs, where either the bounding box or binary mask is represented as a sequence of discrete coordinate tokens. Under this paradigm, visual grounding tasks are unified in our SeqTR network without task-specific branches or heads, e.g., the convolutional mask decoder for RES, which greatly reduces the complexity of multi-task modeling. In addition, SeqTR also shares the same optimization objective for all tasks with a simple cross-entropy loss, further reducing the complexity of deploying hand-crafted loss functions. Experiments on five benchmark datasets demonstrate that the proposed SeqTR outperforms (or is on par with) the existing state-of-the-arts, proving that a simple yet universal approach for visual grounding is indeed feasible. Source code is available at https://github.com/sean-zhuh/SeqTR.

Modern detection transformers (DETRs) use a set of object queries to predict a list of bounding boxes, sort them by their classification confidence scores, and select the top-ranked predictions as the final detection results for the given input image. A highly performant object detector requires accurate ranking for the bounding box predictions. For DETR-based detectors, the top-ranked bounding boxes suffer from less accurate localization quality due to the misalignment between classification scores and localization accuracy, thus impeding the construction of high-quality detectors. In this work, we introduce a simple and highly performant DETR-based object detector by proposing a series of rank-oriented designs, combinedly called Rank-DETR. Our key contributions include: (i) a rank-oriented architecture design that can prompt positive predictions and suppress the negative ones to ensure lower false positive rates, as well as (ii) a rank-oriented loss function and matching cost design that prioritizes predictions of more accurate localization accuracy during ranking to boost the AP under high IoU thresholds. We apply our method to improve the recent SOTA methods (e.g., H-DETR and DINO-DETR) and report strong COCO object detection results when using different backbones such as ResNet-50, Swin-T, and Swin-L, demonstrating the effectiveness of our approach. Code is available at https://github.com/LeapLabTHU/Rank-DETR.

Recent advancements in instruction tuning for large language models (LLMs) suggest that a small, high-quality dataset can significantly equip LLMs with instruction-following capabilities, outperforming large datasets often burdened by quality and redundancy issues. However, the challenge lies in automatically identifying valuable subsets from large datasets to boost both the effectiveness and efficiency of instruction tuning. In this paper, we first establish data selection criteria based on three distinct aspects of data value: diversity, difficulty, and dependability, and then propose the D3 method comprising two key steps of scoring and selection. Specifically, in the scoring step, we define the diversity function to measure sample distinctiveness and introduce the uncertainty-based prediction difficulty to evaluate sample difficulty by mitigating the interference of context-oriented generation diversity. Additionally, we integrate an external LLM for dependability assessment. In the selection step, we formulate the D3 weighted coreset objective, which jointly optimizes three aspects of data value to solve for the most valuable subset. The two steps of D3 can iterate multiple rounds, incorporating feedback to refine the selection focus adaptively. Experiments on both public datasets and the real-world Taobao Live application demonstrate the effectiveness of D3 in endowing LLMs with competitive or even superior instruction-following capabilities using less than 10\% of the entire dataset.

Code completion aims at speeding up code writing by recommending to developers the next tokens they are likely to type. Deep Learning (DL) models pushed the boundaries of code completion by redefining what these coding assistants can do: We moved from predicting few code tokens to automatically generating entire functions. One important factor impacting the performance of DL-based code completion techniques is the context provided as input. With "context" we refer to what the model knows about the code to complete. In a simple scenario, the DL model might be fed with a partially implemented function to complete. In this case, the context is represented by the incomplete function and, based on it, the model must generate a prediction. It is however possible to expand such a context to include additional information, like the whole source code file containing the function to complete, which could be useful to boost the prediction performance. In this work, we present an empirical study investigating how the performance of a DL-based code completion technique is affected by different contexts. We experiment with 8 types of contexts and their combinations. These contexts include: (i) coding contexts, featuring information extracted from the code base in which the code completion is invoked (e.g., code components structurally related to the one to "complete"); (ii) process context, with information aimed at depicting the current status of the project in which a code completion task is triggered (e.g., a textual representation of open issues relevant for the code to complete); and (iii) developer contexts, capturing information about the developer invoking the code completion (e.g., the APIs frequently used). Our results show that additional contextual information can benefit the performance of DL-based code completion, with relative improvements up to +22% in terms of correct predictions.

Recent developments in quantum computing and machine learning have propelled the interdisciplinary study of quantum machine learning. Sequential modeling is an important task with high scientific and commercial value. Existing VQC or QNN-based methods require significant computational resources to perform the gradient-based optimization of a larger number of quantum circuit parameters. The major drawback is that such quantum gradient calculation requires a large amount of circuit evaluation, posing challenges in current near-term quantum hardware and simulation software. In this work, we approach sequential modeling by applying a reservoir computing (RC) framework to quantum recurrent neural networks (QRNN-RC) that are based on classical RNN, LSTM and GRU. The main idea to this RC approach is that the QRNN with randomly initialized weights is treated as a dynamical system and only the final classical linear layer is trained. Our numerical simulations show that the QRNN-RC can reach results comparable to fully trained QRNN models for several function approximation and time series prediction tasks. Since the QRNN training complexity is significantly reduced, the proposed model trains notably faster. In this work we also compare to corresponding classical RNN-based RC implementations and show that the quantum version learns faster by requiring fewer training epochs in most cases. Our results demonstrate a new possibility to utilize quantum neural network for sequential modeling with greater quantum hardware efficiency, an important design consideration for noisy intermediate-scale quantum (NISQ) computers.

We consider the classic supervised learning problem, where a continuous non-negative random label Y (i.e. a random duration) is to be predicted based upon observing a random vector X valued in R^d with dgeq 1 by means of a regression rule with minimum least square error. In various applications, ranging from industrial quality control to public health through credit risk analysis for instance, training observations can be right censored, meaning that, rather than on independent copies of (X,Y), statistical learning relies on a collection of ngeq 1 independent realizations of the triplet (X, ; min{Y,; C},; δ), where C is a nonnegative r.v. with unknown distribution, modeling censorship and δ=I{Yleq C} indicates whether the duration is right censored or not. As ignoring censorship in the risk computation may clearly lead to a severe underestimation of the target duration and jeopardize prediction, we propose to consider a plug-in estimate of the true risk based on a Kaplan-Meier estimator of the conditional survival function of the censorship C given X, referred to as Kaplan-Meier risk, in order to perform empirical risk minimization. It is established, under mild conditions, that the learning rate of minimizers of this biased/weighted empirical risk functional is of order O_{P}(log(n)/n) when ignoring model bias issues inherent to plug-in estimation, as can be attained in absence of censorship. Beyond theoretical results, numerical experiments are presented in order to illustrate the relevance of the approach developed.

Large Language Models are known to capture real-world knowledge, allowing them to excel in many downstream tasks. Despite recent advances, these models are still prone to what are commonly known as hallucinations, causing them to emit unwanted and factually incorrect text. In this work, we propose a novel calibration method that can be used to combat hallucinations. We add a special [IDK] ("I don't know") token to the model's vocabulary and introduce an objective function that shifts probability mass to the [IDK] token for incorrect predictions. This approach allows the model to express uncertainty in its output explicitly. We evaluate our proposed method across multiple model architectures and factual downstream tasks. We find that models trained with our method are able to express uncertainty in places where they would previously make mistakes while suffering only a small loss of encoded knowledge. We further perform extensive ablation studies of multiple variations of our approach and provide a detailed analysis of the precision-recall tradeoff of our method.

Visual language models (VLMs) have attracted increasing interest in autonomous driving due to their powerful reasoning capabilities. However, existing VLMs typically utilize discrete text Chain-of-Thought (CoT) tailored to the current scenario, which essentially represents highly abstract and symbolic compression of visual information, potentially leading to spatio-temporal relationship ambiguity and fine-grained information loss. Is autonomous driving better modeled on real-world simulation and imagination than on pure symbolic logic? In this paper, we propose a spatio-temporal CoT reasoning method that enables models to think visually. First, VLM serves as a world model to generate unified image frame for predicting future world states: where perception results (e.g., lane divider and 3D detection) represent the future spatial relationships, and ordinary future frame represent the temporal evolution relationships. This spatio-temporal CoT then serves as intermediate reasoning steps, enabling the VLM to function as an inverse dynamics model for trajectory planning based on current observations and future predictions. To implement visual generation in VLMs, we propose a unified pretraining paradigm integrating visual generation and understanding, along with a progressive visual CoT enhancing autoregressive image generation. Extensive experimental results demonstrate the effectiveness of the proposed method, advancing autonomous driving towards visual reasoning.

Tracing the water snowline in low-mass young stellar objects (YSOs) is important because dust grain growth is promoted and the chemical composition varies at the water snowline, which influences planet formation and its properties. In protostellar envelopes, the water snowline can be estimated as a function of luminosity using a relation derived from radiative transfer models, and these predictions are consistent with observations. However, accurately estimating the water snowline in protoplanetary disks requires new relations that account for the disk structure. We present the relations between luminosity and water snowline using the dust continuum radiative transfer models with various density structures. We adopt two-dimensional density structures for an envelope-only model (Model E), an envelope+disk+cavity model (Model E+D), and a protoplanetary disk model (Model PPD). The relations between the water snowline, where T_dust = 100 K, and the total luminosity, ranging 0.1-1,000 solar luminosity, are well fitted by a power-law relation, R_snow=a * (L/L_solar)^p au. The factor a decreases with increasing disk density, while the power index p has values around 0.5 in all models. As the disk becomes denser, the water snowline forms at smaller radii even at the same luminosity, since dense dust hinders photon propagation. We also explore the effect of viscous heating on the water snowline. In Model PPD with viscous heating, the water snowline shifts outward by a few au up to 15 au, increasing the factor a and decreasing the power index p. In Model E+D with lower disk mass, the effect of viscous heating is negligible, indicating that the disk mass controls the effect. The discrepancy between our models and direct observations provides insights into the recent outburst event and the presence of a disk structure in low-mass YSOs.

Large language models (LLMs) often generate inaccurate or fabricated information and generally fail to indicate their confidence, which limits their broader applications. Previous work elicits confidence from LLMs by direct or self-consistency prompting, or constructing specific datasets for supervised finetuning. The prompting-based approaches have inferior performance, and the training-based approaches are limited to binary or inaccurate group-level confidence estimates. In this work, we present the advanced SaySelf, a training framework that teaches LLMs to express more accurate fine-grained confidence estimates. In addition, beyond the confidence scores, SaySelf initiates the process of directing LLMs to produce self-reflective rationales that clearly identify gaps in their parametric knowledge and explain their uncertainty. This is achieved by using an LLM to automatically summarize the uncertainties in specific knowledge via natural language. The summarization is based on the analysis of the inconsistency in multiple sampled reasoning chains, and the resulting data is utilized for supervised fine-tuning. Moreover, we utilize reinforcement learning with a meticulously crafted reward function to calibrate the confidence estimates, motivating LLMs to deliver accurate, high-confidence predictions and to penalize overconfidence in erroneous outputs. Experimental results in both in-distribution and out-of-distribution datasets demonstrate the effectiveness of SaySelf in reducing the confidence calibration error and maintaining the task performance. We show that the generated self-reflective rationales are reasonable and can further contribute to the calibration. The code is made public at https://github.com/xu1868/SaySelf.

Despite their remarkable effectiveness and broad application, the drivers of success underlying ensembles of trees are still not fully understood. In this paper, we highlight how interpreting tree ensembles as adaptive and self-regularizing smoothers can provide new intuition and deeper insight to this topic. We use this perspective to show that, when studied as smoothers, randomized tree ensembles not only make predictions that are quantifiably more smooth than the predictions of the individual trees they consist of, but also further regulate their smoothness at test-time based on the dissimilarity between testing and training inputs. First, we use this insight to revisit, refine and reconcile two recent explanations of forest success by providing a new way of quantifying the conjectured behaviors of tree ensembles objectively by measuring the effective degree of smoothing they imply. Then, we move beyond existing explanations for the mechanisms by which tree ensembles improve upon individual trees and challenge the popular wisdom that the superior performance of forests should be understood as a consequence of variance reduction alone. We argue that the current high-level dichotomy into bias- and variance-reduction prevalent in statistics is insufficient to understand tree ensembles -- because the prevailing definition of bias does not capture differences in the expressivity of the hypothesis classes formed by trees and forests. Instead, we show that forests can improve upon trees by three distinct mechanisms that are usually implicitly entangled. In particular, we demonstrate that the smoothing effect of ensembling can reduce variance in predictions due to noise in outcome generation, reduce variability in the quality of the learned function given fixed input data and reduce potential bias in learnable functions by enriching the available hypothesis space.

We present a novel variational framework for performing inference in (neural) stochastic differential equations (SDEs) driven by Markov-approximate fractional Brownian motion (fBM). SDEs offer a versatile tool for modeling real-world continuous-time dynamic systems with inherent noise and randomness. Combining SDEs with the powerful inference capabilities of variational methods, enables the learning of representative function distributions through stochastic gradient descent. However, conventional SDEs typically assume the underlying noise to follow a Brownian motion (BM), which hinders their ability to capture long-term dependencies. In contrast, fractional Brownian motion (fBM) extends BM to encompass non-Markovian dynamics, but existing methods for inferring fBM parameters are either computationally demanding or statistically inefficient. In this paper, building upon the Markov approximation of fBM, we derive the evidence lower bound essential for efficient variational inference of posterior path measures, drawing from the well-established field of stochastic analysis. Additionally, we provide a closed-form expression to determine optimal approximation coefficients. Furthermore, we propose the use of neural networks to learn the drift, diffusion and control terms within our variational posterior, leading to the variational training of neural-SDEs. In this framework, we also optimize the Hurst index, governing the nature of our fractional noise. Beyond validation on synthetic data, we contribute a novel architecture for variational latent video prediction,-an approach that, to the best of our knowledge, enables the first variational neural-SDE application to video perception.

Although many pretrained models exist for text or images, there have been relatively fewer attempts to train representations specifically for dialog understanding. Prior works usually relied on finetuned representations based on generic text representation models like BERT or GPT-2. But such language modeling pretraining objectives do not take the structural information of conversational text into consideration. Although generative dialog models can learn structural features too, we argue that the structure-unaware word-by-word generation is not suitable for effective conversation modeling. We empirically demonstrate that such representations do not perform consistently across various dialog understanding tasks. Hence, we propose a structure-aware Mutual Information based loss-function DMI (Discourse Mutual Information) for training dialog-representation models, that additionally captures the inherent uncertainty in response prediction. Extensive evaluation on nine diverse dialog modeling tasks shows that our proposed DMI-based models outperform strong baselines by significant margins.

We present an empirical study of scaling properties of encoder-decoder Transformer models used in neural machine translation (NMT). We show that cross-entropy loss as a function of model size follows a certain scaling law. Specifically (i) We propose a formula which describes the scaling behavior of cross-entropy loss as a bivariate function of encoder and decoder size, and show that it gives accurate predictions under a variety of scaling approaches and languages; we show that the total number of parameters alone is not sufficient for such purposes. (ii) We observe different power law exponents when scaling the decoder vs scaling the encoder, and provide recommendations for optimal allocation of encoder/decoder capacity based on this observation. (iii) We also report that the scaling behavior of the model is acutely influenced by composition bias of the train/test sets, which we define as any deviation from naturally generated text (either via machine generated or human translated text). We observe that natural text on the target side enjoys scaling, which manifests as successful reduction of the cross-entropy loss. (iv) Finally, we investigate the relationship between the cross-entropy loss and the quality of the generated translations. We find two different behaviors, depending on the nature of the test data. For test sets which were originally translated from target language to source language, both loss and BLEU score improve as model size increases. In contrast, for test sets originally translated from source language to target language, the loss improves, but the BLEU score stops improving after a certain threshold. We release generated text from all models used in this study.