new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Dec 9

XR-NPE: High-Throughput Mixed-precision SIMD Neural Processing Engine for Extended Reality Perception Workloads

This work proposes XR-NPE, a high-throughput Mixed-precision SIMD Neural Processing Engine, designed for extended reality (XR) perception workloads like visual inertial odometry (VIO), object classification, and eye gaze extraction. XR-NPE is first to support FP4, Posit (4,1), Posit (8,0), and Posit (16,1) formats, with layer adaptive hybrid-algorithmic implementation supporting ultra-low bit precision to significantly reduce memory bandwidth requirements, and accompanied by quantization-aware training for minimal accuracy loss. The proposed Reconfigurable Mantissa Multiplication and Exponent processing Circuitry (RMMEC) reduces dark silicon in the SIMD MAC compute engine, assisted by selective power gating to reduce energy consumption, providing 2.85x improved arithmetic intensity. XR-NPE achieves a maximum operating frequency of 1.72 GHz, area 0.016 mm2 , and arithmetic intensity 14 pJ at CMOS 28nm, reducing 42% area, 38% power compared to the best of state-of-the-art MAC approaches. The proposed XR-NPE based AXI-enabled Matrix-multiplication co-processor consumes 1.4x fewer LUTs, 1.77x fewer FFs, and provides 1.2x better energy efficiency compared to SoTA accelerators on VCU129. The proposed co-processor provides 23% better energy efficiency and 4% better compute density for VIO workloads. XR-NPE establishes itself as a scalable, precision-adaptive compute engine for future resource-constrained XR devices. The complete set for codes for results reproducibility are released publicly, enabling designers and researchers to readily adopt and build upon them. https://github.com/mukullokhande99/XR-NPE.

  • 5 authors
·
Aug 18 1

ZO2: Scalable Zeroth-Order Fine-Tuning for Extremely Large Language Models with Limited GPU Memory

Fine-tuning large pre-trained LLMs generally demands extensive GPU memory. Traditional first-order optimizers like SGD encounter substantial difficulties due to increased memory requirements from storing activations and gradients during both the forward and backward phases as the model size expands. Alternatively, zeroth-order (ZO) techniques can compute gradients using just forward operations, eliminating the need to store activations. Furthermore, by leveraging CPU capabilities, it's feasible to enhance both the memory and processing power available to a single GPU. We propose a novel framework, ZO2 (Zeroth-Order Offloading), for efficient zeroth-order fine-tuning of LLMs with only limited GPU memory. Our framework dynamically shifts model parameters between the CPU and GPU as required, optimizing computation flow and maximizing GPU usage by minimizing downtime. This integration of parameter adjustments with ZO's double forward operations reduces unnecessary data movement, enhancing the fine-tuning efficacy. Additionally, our framework supports an innovative low-bit precision approach in AMP mode to streamline data exchanges between the CPU and GPU. Employing this approach allows us to fine-tune extraordinarily large models, such as the OPT-175B with more than 175 billion parameters, on a mere 18GB GPU--achievements beyond the reach of traditional methods. Moreover, our framework achieves these results with almost no additional time overhead and absolutely no accuracy loss compared to standard zeroth-order methods. ZO2's code has been open-sourced in https://github.com/liangyuwang/zo2.

  • 7 authors
·
Mar 16

PowerWalk: Scalable Personalized PageRank via Random Walks with Vertex-Centric Decomposition

Most methods for Personalized PageRank (PPR) precompute and store all accurate PPR vectors, and at query time, return the ones of interest directly. However, the storage and computation of all accurate PPR vectors can be prohibitive for large graphs, especially in caching them in memory for real-time online querying. In this paper, we propose a distributed framework that strikes a better balance between offline indexing and online querying. The offline indexing attains a fingerprint of the PPR vector of each vertex by performing billions of "short" random walks in parallel across a cluster of machines. We prove that our indexing method has an exponential convergence, achieving the same precision with previous methods using a much smaller number of random walks. At query time, the new PPR vector is composed by a linear combination of related fingerprints, in a highly efficient vertex-centric decomposition manner. Interestingly, the resulting PPR vector is much more accurate than its offline counterpart because it actually uses more random walks in its estimation. More importantly, we show that such decomposition for a batch of queries can be very efficiently processed using a shared decomposition. Our implementation, PowerWalk, takes advantage of advanced distributed graph engines and it outperforms the state-of-the-art algorithms by orders of magnitude. Particularly, it responses to tens of thousands of queries on graphs with billions of edges in just a few seconds.

  • 4 authors
·
Aug 22, 2016

Gaussian Weight Sampling for Scalable, Efficient and Stable Pseudo-Quantization Training

Ever-growing scale of large language models (LLMs) is pushing for improved efficiency, favoring fully quantized training (FQT) over BF16. While FQT accelerates training, it faces consistency challenges and requires searching over an exponential number of cases, each needing over 200B tokens to ensure stability. Pseudo-quantization training (PQT) addresses the issues of FQT, although it is not well-studied. We explore the practical implications of PQT in detail and propose a noise distribution R that is floating-point (FP)-friendly, with ideal properties including stochastic precision annealing. As a result, the proposed method serves as an effective theoretical foundation for low-precision FP parameters through PQT, utilizing efficient fake quantization via an addition and subsequent FP casting. We demonstrate that Gaussian weight sampling is (1) scalable: supports low-precision FP parameters down to FP6 and high-precision noise up to 9-bit with BF16 operator. The proposed method is (2) efficient: incurring computational overhead as low as 1.40\% on the A100 GPU in terms of Llama2 training tokens per second, and requiring 2 bytes per parameter in GPU memory. We demonstrate that PQT with Gaussian weight sampling is (3) stable: closely following or even surpassing performance of the BF16 baseline while pre-training GPT2 and Llama2 models with up to 1B parameters and 300B tokens.

  • 2 authors
·
May 16

Scalable MatMul-free Language Modeling

Matrix multiplication (MatMul) typically dominates the overall computational cost of large language models (LLMs). This cost only grows as LLMs scale to larger embedding dimensions and context lengths. In this work, we show that MatMul operations can be completely eliminated from LLMs while maintaining strong performance at billion-parameter scales. Our experiments show that our proposed MatMul-free models achieve performance on-par with state-of-the-art Transformers that require far more memory during inference at a scale up to at least 2.7B parameters. We investigate the scaling laws and find that the performance gap between our MatMul-free models and full precision Transformers narrows as the model size increases. We also provide a GPU-efficient implementation of this model which reduces memory usage by up to 61% over an unoptimized baseline during training. By utilizing an optimized kernel during inference, our model's memory consumption can be reduced by more than 10x compared to unoptimized models. To properly quantify the efficiency of our architecture, we build a custom hardware solution on an FPGA which exploits lightweight operations beyond what GPUs are capable of. We processed billion-parameter scale models at 13W beyond human readable throughput, moving LLMs closer to brain-like efficiency. This work not only shows how far LLMs can be stripped back while still performing effectively, but also points at the types of operations future accelerators should be optimized for in processing the next generation of lightweight LLMs. Our code implementation is available at https://github.com/ridgerchu/matmulfreellm.

  • 8 authors
·
Jun 4, 2024

Fitness aligned structural modeling enables scalable virtual screening with AuroBind

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.

Peer-Ranked Precision: Creating a Foundational Dataset for Fine-Tuning Vision Models from DataSeeds' Annotated Imagery

The development of modern Artificial Intelligence (AI) models, particularly diffusion-based models employed in computer vision and image generation tasks, is undergoing a paradigmatic shift in development methodologies. Traditionally dominated by a "Model Centric" approach, in which performance gains were primarily pursued through increasingly complex model architectures and hyperparameter optimization, the field is now recognizing a more nuanced "Data-Centric" approach. This emergent framework foregrounds the quality, structure, and relevance of training data as the principal driver of model performance. To operationalize this paradigm shift, we introduce the DataSeeds.AI sample dataset (the "DSD"), initially comprised of approximately 10,610 high-quality human peer-ranked photography images accompanied by extensive multi-tier annotations. The DSD is a foundational computer vision dataset designed to usher in a new standard for commercial image datasets. Representing a small fraction of DataSeed.AI's 100 million-plus image catalog, the DSD provides a scalable foundation necessary for robust commercial and multimodal AI development. Through this in-depth exploratory analysis, we document the quantitative improvements generated by the DSD on specific models against known benchmarks and make the code and the trained models used in our evaluation publicly available.

  • 4 authors
·
Jun 5 2

Sparse Autoencoders Enable Scalable and Reliable Circuit Identification in Language Models

This paper introduces an efficient and robust method for discovering interpretable circuits in large language models using discrete sparse autoencoders. Our approach addresses key limitations of existing techniques, namely computational complexity and sensitivity to hyperparameters. We propose training sparse autoencoders on carefully designed positive and negative examples, where the model can only correctly predict the next token for the positive examples. We hypothesise that learned representations of attention head outputs will signal when a head is engaged in specific computations. By discretising the learned representations into integer codes and measuring the overlap between codes unique to positive examples for each head, we enable direct identification of attention heads involved in circuits without the need for expensive ablations or architectural modifications. On three well-studied tasks - indirect object identification, greater-than comparisons, and docstring completion - the proposed method achieves higher precision and recall in recovering ground-truth circuits compared to state-of-the-art baselines, while reducing runtime from hours to seconds. Notably, we require only 5-10 text examples for each task to learn robust representations. Our findings highlight the promise of discrete sparse autoencoders for scalable and efficient mechanistic interpretability, offering a new direction for analysing the inner workings of large language models.

  • 2 authors
·
May 21, 2024

Gradient Multi-Normalization for Stateless and Scalable LLM Training

Training large language models (LLMs) typically relies on adaptive optimizers like Adam (Kingma & Ba, 2015) which store additional state information to accelerate convergence but incur significant memory overhead. Recent efforts, such as SWAN (Ma et al., 2024) address this by eliminating the need for optimizer states while achieving performance comparable to Adam via a multi-step preprocessing procedure applied to instantaneous gradients. Motivated by the success of SWAN, we introduce a novel framework for designing stateless optimizers that normalizes stochastic gradients according to multiple norms. To achieve this, we propose a simple alternating scheme to enforce the normalization of gradients w.r.t these norms. We show that our procedure can produce, up to an arbitrary precision, a fixed-point of the problem, and that SWAN is a particular instance of our approach with carefully chosen norms, providing a deeper understanding of its design. However, SWAN's computationally expensive whitening/orthogonalization step limit its practicality for large LMs. Using our principled perspective, we develop of a more efficient, scalable, and practical stateless optimizer. Our algorithm relaxes the properties of SWAN, significantly reducing its computational cost while retaining its memory efficiency, making it applicable to training large-scale models. Experiments on pre-training LLaMA models with up to 1 billion parameters demonstrate a 3X speedup over Adam with significantly reduced memory requirements, outperforming other memory-efficient baselines.

  • 4 authors
·
Feb 10

LLMCad: Fast and Scalable On-device Large Language Model Inference

Generative tasks, such as text generation and question answering, hold a crucial position in the realm of mobile applications. Due to their sensitivity to privacy concerns, there is a growing demand for their execution directly on mobile devices. Currently, the execution of these generative tasks heavily depends on Large Language Models (LLMs). Nevertheless, the limited memory capacity of these devices presents a formidable challenge to the scalability of such models. In our research, we introduce LLMCad, an innovative on-device inference engine specifically designed for efficient generative Natural Language Processing (NLP) tasks. The core idea behind LLMCad revolves around model collaboration: a compact LLM, residing in memory, takes charge of generating the most straightforward tokens, while a high-precision LLM steps in to validate these tokens and rectify any identified errors. LLMCad incorporates three novel techniques: (1) Instead of generating candidate tokens in a sequential manner, LLMCad employs the smaller LLM to construct a token tree, encompassing a wider range of plausible token pathways. Subsequently, the larger LLM can efficiently validate all of these pathways simultaneously. (2) It employs a self-adjusting fallback strategy, swiftly initiating the verification process whenever the smaller LLM generates an erroneous token. (3) To ensure a continuous flow of token generation, LLMCad speculatively generates tokens during the verification process by implementing a compute-IO pipeline. Through an extensive series of experiments, LLMCad showcases an impressive token generation speed, achieving rates up to 9.3x faster than existing inference engines.

  • 7 authors
·
Sep 8, 2023

Building Flexible, Scalable, and Machine Learning-ready Multimodal Oncology Datasets

The advancements in data acquisition, storage, and processing techniques have resulted in the rapid growth of heterogeneous medical data. Integrating radiological scans, histopathology images, and molecular information with clinical data is essential for developing a holistic understanding of the disease and optimizing treatment. The need for integrating data from multiple sources is further pronounced in complex diseases such as cancer for enabling precision medicine and personalized treatments. This work proposes Multimodal Integration of Oncology Data System (MINDS) - a flexible, scalable, and cost-effective metadata framework for efficiently fusing disparate data from public sources such as the Cancer Research Data Commons (CRDC) into an interconnected, patient-centric framework. MINDS offers an interface for exploring relationships across data types and building cohorts for developing large-scale multimodal machine learning models. By harmonizing multimodal data, MINDS aims to potentially empower researchers with greater analytical ability to uncover diagnostic and prognostic insights and enable evidence-based personalized care. MINDS tracks granular end-to-end data provenance, ensuring reproducibility and transparency. The cloud-native architecture of MINDS can handle exponential data growth in a secure, cost-optimized manner while ensuring substantial storage optimization, replication avoidance, and dynamic access capabilities. Auto-scaling, access controls, and other mechanisms guarantee pipelines' scalability and security. MINDS overcomes the limitations of existing biomedical data silos via an interoperable metadata-driven approach that represents a pivotal step toward the future of oncology data integration.

  • 5 authors
·
Sep 30, 2023

ZeroGR: A Generalizable and Scalable Framework for Zero-Shot Generative Retrieval

Generative retrieval (GR) reformulates information retrieval (IR) by framing it as the generation of document identifiers (docids), thereby enabling an end-to-end optimization and seamless integration with generative language models (LMs). Despite notable progress under supervised training, GR still struggles to generalize to zero-shot IR scenarios, which are prevalent in real-world applications. To tackle this challenge, we propose ZeroGR, a zero-shot generative retrieval framework that leverages natural language instructions to extend GR across a wide range of IR tasks. Specifically, ZeroGR is composed of three key components: (i) an LM-based docid generator that unifies heterogeneous documents (e.g., text, tables, code) into semantically meaningful docids; (ii) an instruction-tuned query generator that generates diverse types of queries from natural language task descriptions to enhance corpus indexing; and (iii) a reverse annealing decoding strategy to balance precision and recall during docid generation. We investigate the impact of instruction fine-tuning scale and find that performance consistently improves as the number of IR tasks encountered during training increases. Empirical results on the BEIR and MAIR benchmarks demonstrate that ZeroGR outperforms strong dense retrieval and generative baselines in zero-shot settings, establishing a new state-of-the-art for instruction-driven GR.

  • 8 authors
·
Oct 11

Comprehensive Benchmarking of YOLOv11 Architectures for Scalable and Granular Peripheral Blood Cell Detection

Manual peripheral blood smear (PBS) analysis is labor intensive and subjective. While deep learning offers a promising alternative, a systematic evaluation of state of the art models such as YOLOv11 for fine grained PBS detection is still lacking. In this work, we make two key contributions. First, we curate a large scale annotated dataset for blood cell detection and classification, comprising 16,891 images across 12 peripheral blood cell (PBC) classes, along with the red blood cell class, all carefully re annotated for object detection tasks. In total, the dataset contains 298,850 annotated cells. Second, we leverage this dataset to conduct a comprehensive evaluation of five YOLOv11 variants (ranging from Nano to XLarge). These models are rigorously benchmarked under two data splitting strategies (70:20:10 and 80:10:10) and systematically assessed using multiple performance criteria, including mean Average Precision (mAP), precision, recall, F1 score, and computational efficiency. Our experiments show that the YOLOv11 Medium variant achieves the best trade off, reaching a [email protected] of 0.934 under the 8:1:1 split. Larger models (Large and XLarge) provide only marginal accuracy gains at substantially higher computational cost. Moreover, the 8:1:1 split consistently outperforms the 7:2:1 split across all models. These findings highlight YOLOv11, particularly the Medium variant, as a highly effective framework for automated, fine grained PBS detection. Beyond benchmarking, our publicly released dataset (github.com/Mohamad-AbouAli/OI-PBC-Dataset) offers a valuable resource to advance research on blood cell detection and classification in hematology.

  • 7 authors
·
Sep 29

GALAX: Graph-Augmented Language Model for Explainable Reinforcement-Guided Subgraph Reasoning in Precision Medicine

In precision medicine, quantitative multi-omic features, topological context, and textual biological knowledge play vital roles in identifying disease-critical signaling pathways and targets. Existing pipelines capture only part of these-numerical omics ignore topological context, text-centric LLMs lack quantitative grounded reasoning, and graph-only models underuse node semantics and the generalization of LLMs-limiting mechanistic interpretability. Although Process Reward Models (PRMs) aim to guide reasoning in LLMs, they remain limited by unreliable intermediate evaluation, and vulnerability to reward hacking with computational cost. These gaps motivate integrating quantitative multi-omic signals, topological structure with node annotations, and literature-scale text via LLMs, using subgraph reasoning as the principle bridge linking numeric evidence, topological knowledge and language context. Therefore, we propose GALAX (Graph Augmented LAnguage model with eXplainability), an innovative framework that integrates pretrained Graph Neural Networks (GNNs) into Large Language Models (LLMs) via reinforcement guided by a Graph Process Reward Model (GPRM), which generates disease-relevant subgraphs in a step-wise manner initiated by an LLM and iteratively evaluated by a pretrained GNN, enabling process-level supervision without explicit intermediate reasoning annotations. As an application, we also introduced Target-QA, a benchmark combining CRISPR-identified targets, multi-omic profiles, and biomedical graph knowledge across diverse cancer cell lines, which enables GNN pretraining for supervising step-wise graph construction and supports long-context reasoning over text-numeric graphs (TNGs), providing a scalable and biologically grounded framework for explainable, reinforcement-guided subgraph reasoning toward reliable and interpretable target and pathway discovery in precision medicine.

  • 7 authors
·
Sep 25

Reliable End-to-End Material Information Extraction from the Literature with Source-Tracked Multi-Stage Large Language Models

Data-driven materials discovery requires large-scale experimental datasets, yet most of the information remains trapped in unstructured literature. Existing extraction efforts often focus on a limited set of features and have not addressed the integrated composition-processing-microstructure-property relationships essential for understanding materials behavior, thereby posing challenges for building comprehensive databases. To address this gap, we propose a multi-stage information extraction pipeline powered by large language models, which captures 47 features spanning composition, processing, microstructure, and properties exclusively from experimentally reported materials. The pipeline integrates iterative extraction with source tracking to enhance both accuracy and reliability. Evaluations at the feature level (independent attributes) and tuple level (interdependent features) yielded F1 scores around 0.96. Compared with single-pass extraction without source tracking, our approach improved F1 scores of microstructure category by 10.0% (feature level) and 13.7% (tuple level), and reduced missed materials from 49 to 13 out of 396 materials in 100 articles on precipitate-containing multi-principal element alloys (miss rate reduced from 12.4% to 3.3%). The pipeline enables scalable and efficient literature mining, producing databases with high precision, minimal omissions, and zero false positives. These datasets provide trustworthy inputs for machine learning and materials informatics, while the modular design generalizes to diverse material classes, enabling comprehensive materials information extraction.

  • 6 authors
·
Oct 1

Are LLMs Better than Reported? Detecting Label Errors and Mitigating Their Effect on Model Performance

NLP benchmarks rely on standardized datasets for training and evaluating models and are crucial for advancing the field. Traditionally, expert annotations ensure high-quality labels; however, the cost of expert annotation does not scale well with the growing demand for larger datasets required by modern models. While crowd-sourcing provides a more scalable solution, it often comes at the expense of annotation precision and consistency. Recent advancements in large language models (LLMs) offer new opportunities to enhance the annotation process, particularly for detecting label errors in existing datasets. In this work, we consider the recent approach of LLM-as-a-judge, leveraging an ensemble of LLMs to flag potentially mislabeled examples. Through a case study of four datasets from the TRUE benchmark, covering different tasks and domains, we empirically analyze the labeling quality of existing datasets, and compare expert, crowd-sourced, and our LLM-based annotations in terms of agreement, label quality, and efficiency, demonstrating the strengths and limitations of each annotation method. Our findings reveal a substantial number of label errors, which, when corrected, induce a significant upward shift in reported model performance. This suggests that many of the LLMs so-called mistakes are due to label errors rather than genuine model failures. Additionally, we discuss the implications of mislabeled data and propose methods to mitigate them in training to improve model performance.

  • 5 authors
·
Oct 24, 2024 2

AgroSense: An Integrated Deep Learning System for Crop Recommendation via Soil Image Analysis and Nutrient Profiling

Meeting the increasing global demand for food security and sustainable farming requires intelligent crop recommendation systems that operate in real time. Traditional soil analysis techniques are often slow, labor-intensive, and not suitable for on-field decision-making. To address these limitations, we introduce AgroSense, a deep-learning framework that integrates soil image classification and nutrient profiling to produce accurate and contextually relevant crop recommendations. AgroSense comprises two main components: a Soil Classification Module, which leverages ResNet-18, EfficientNet-B0, and Vision Transformer architectures to categorize soil types from images; and a Crop Recommendation Module, which employs a Multi-Layer Perceptron, XGBoost, LightGBM, and TabNet to analyze structured soil data, including nutrient levels, pH, and rainfall. We curated a multimodal dataset of 10,000 paired samples drawn from publicly available Kaggle repositories, approximately 50,000 soil images across seven classes, and 25,000 nutrient profiles for experimental evaluation. The fused model achieves 98.0% accuracy, with a precision of 97.8%, a recall of 97.7%, and an F1-score of 96.75%, while RMSE and MAE drop to 0.32 and 0.27, respectively. Ablation studies underscore the critical role of multimodal coupling, and statistical validation via t-tests and ANOVA confirms the significance of our improvements. AgroSense offers a practical, scalable solution for real-time decision support in precision agriculture and paves the way for future lightweight multimodal AI systems in resource-constrained environments.

  • 3 authors
·
Sep 1

MoTE: Mixture of Ternary Experts for Memory-efficient Large Multimodal Models

Large multimodal Mixture-of-Experts (MoEs) effectively scale the model size to boost performance while maintaining fixed active parameters. However, previous works primarily utilized full-precision experts during sparse up-cycling. Despite they show superior performance on end tasks, the large amount of experts introduces higher memory footprint, which poses significant challenges for the deployment on edge devices. In this work, we propose MoTE, a scalable and memory-efficient approach to train Mixture-of-Ternary-Experts models from dense checkpoint. Instead of training fewer high-precision experts, we propose to train more low-precision experts during up-cycling. Specifically, we use the pre-trained FFN as a shared expert and train ternary routed experts with parameters in {-1, 0, 1}. Extensive experiments show that our approach has promising scaling trend along model size. MoTE achieves comparable performance to full-precision baseline MoE-LLaVA while offering lower memory footprint. Furthermore, our approach is compatible with post-training quantization methods and the advantage further amplifies when memory-constraint goes lower. Given the same amount of expert memory footprint of 3.4GB and combined with post-training quantization, MoTE outperforms MoE-LLaVA by a gain of 4.3% average accuracy on end tasks, demonstrating its effectiveness and potential for memory-constrained devices.

  • 8 authors
·
Jun 17 2

Gene-DML: Dual-Pathway Multi-Level Discrimination for Gene Expression Prediction from Histopathology Images

Accurately predicting gene expression from histopathology images offers a scalable and non-invasive approach to molecular profiling, with significant implications for precision medicine and computational pathology. However, existing methods often underutilize the cross-modal representation alignment between histopathology images and gene expression profiles across multiple representational levels, thereby limiting their prediction performance. To address this, we propose Gene-DML, a unified framework that structures latent space through Dual-pathway Multi-Level discrimination to enhance correspondence between morphological and transcriptional modalities. The multi-scale instance-level discrimination pathway aligns hierarchical histopathology representations extracted at local, neighbor, and global levels with gene expression profiles, capturing scale-aware morphological-transcriptional relationships. In parallel, the cross-level instance-group discrimination pathway enforces structural consistency between individual (image/gene) instances and modality-crossed (gene/image, respectively) groups, strengthening the alignment across modalities. By jointly modelling fine-grained and structural-level discrimination, Gene-DML is able to learn robust cross-modal representations, enhancing both predictive accuracy and generalization across diverse biological contexts. Extensive experiments on public spatial transcriptomics datasets demonstrate that Gene-DML achieves state-of-the-art performance in gene expression prediction. The code and checkpoints will be released soon.

  • 4 authors
·
Jul 19

MonkeyOCR: Document Parsing with a Structure-Recognition-Relation Triplet Paradigm

We introduce MonkeyOCR, a vision-language model for document parsing that advances the state of the art by leveraging a Structure-Recognition-Relation (SRR) triplet paradigm. This design simplifies what would otherwise be a complex multi-tool pipeline (as in MinerU's modular approach) and avoids the inefficiencies of processing full pages with giant end-to-end models (e.g., large multimodal LLMs like Qwen-VL). In SRR, document parsing is abstracted into three fundamental questions - "Where is it?" (structure), "What is it?" (recognition), and "How is it organized?" (relation) - corresponding to layout analysis, content identification, and logical ordering. This focused decomposition balances accuracy and speed: it enables efficient, scalable processing without sacrificing precision. To train and evaluate this approach, we introduce the MonkeyDoc (the most comprehensive document parsing dataset to date), with 3.9 million instances spanning over ten document types in both Chinese and English. Experiments show that MonkeyOCR outperforms MinerU by an average of 5.1%, with particularly notable improvements on challenging content such as formulas (+15.0%) and tables (+8.6%). Remarkably, our 3B-parameter model surpasses much larger and top-performing models, including Qwen2.5-VL (72B) and Gemini 2.5 Pro, achieving state-of-the-art average performance on English document parsing tasks. In addition, MonkeyOCR processes multi-page documents significantly faster (0.84 pages per second compared to 0.65 for MinerU and 0.12 for Qwen2.5-VL-7B). The 3B model can be efficiently deployed for inference on a single NVIDIA 3090 GPU. Code and models will be released at https://github.com/Yuliang-Liu/MonkeyOCR.

ProVision: Programmatically Scaling Vision-centric Instruction Data for Multimodal Language Models

With the rise of multimodal applications, instruction data has become critical for training multimodal language models capable of understanding complex image-based queries. Existing practices rely on powerful but costly large language models (LLMs) or multimodal language models (MLMs) to produce instruction data. These are often prone to hallucinations, licensing issues and the generation process is often hard to scale and interpret. In this work, we present a programmatic approach that employs scene graphs as symbolic representations of images and human-written programs to systematically synthesize vision-centric instruction data. Our approach ensures the interpretability and controllability of the data generation process and scales efficiently while maintaining factual accuracy. By implementing a suite of 24 single-image, 14 multi-image instruction generators, and a scene graph generation pipeline, we build a scalable, cost-effective system: ProVision which produces diverse question-answer pairs concerning objects, attributes, relations, depth, etc., for any given image. Applied to Visual Genome and DataComp datasets, we generate over 10 million instruction data points, ProVision-10M, and leverage them in both pretraining and instruction tuning stages of MLMs. When adopted in the instruction tuning stage, our single-image instruction data yields up to a 7% improvement on the 2D split and 8% on the 3D split of CVBench, along with a 3% increase in performance on QBench2, RealWorldQA, and MMMU. Our multi-image instruction data leads to an 8% improvement on Mantis-Eval. Incorporation of our data in both pre-training and fine-tuning stages of xGen-MM-4B leads to an averaged improvement of 1.6% across 11 benchmarks.

  • 14 authors
·
Dec 9, 2024