Lost in Tokenization: Context as the Key to Unlocking Biomolecular Understanding in Scientific LLMs

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at github.com/opendatalab-raise-dev/CoKE.

AudioMarathon: A Comprehensive Benchmark for Long-Context Audio Understanding and Efficiency in Audio LLMs

Processing long-form audio is a major challenge for Large Audio Language models (LALMs). These models struggle with the quadratic cost of attention ($O(N^2)$) and with modeling long-range temporal dependencies. Existing audio benchmarks are built mostly from short clips and do not evaluate models in realistic long context settings. To address this gap, we introduce AudioMarathon, a benchmark designed to evaluate both understanding and inference efficiency on long-form audio. AudioMarathon provides a diverse set of tasks built upon three pillars: long-context audio inputs with durations ranging from 90.0 to 300.0 seconds, which correspond to encoded sequences of 2,250 to 7,500 audio tokens, respectively, full domain coverage across speech, sound, and music, and complex reasoning that requires multi-hop inference. We evaluate state-of-the-art LALMs and observe clear performance drops as audio length grows. We also study acceleration techniques and analyze the trade-offs of token pruning and KV cache eviction. The results show large gaps across current LALMs and highlight the need for better temporal reasoning and memory-efficient architectures. We believe AudioMarathon will drive the audio and multimodal research community to develop more advanced audio understanding models capable of solving complex audio tasks.

MinerU2.5: A Decoupled Vision-Language Model for Efficient High-Resolution Document Parsing

We introduce MinerU2.5, a 1.2B-parameter document parsing vision-language model that achieves state-of-the-art recognition accuracy while maintaining exceptional computational efficiency. Our approach employs a coarse-to-fine, two-stage parsing strategy that decouples global layout analysis from local content recognition. In the first stage, the model performs efficient layout analysis on downsampled images to identify structural elements, circumventing the computational overhead of processing high-resolution inputs. In the second stage, guided by the global layout, it performs targeted content recognition on native-resolution crops extracted from the original image, preserving fine-grained details in dense text, complex formulas, and tables. To support this strategy, we developed a comprehensive data engine that generates diverse, large-scale training corpora for both pretraining and fine-tuning. Ultimately, MinerU2.5 demonstrates strong document parsing ability, achieving state-of-the-art performance on multiple benchmarks, surpassing both general-purpose and domain-specific models across various recognition tasks, while maintaining significantly lower computational overhead.

Middo: Model-Informed Dynamic Data Optimization for Enhanced LLM Fine-Tuning via Closed-Loop Learning

Supervised Fine-Tuning (SFT) Large Language Models (LLM) fundamentally rely on high-quality training data. While data selection and data synthesis are two common strategies to improve data quality, existing approaches often face limitations in static dataset curation that fail to adapt to evolving model capabilities. In this paper, we introduce Middo, a self-evolving Model-informed dynamic data optimization framework that uses model-aware data selection and context-preserving data refinement. Unlike conventional one-off filtering/synthesis methods, our framework establishes a closed-loop optimization system: (1) A self-referential diagnostic module proactively identifies suboptimal samples through tri-axial model signals - loss patterns (complexity), embedding cluster dynamics (diversity), and self-alignment scores (quality); (2) An adaptive optimization engine then transforms suboptimal samples into pedagogically valuable training points while preserving semantic integrity; (3) This optimization process continuously evolves with model capability through dynamic learning principles. Experiments on multiple benchmarks demonstrate that our \method consistently enhances the quality of seed data and boosts LLM's performance with improving accuracy by 7.15% on average while maintaining the original dataset scale. This work establishes a new paradigm for sustainable LLM training through dynamic human-AI co-evolution of data and models. Our datasets, models, and code are coming soon.

A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

InternVL3.5: Advancing Open-Source Multimodal Models in Versatility, Reasoning, and Efficiency

We introduce InternVL 3.5, a new family of open-source multimodal models that significantly advances versatility, reasoning capability, and inference efficiency along the InternVL series. A key innovation is the Cascade Reinforcement Learning (Cascade RL) framework, which enhances reasoning through a two-stage process: offline RL for stable convergence and online RL for refined alignment. This coarse-to-fine training strategy leads to substantial improvements on downstream reasoning tasks, e.g., MMMU and MathVista. To optimize efficiency, we propose a Visual Resolution Router (ViR) that dynamically adjusts the resolution of visual tokens without compromising performance. Coupled with ViR, our Decoupled Vision-Language Deployment (DvD) strategy separates the vision encoder and language model across different GPUs, effectively balancing computational load. These contributions collectively enable InternVL3.5 to achieve up to a +16.0\% gain in overall reasoning performance and a 4.05$\times$ inference speedup compared to its predecessor, i.e., InternVL3. In addition, InternVL3.5 supports novel capabilities such as GUI interaction and embodied agency. Notably, our largest model, i.e., InternVL3.5-241B-A28B, attains state-of-the-art results among open-source MLLMs across general multimodal, reasoning, text, and agentic tasks -- narrowing the performance gap with leading commercial models like GPT-5. All models and code are publicly released.

Echo-4o: Harnessing the Power of GPT-4o Synthetic Images for Improved Image Generation

Recently, GPT-4o has garnered significant attention for its strong performance in image generation, yet open-source models still lag behind. Several studies have explored distilling image data from GPT-4o to enhance open-source models, achieving notable progress. However, a key question remains: given that real-world image datasets already constitute a natural source of high-quality data, why should we use GPT-4o-generated synthetic data? In this work, we identify two key advantages of synthetic images. First, they can complement rare scenarios in real-world datasets, such as surreal fantasy or multi-reference image generation, which frequently occur in user queries. Second, they provide clean and controllable supervision. Real-world data often contains complex background noise and inherent misalignment between text descriptions and image content, whereas synthetic images offer pure backgrounds and long-tailed supervision signals, facilitating more accurate text-to-image alignment. Building on these insights, we introduce Echo-4o-Image, a 180K-scale synthetic dataset generated by GPT-4o, harnessing the power of synthetic image data to address blind spots in real-world coverage. Using this dataset, we fine-tune the unified multimodal generation baseline Bagel to obtain Echo-4o. In addition, we propose two new evaluation benchmarks for a more accurate and challenging assessment of image generation capabilities: GenEval++, which increases instruction complexity to mitigate score saturation, and Imagine-Bench, which focuses on evaluating both the understanding and generation of imaginative content. Echo-4o demonstrates strong performance across standard benchmarks. Moreover, applying Echo-4o-Image to other foundation models (e.g., OmniGen2, BLIP3-o) yields consistent performance gains across multiple metrics, highlighting the datasets strong transferability.

Can One Domain Help Others? A Data-Centric Study on Multi-Domain Reasoning via Reinforcement Learning

Reinforcement Learning with Verifiable Rewards (RLVR) has emerged as a powerful paradigm for enhancing the reasoning capabilities of LLMs. Existing research has predominantly concentrated on isolated reasoning domains such as mathematical problem-solving, coding tasks, or logical reasoning. However, real world reasoning scenarios inherently demand an integrated application of multiple cognitive skills. Despite this, the interplay among these reasoning skills under reinforcement learning remains poorly understood. To bridge this gap, we present a systematic investigation of multi-domain reasoning within the RLVR framework, explicitly focusing on three primary domains: mathematical reasoning, code generation, and logical puzzle solving. We conduct a comprehensive study comprising four key components: (1) Leveraging the GRPO algorithm and the Qwen-2.5-7B model family, our study thoroughly evaluates the models' in-domain improvements and cross-domain generalization capabilities when trained on single-domain datasets. (2) Additionally, we examine the intricate interactions including mutual enhancements and conflicts that emerge during combined cross-domain training. (3) To further understand the influence of SFT on RL, we also analyze and compare performance differences between base and instruct models under identical RL configurations. (4) Furthermore, we delve into critical RL training details, systematically exploring the impacts of curriculum learning strategies, variations in reward design, and language-specific factors. Through extensive experiments, our results offer significant insights into the dynamics governing domain interactions, revealing key factors influencing both specialized and generalizable reasoning performance. These findings provide valuable guidance for optimizing RL methodologies to foster comprehensive, multi-domain reasoning capabilities in LLMs.

Native Visual Understanding: Resolving Resolution Dilemmas in Vision-Language Models

Vision-Language Models (VLMs) face significant challenges when dealing with the diverse resolutions and aspect ratios of real-world images, as most existing models rely on fixed, low-resolution inputs. While recent studies have explored integrating native resolution visual encoding to improve model performance, such efforts remain fragmented and lack a systematic framework within the open-source community. Moreover, existing benchmarks fall short in evaluating VLMs under varied visual conditions, often neglecting resolution as a critical factor. To address the "Resolution Dilemma" stemming from both model design and benchmark limitations, we introduce RC-Bench, a novel benchmark specifically designed to systematically evaluate VLM capabilities under extreme visual conditions, with an emphasis on resolution and aspect ratio variations. In conjunction, we propose NativeRes-LLaVA, an open-source training framework that empowers VLMs to effectively process images at their native resolutions and aspect ratios. Based on RC-Bench and NativeRes-LLaVA, we conduct comprehensive experiments on existing visual encoding strategies. The results show that Native Resolution Visual Encoding significantly improves the performance of VLMs on RC-Bench as well as other resolution-centric benchmarks. Code is available at https://github.com/Niujunbo2002/NativeRes-LLaVA.

VRBench: A Benchmark for Multi-Step Reasoning in Long Narrative Videos

We present VRBench, the first long narrative video benchmark crafted for evaluating large models' multi-step reasoning capabilities, addressing limitations in existing evaluations that overlook temporal reasoning and procedural validity. It comprises 1,010 long videos (with an average duration of 1.6 hours), along with 9,468 human-labeled multi-step question-answering pairs and 30,292 reasoning steps with timestamps. These videos are curated via a multi-stage filtering process including expert inter-rater reviewing to prioritize plot coherence. We develop a human-AI collaborative framework that generates coherent reasoning chains, each requiring multiple temporally grounded steps, spanning seven types (e.g., event attribution, implicit inference). VRBench designs a multi-phase evaluation pipeline that assesses models at both the outcome and process levels. Apart from the MCQs for the final results, we propose a progress-level LLM-guided scoring metric to evaluate the quality of the reasoning chain from multiple dimensions comprehensively. Through extensive evaluations of 12 LLMs and 16 VLMs on VRBench, we undertake a thorough analysis and provide valuable insights that advance the field of multi-step reasoning.