Automating Exploratory Multiomics Research via Language Models

This paper introduces PROTEUS, a fully automated system that produces data-driven hypotheses from raw data files. We apply PROTEUS to clinical proteogenomics, a field where effective downstream data analysis and hypothesis proposal is crucial for producing novel discoveries. PROTEUS uses separate modules to simulate different stages of the scientific process, from open-ended data exploration to specific statistical analysis and hypothesis proposal. It formulates research directions, tools, and results in terms of relationships between biological entities, using unified graph structures to manage complex research processes. We applied PROTEUS to 10 clinical multiomics datasets from published research, arriving at 360 total hypotheses. Results were evaluated through external data validation and automatic open-ended scoring. Through exploratory and iterative research, the system can navigate high-throughput and heterogeneous multiomics data to arrive at hypotheses that balance reliability and novelty. In addition to accelerating multiomic analysis, PROTEUS represents a path towards tailoring general autonomous systems to specialized scientific domains to achieve open-ended hypothesis generation from data.

AutoSDT: Scaling Data-Driven Discovery Tasks Toward Open Co-Scientists

Despite long-standing efforts in accelerating scientific discovery with AI, building AI co-scientists remains challenging due to limited high-quality data for training and evaluation. To tackle this data scarcity issue, we present AutoSDT, an automatic pipeline that collects high-quality coding tasks in real-world data-driven discovery workflows. AutoSDT leverages the coding capabilities and parametric knowledge of LLMs to search for diverse sources, select ecologically valid tasks, and synthesize accurate task instructions and code solutions. Using our pipeline, we construct AutoSDT-5K, a dataset of 5,404 coding tasks for data-driven discovery that covers four scientific disciplines and 756 unique Python packages. To the best of our knowledge, AutoSDT-5K is the only automatically collected and the largest open dataset for data-driven scientific discovery. Expert feedback on a subset of 256 tasks shows the effectiveness of AutoSDT: 93% of the collected tasks are ecologically valid, and 92.2% of the synthesized programs are functionally correct. Trained on AutoSDT-5K, the Qwen2.5-Coder-Instruct LLM series, dubbed AutoSDT-Coder, show substantial improvement on two challenging data-driven discovery benchmarks, ScienceAgentBench and DiscoveryBench. Most notably, AutoSDT-Coder-32B reaches the same level of performance as GPT-4o on ScienceAgentBench with a success rate of 7.8%, doubling the performance of its base model. On DiscoveryBench, it lifts the hypothesis matching score to 8.1, bringing a 17.4% relative improvement and closing the gap between open-weight models and GPT-4o.

ChartSketcher: Reasoning with Multimodal Feedback and Reflection for Chart Understanding

Charts are high-density visualization carriers for complex data, serving as a crucial medium for information extraction and analysis. Automated chart understanding poses significant challenges to existing multimodal large language models (MLLMs) due to the need for precise and complex visual reasoning. Current step-by-step reasoning models primarily focus on text-based logical reasoning for chart understanding. However, they struggle to refine or correct their reasoning when errors stem from flawed visual understanding, as they lack the ability to leverage multimodal interaction for deeper comprehension. Inspired by human cognitive behavior, we propose ChartSketcher, a multimodal feedback-driven step-by-step reasoning method designed to address these limitations. ChartSketcher is a chart understanding model that employs Sketch-CoT, enabling MLLMs to annotate intermediate reasoning steps directly onto charts using a programmatic sketching library, iteratively feeding these visual annotations back into the reasoning process. This mechanism enables the model to visually ground its reasoning and refine its understanding over multiple steps. We employ a two-stage training strategy: a cold start phase to learn sketch-based reasoning patterns, followed by off-policy reinforcement learning to enhance reflection and generalization. Experiments demonstrate that ChartSketcher achieves promising performance on chart understanding benchmarks and general vision tasks, providing an interactive and interpretable approach to chart comprehension.

Enhancing Large Language Models with Reward-guided Tree Search for Knowledge Graph Question and Answering

Recently, large language models (LLMs) have demonstrated impressive performance in Knowledge Graph Question Answering (KGQA) tasks, which aim to find answers based on knowledge graphs (KGs) for natural language questions. Existing LLMs-based KGQA methods typically follow the Graph Retrieval-Augmented Generation (GraphRAG) paradigm, which first retrieves reasoning paths from the large KGs, and then generates the answers based on them. However, these methods emphasize the exploration of new optimal reasoning paths in KGs while ignoring the exploitation of historical reasoning paths, which may lead to sub-optimal reasoning paths. Additionally, the complex semantics contained in questions may lead to the retrieval of inaccurate reasoning paths. To address these issues, this paper proposes a novel and training-free framework for KGQA tasks called Reward-guided Tree Search on Graph (RTSoG). RTSoG decomposes an original question into a series of simpler and well-defined sub-questions to handle the complex semantics. Then, a Self-Critic Monte Carlo Tree Search (SC-MCTS) guided by a reward model is introduced to iteratively retrieve weighted reasoning paths as contextual knowledge. Finally, it stacks the weighted reasoning paths according to their weights to generate the final answers. Extensive experiments on four datasets demonstrate the effectiveness of RTSoG. Notably, it achieves 8.7\% and 7.0\% performance improvement over the state-of-the-art method on the GrailQA and the WebQSP respectively.

Wan: Open and Advanced Large-Scale Video Generative Models

This report presents Wan, a comprehensive and open suite of video foundation models designed to push the boundaries of video generation. Built upon the mainstream diffusion transformer paradigm, Wan achieves significant advancements in generative capabilities through a series of innovations, including our novel VAE, scalable pre-training strategies, large-scale data curation, and automated evaluation metrics. These contributions collectively enhance the model's performance and versatility. Specifically, Wan is characterized by four key features: Leading Performance: The 14B model of Wan, trained on a vast dataset comprising billions of images and videos, demonstrates the scaling laws of video generation with respect to both data and model size. It consistently outperforms the existing open-source models as well as state-of-the-art commercial solutions across multiple internal and external benchmarks, demonstrating a clear and significant performance superiority. Comprehensiveness: Wan offers two capable models, i.e., 1.3B and 14B parameters, for efficiency and effectiveness respectively. It also covers multiple downstream applications, including image-to-video, instruction-guided video editing, and personal video generation, encompassing up to eight tasks. Consumer-Grade Efficiency: The 1.3B model demonstrates exceptional resource efficiency, requiring only 8.19 GB VRAM, making it compatible with a wide range of consumer-grade GPUs. Openness: We open-source the entire series of Wan, including source code and all models, with the goal of fostering the growth of the video generation community. This openness seeks to significantly expand the creative possibilities of video production in the industry and provide academia with high-quality video foundation models. All the code and models are available at https://github.com/Wan-Video/Wan2.1.

LocalEscaper: A Weakly-supervised Framework with Regional Reconstruction for Scalable Neural TSP Solvers

Neural solvers have shown significant potential in solving the Traveling Salesman Problem (TSP), yet current approaches face significant challenges. Supervised learning (SL)-based solvers require large amounts of high-quality labeled data, while reinforcement learning (RL)-based solvers, though less dependent on such data, often suffer from inefficiencies. To address these limitations, we propose LocalEscaper, a novel weakly-supervised learning framework for large-scale TSP. LocalEscaper effectively combines the advantages of both SL and RL, enabling effective training on datasets with low-quality labels. To further enhance solution quality, we introduce a regional reconstruction strategy, which mitigates the problem of local optima, a common issue in existing local reconstruction methods. Additionally, we propose a linear-complexity attention mechanism that reduces computational overhead, enabling the efficient solution of large-scale TSPs without sacrificing performance. Experimental results on both synthetic and real-world datasets demonstrate that LocalEscaper outperforms existing neural solvers, achieving state-of-the-art results. Notably, it sets a new benchmark for scalability and efficiency, solving TSP instances with up to 50,000 cities.

MedXpertQA: Benchmarking Expert-Level Medical Reasoning and Understanding

We introduce MedXpertQA, a highly challenging and comprehensive benchmark to evaluate expert-level medical knowledge and advanced reasoning. MedXpertQA includes 4,460 questions spanning 17 specialties and 11 body systems. It includes two subsets, Text for text evaluation and MM for multimodal evaluation. Notably, MM introduces expert-level exam questions with diverse images and rich clinical information, including patient records and examination results, setting it apart from traditional medical multimodal benchmarks with simple QA pairs generated from image captions. MedXpertQA applies rigorous filtering and augmentation to address the insufficient difficulty of existing benchmarks like MedQA, and incorporates specialty board questions to improve clinical relevance and comprehensiveness. We perform data synthesis to mitigate data leakage risk and conduct multiple rounds of expert reviews to ensure accuracy and reliability. We evaluate 16 leading models on MedXpertQA. Moreover, medicine is deeply connected to real-world decision-making, providing a rich and representative setting for assessing reasoning abilities beyond mathematics and code. To this end, we develop a reasoning-oriented subset to facilitate the assessment of o1-like models.

Static Batching of Irregular Workloads on GPUs: Framework and Application to Efficient MoE Model Inference

It has long been a problem to arrange and execute irregular workloads on massively parallel devices. We propose a general framework for statically batching irregular workloads into a single kernel with a runtime task mapping mechanism on GPUs. We further apply this framework to Mixture-of-Experts (MoE) model inference and implement an optimized and efficient CUDA kernel. Our MoE kernel achieves up to 91% of the peak Tensor Core throughput on NVIDIA H800 GPU and 95% on NVIDIA H20 GPU.

OVO-Bench: How Far is Your Video-LLMs from Real-World Online Video Understanding?

Temporal Awareness, the ability to reason dynamically based on the timestamp when a question is raised, is the key distinction between offline and online video LLMs. Unlike offline models, which rely on complete videos for static, post hoc analysis, online models process video streams incrementally and dynamically adapt their responses based on the timestamp at which the question is posed. Despite its significance, temporal awareness has not been adequately evaluated in existing benchmarks. To fill this gap, we present OVO-Bench (Online-VideO-Benchmark), a novel video benchmark that emphasizes the importance of timestamps for advanced online video understanding capability benchmarking. OVO-Bench evaluates the ability of video LLMs to reason and respond to events occurring at specific timestamps under three distinct scenarios: (1) Backward tracing: trace back to past events to answer the question. (2) Real-time understanding: understand and respond to events as they unfold at the current timestamp. (3) Forward active responding: delay the response until sufficient future information becomes available to answer the question accurately. OVO-Bench comprises 12 tasks, featuring 644 unique videos and approximately human-curated 2,800 fine-grained meta-annotations with precise timestamps. We combine automated generation pipelines with human curation. With these high-quality samples, we further developed an evaluation pipeline to systematically query video LLMs along the video timeline. Evaluations of nine Video-LLMs reveal that, despite advancements on traditional benchmarks, current models struggle with online video understanding, showing a significant gap compared to human agents. We hope OVO-Bench will drive progress in video LLMs and inspire future research in online video reasoning. Our benchmark and code can be accessed at https://github.com/JoeLeelyf/OVO-Bench.

InternLM-XComposer2.5-OmniLive: A Comprehensive Multimodal System for Long-term Streaming Video and Audio Interactions

Creating AI systems that can interact with environments over long periods, similar to human cognition, has been a longstanding research goal. Recent advancements in multimodal large language models (MLLMs) have made significant strides in open-world understanding. However, the challenge of continuous and simultaneous streaming perception, memory, and reasoning remains largely unexplored. Current MLLMs are constrained by their sequence-to-sequence architecture, which limits their ability to process inputs and generate responses simultaneously, akin to being unable to think while perceiving. Furthermore, relying on long contexts to store historical data is impractical for long-term interactions, as retaining all information becomes costly and inefficient. Therefore, rather than relying on a single foundation model to perform all functions, this project draws inspiration from the concept of the Specialized Generalist AI and introduces disentangled streaming perception, reasoning, and memory mechanisms, enabling real-time interaction with streaming video and audio input. The proposed framework InternLM-XComposer2.5-OmniLive (IXC2.5-OL) consists of three key modules: (1) Streaming Perception Module: Processes multimodal information in real-time, storing key details in memory and triggering reasoning in response to user queries. (2) Multi-modal Long Memory Module: Integrates short-term and long-term memory, compressing short-term memories into long-term ones for efficient retrieval and improved accuracy. (3) Reasoning Module: Responds to queries and executes reasoning tasks, coordinating with the perception and memory modules. This project simulates human-like cognition, enabling multimodal large language models to provide continuous and adaptive service over time.