arXiv subjects

Yuchen Ren

Publications and source records attributed to Yuchen Ren.

At least 19 recordsLinked to original sources

arXiv2026

On Success and Simplicity: A Second Look at Transferable Vision-Language Attack Pipeline

Vision-Language Pre-training Models (VLPMs) are known to be vulnerable to adversarial attacks. Recent transferable attacks on VLPMs have followed a common pipeline with complicated loss functions or multi-stage text/image attacks. However, in this paper, we demonstrate that such a sophisticated attack pipeline can be simpler yet more successful. Specifically, we identify three previously overlooked issues caused by inappropriate cross-modal interactions and excessive operations. To address them, we propose the Simple Vision-Language Attack (SimVLA) pipeline, which observably improves transferability and efficiency. Experiments on four datasets and three downstream tasks validate the superiority of our pipeline. For instance, on Flickr30k text-image retrieval dataset, our SimVLA outperforms the SOTA baseline in R@1 transferability by 8.01\%-14.71\%, while consuming only about 35.73\% of the time and 46.26\% of the max VRAM. Overall, the superiority of our SimVLA highlights the importance of leveraging domain knowledge (e.g., our proposed cross-modal word identification), while blindly pursuing intricate operations (e.g, complex loss functions and redundant multi-stage designs) may even be harmful. We hope our SimVLA can serve as a simple yet effective backbone for future extensions. Code is available at https://github.com/RYC-98/SimVLA.

cs.CV↗

arXiv2026

Faithful, Enriched, and Precise: Benchmarking Natural-Science Illustration Generation by T2I models

Scientific illustrations are essential tools for communicating research findings, especially in natural science, where they visualize complex concepts and processes. As Text-to-Image (T2I) models become increasingly capable, researchers have started to use them for scientific illustration generation. However, existing benchmarks often assess outputs at a holistic level, overlooking fine-grained elements, while scientific reasoning ability and output conciseness remain under-quantified. We introduce FEPBench, a benchmark built from carefully selected high-quality scientific illustrations across multiple disciplines and layout types. With the assistance of multimodal large language models (MLLMs) and human experts, we provide fine-grained atom set annotations and systematically evaluate T2I models along three dimensions: instruction faithfulness, reasoning enrichment, and semantic precision. Our evaluation further decomposes model performance across visual, textual, relation, and layout elements. Results show that even state-of-the-art (SOTA) closed-source models, such as GPT Image 2 and Nano Banana Pro, still suffer from text-rendering bottlenecks, limited reasoning enrichment, and difficulty balancing generation richness with precision. These findings provide practical guidance for improving and deploying T2I models in scientific illustration generation. Benchmark data, atom set annotations, and evaluation code will be released by us.

cs.CV↗

arXiv2026

KORE: Enhancing Knowledge Injection for Large Multimodal Models via Knowledge-Oriented Controls

Large Multimodal Models encode extensive factual knowledge in their pre-trained weights. However, its knowledge remains static and limited, unable to keep pace with real-world developments, which hinders continuous knowledge acquisition. Effective knowledge injection thus becomes critical, involving two goals: knowledge adaptation (injecting new knowledge) and knowledge retention (preserving old knowledge). Existing methods often struggle to learn new knowledge and suffer from catastrophic forgetting. To address this, we propose KORE, a synergistic method of KnOwledge-oRientEd augmentations and constraints for injecting new knowledge into large multimodal models while preserving old knowledge. Unlike general text or image data augmentation, KORE automatically converts individual knowledge items into structured and comprehensive knowledge to ensure that the model accurately learns new knowledge, enabling accurate adaptation. Meanwhile, KORE stores previous knowledge in the covariance matrix of LMM's linear layer activations and initializes the adapter by projecting the original weights into the matrix's null space, defining a fine-tuning direction that minimizes interference with previous knowledge, enabling powerful retention. Extensive experiments on various LMMs, including LLaVA-v1.5-7B, LLaVA-v1.5-13B, and Qwen2.5-VL-7B, show that KORE achieves superior new knowledge injection performance and effectively mitigates catastrophic forgetting.

cs.CL↗

arXiv2026

MINED: Probing and Updating with Multimodal Time-Sensitive Knowledge for Large Multimodal Models

Large Multimodal Models (LMMs) encode rich factual knowledge via cross-modal pre-training, yet their static representations struggle to maintain an accurate understanding of time-sensitive factual knowledge. Existing benchmarks remain constrained by static designs, inadequately evaluating LMMs' ability to understand time-sensitive knowledge. To address this gap, we propose MINED, a comprehensive benchmark that evaluates temporal awareness along 6 key dimensions and 11 challenging tasks: cognition, awareness, trustworthiness, understanding, reasoning, and robustness. MINED is constructed from Wikipedia by two professional annotators, containing 2,104 time-sensitive knowledge samples spanning six knowledge types. Evaluating 15 widely used LMMs on MINED shows that Gemini-2.5-Pro achieves the highest average CEM score of 63.07, while most open-source LMMs still lack time understanding ability. Meanwhile, LMMs perform best on organization knowledge, whereas their performance is weakest on sport. To address these challenges, we investigate the feasibility of updating time-sensitive knowledge in LMMs through knowledge editing methods and observe that LMMs can effectively update knowledge via knowledge editing methods in single editing scenarios.

cs.CL↗

arXiv2026

Intern-S1-Pro: Scientific Multimodal Foundation Model at Trillion Scale

We introduce Intern-S1-Pro, the first one-trillion-parameter scientific multimodal foundation model. Scaling to this unprecedented size, the model delivers a comprehensive enhancement across both general and scientific domains. Beyond stronger reasoning and image-text understanding capabilities, its intelligence is augmented with advanced agent capabilities. Simultaneously, its scientific expertise has been vastly expanded to master over 100 specialized tasks across critical science fields, including chemistry, materials, life sciences, and earth sciences. Achieving this massive scale is made possible by the robust infrastructure support of XTuner and LMDeploy, which facilitates highly efficient Reinforcement Learning (RL) training at the 1-trillion parameter level while ensuring strict precision consistency between training and inference. By seamlessly integrating these advancements, Intern-S1-Pro further fortifies the fusion of general and specialized intelligence, working as a Specializable Generalist, demonstrating its position in the top tier of open-source models for general capabilities, while outperforming proprietary models in the depth of specialized scientific tasks.

cs.LG↗

arXiv2026

When Large Multimodal Models Confront Evolving Knowledge: Challenges and Explorations

Large Multimodal Models (LMMs) store vast amounts of pretrained knowledge but struggle to remain aligned with real-world updates, making it difficult to avoid capability degradation when acquiring evolving knowledge. Furthermore, most current work focuses on exploring static textual knowledge injection, neglecting dynamic multimodal evolving knowledge injection, leaving the potential of LMMs for multimodal knowledge injection as an open question. To address this, we first propose a pipeline to construct MMEVOKE, a benchmark for evaluating LMMs' ability in multimodal evolving knowledge injection. MMEVOKE contains 9,422 samples spanning 159 subtypes. Then, based on extensive experiments with MMEVOKE, we reveal challenges such as poor injection performance and capability degradation in existing knowledge injection methods through knowledge injection tests and general capability tests. Finally, to tackle these challenges, we introduce knowledge augmentation and knowledge retention methods, finding that knowledge-aware augmentation strengthens knowledge injection performance, and that Data Replay and MoE methods effectively mitigate capability degradation.

cs.CL↗

arXiv2025

Probing Scientific General Intelligence of LLMs with Scientist-Aligned Workflows

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

cs.AI↗

arXiv2025

SciReasoner: Laying the Scientific Reasoning Ground Across Disciplines

We present a scientific reasoning foundation model that aligns natural language with heterogeneous scientific representations. The model is pretrained on a 206B-token corpus spanning scientific text, pure sequences, and sequence-text pairs, then aligned via SFT on 40M instructions, annealed cold-start bootstrapping to elicit long-form chain-of-thought, and reinforcement learning with task-specific reward shaping, which instills deliberate scientific reasoning. It supports four capability families, covering up to 103 tasks across workflows: (i) faithful translation between text and scientific formats, (ii) text/knowledge extraction, (iii) property prediction, (iv) property classification, (v) unconditional and conditional sequence generation and design. Compared with specialist systems, our approach broadens instruction coverage, improves cross-domain generalization, and enhances fidelity. We detail data curation and training and show that cross-discipline learning strengthens transfer and downstream reliability. The model, instruct tuning datasets and the evaluation code are open-sourced at https://huggingface.co/SciReason and https://github.com/open-sciencelab/SciReason.

cs.CL↗

arXiv2025

ChronusOmni: Improving Time Awareness of Omni Large Language Models

Time awareness is a fundamental ability of omni large language models, especially for understanding long videos and answering complex questions. Previous approaches mainly target vision-language scenarios and focus on the explicit temporal grounding questions, such as identifying when a visual event occurs or determining what event happens at aspecific time. However, they often make insufficient use of the audio modality, and overlook implicit temporal grounding across modalities--for example, identifying what is visually present when a character speaks, or determining what is said when a visual event occurs--despite such cross-modal temporal relations being prevalent in real-world scenarios. In this paper, we propose ChronusOmni, an omni large language model designed to enhance temporal awareness for both explicit and implicit audiovisual temporal grounding. First, we interleave text-based timestamp tokens with visual and audio representations at each time unit, enabling unified temporal modeling across modalities. Second, to enforce correct temporal ordering and strengthen fine-grained temporal reasoning, we incorporate reinforcement learning with specially designed reward functions. Moreover, we construct ChronusAV, a temporally-accurate, modality-complete, and cross-modal-aligned dataset to support the training and evaluation on audiovisual temporal grounding task. Experimental results demonstrate that ChronusOmni achieves state-of-the-art performance on ChronusAV with more than 30% improvement and top results on most metrics upon other temporal grounding benchmarks. This highlights the strong temporal awareness of our model across modalities, while preserving general video and audio understanding capabilities.

cs.CL↗

arXiv2025

Use as Many Surrogates as You Want: Selective Ensemble Attack to Unleash Transferability without Sacrificing Resource Efficiency

In surrogate ensemble attacks, using more surrogate models yields higher transferability but lower resource efficiency. This practical trade-off between transferability and efficiency has largely limited existing attacks despite many pre-trained models are easily accessible online. In this paper, we argue that such a trade-off is caused by an unnecessary common assumption, i.e., all models should be \textit{identical} across iterations. By lifting this assumption, we can use as many surrogates as we want to unleash transferability without sacrificing efficiency. Concretely, we propose Selective Ensemble Attack (SEA), which dynamically selects diverse models (from easily accessible pre-trained models) across iterations based on our new interpretation of decoupling within-iteration and cross-iteration model diversity. In this way, the number of within-iteration models is fixed for maintaining efficiency, while only cross-iteration model diversity is increased for higher transferability. Experiments on ImageNet demonstrate the superiority of SEA in various scenarios. For example, when dynamically selecting 4 from 20 accessible models, SEA yields 8.5% higher transferability than existing attacks under the same efficiency. The superiority of SEA also generalizes to real-world systems, such as commercial vision APIs and large vision-language models. Overall, SEA opens up the possibility of adaptively balancing transferability and efficiency according to specific resource requirements.

cs.CV↗

arXiv2025

GoRA: Gradient-driven Adaptive Low Rank Adaptation

Low-Rank Adaptation (LoRA) is a crucial method for efficiently fine-tuning large language models (LLMs), with its effectiveness influenced by two key factors: rank selection and weight initialization. While numerous LoRA variants have been proposed to improve performance by addressing one of these aspects, they often compromise usability or computational efficiency. In this paper, we analyze and identify the core limitations of existing approaches and propose a novel framework--GoRA (Gradient-driven Adaptive Low Rank Adaptation)--that simultaneously adapts both the rank and initialization strategy within a unified framework. GoRA leverages gradient information during training to dynamically assign optimal ranks and initialize low-rank adapter weights in an adaptive manner. To our knowledge, GoRA is the first method that not only addresses the limitations of prior approaches--which often focus on either rank selection or initialization in isolation--but also unifies both aspects within a single framework, enabling more effective and efficient adaptation. Extensive experiments across various architectures and modalities show that GoRA consistently outperforms existing LoRA-based methods while preserving the efficiency of vanilla LoRA. For example, when fine-tuning Llama3.1-8B-Base for mathematical reasoning, GoRA achieves a 5.13-point improvement over standard LoRA and even outperforms full fine-tuning by 2.05 points under high-rank settings. Code is available at: https://github.com/hhnqqq/MyTransformers.

cs.LG↗

arXiv2025

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.

cs.CL↗

arXiv2025

Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models

Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale instruction-tuning dataset for multi-omics biological sequences, including DNA, RNA, proteins, and multi-molecules. This dataset bridges LLMs and complex biological sequence-related tasks, enhancing their versatility and reasoning while maintaining conversational fluency. We also highlight significant limitations of current state-of-the-art LLMs on multi-omics tasks without specialized training. To overcome this, we propose ChatMultiOmics, a strong baseline with a novel three-stage training pipeline, demonstrating superior biological understanding through Biology-Instructions. Both resources are publicly available, paving the way for better integration of LLMs in multi-omics analysis. The Biology-Instructions is publicly available at: https://github.com/hhnqqq/Biology-Instructions.

q-bio.BM↗

arXiv2025

Improving Adversarial Transferability on Vision Transformers via Forward Propagation Refinement

Vision Transformers (ViTs) have been widely applied in various computer vision and vision-language tasks. To gain insights into their robustness in practical scenarios, transferable adversarial examples on ViTs have been extensively studied. A typical approach to improving adversarial transferability is by refining the surrogate model. However, existing work on ViTs has restricted their surrogate refinement to backward propagation. In this work, we instead focus on Forward Propagation Refinement (FPR) and specifically refine two key modules of ViTs: attention maps and token embeddings. For attention maps, we propose Attention Map Diversification (AMD), which diversifies certain attention maps and also implicitly imposes beneficial gradient vanishing during backward propagation. For token embeddings, we propose Momentum Token Embedding (MTE), which accumulates historical token embeddings to stabilize the forward updates in both the Attention and MLP blocks. We conduct extensive experiments with adversarial examples transferred from ViTs to various CNNs and ViTs, demonstrating that our FPR outperforms the current best (backward) surrogate refinement by up to 7.0\% on average. We also validate its superiority against popular defenses and its compatibility with other transfer methods. Codes and appendix are available at https://github.com/RYC-98/FPR.

cs.CV↗

arXiv2024

Improving Integrated Gradient-based Transferable Adversarial Examples by Refining the Integration Path

Transferable adversarial examples are known to cause threats in practical, black-box attack scenarios. A notable approach to improving transferability is using integrated gradients (IG), originally developed for model interpretability. In this paper, we find that existing IG-based attacks have limited transferability due to their naive adoption of IG in model interpretability. To address this limitation, we focus on the IG integration path and refine it in three aspects: multiplicity, monotonicity, and diversity, supported by theoretical analyses. We propose the Multiple Monotonic Diversified Integrated Gradients (MuMoDIG) attack, which can generate highly transferable adversarial examples on different CNN and ViT models and defenses. Experiments validate that MuMoDIG outperforms the latest IG-based attack by up to 37.3\% and other state-of-the-art attacks by 8.4\%. In general, our study reveals that migrating established techniques to improve transferability may require non-trivial efforts. Code is available at \url{https://github.com/RYC-98/MuMoDIG}.

cs.CR↗

arXiv2024

Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA

Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed for natural language, which are unsuitable for DNA sequences due to their unique characteristics. In addition, the optimal approach to tokenize DNA remains largely under-explored, and may not be intuitively understood by humans even if discovered. To address these challenges, we introduce MxDNA, a novel framework where the model autonomously learns an effective DNA tokenization strategy through gradient decent. MxDNA employs a sparse Mixture of Convolution Experts coupled with a deformable convolution to model the tokenization process, with the discontinuous, overlapping, and ambiguous nature of meaningful genomic segments explicitly considered. On Nucleotide Transformer Benchmarks and Genomic Benchmarks, MxDNA demonstrates superior performance to existing methods with less pretraining data and time, highlighting its effectiveness. Finally, we show that MxDNA learns unique tokenization strategy distinct to those of previous methods and captures genomic functionalities at a token level during self-supervised pretraining. Our MxDNA aims to provide a new perspective on DNA tokenization, potentially offering broad applications in various domains and yielding profound insights.

q-bio.GN↗

arXiv2024

COMET: Benchmark for Comprehensive Biological Multi-omics Evaluation Tasks and Language Models

As key elements within the central dogma, DNA, RNA, and proteins play crucial roles in maintaining life by guaranteeing accurate genetic expression and implementation. Although research on these molecules has profoundly impacted fields like medicine, agriculture, and industry, the diversity of machine learning approaches-from traditional statistical methods to deep learning models and large language models-poses challenges for researchers in choosing the most suitable models for specific tasks, especially for cross-omics and multi-omics tasks due to the lack of comprehensive benchmarks. To address this, we introduce the first comprehensive multi-omics benchmark COMET (Benchmark for Biological COmprehensive Multi-omics Evaluation Tasks and Language Models), designed to evaluate models across single-omics, cross-omics, and multi-omics tasks. First, we curate and develop a diverse collection of downstream tasks and datasets covering key structural and functional aspects in DNA, RNA, and proteins, including tasks that span multiple omics levels. Then, we evaluate existing foundational language models for DNA, RNA, and proteins, as well as the newly proposed multi-omics method, offering valuable insights into their performance in integrating and analyzing data from different biological modalities. This benchmark aims to define critical issues in multi-omics research and guide future directions, ultimately promoting advancements in understanding biological processes through integrated and different omics data analysis.

q-bio.BM↗

arXiv2024

BEACON: Benchmark for Comprehensive RNA Tasks and Language Models

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (\textbf{BE}nchm\textbf{A}rk for \textbf{CO}mprehensive R\textbf{N}A Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

q-bio.QM↗