Daily Papers

Large language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored. To fill this research gap, we first introduce Biology-Instructions, the first large-scale multi-omics biological sequences-related instruction-tuning dataset including DNA, RNA, proteins, and multi-molecules, designed to bridge the gap between large language models (LLMs) and complex biological sequences-related tasks. This dataset can enhance the versatility of LLMs by integrating diverse biological sequenced-based prediction tasks with advanced reasoning capabilities, while maintaining conversational fluency. Additionally, we reveal significant performance limitations in even state-of-the-art LLMs on biological sequence-related multi-omics tasks without specialized pre-training and instruction-tuning. We further develop a strong baseline called ChatMultiOmics with a novel three-stage training pipeline, demonstrating the powerful ability to understand biology by using Biology-Instructions. Biology-Instructions and ChatMultiOmics are publicly available and crucial resources for enabling more effective integration of LLMs with multi-omics sequence analysis.

Scientific discovery increasingly requires AI systems that can reason over scientific evidence of heterogeneous modalities, interact with scientific tools and environments, and sustain progress across long task horizons. We present Intern-S2-Preview, a series of scientific agentic foundation models designed to support multimodal scientific understanding, reasoning, generation, and long-horizon tasks. The training pipeline begins with scientific multimodal pre-training over rendered scientific documents, interleaved image-text data, and diverse scientific corpora. Starting from the pretrained checkpoint, we apply a unified post-training pipeline consisting of supervised fine-tuning, scalable multi-task reinforcement learning (RL), black- and white-box agentic RL, and on-policy distillation. This pipeline is supported by practical techniques that improve rollout and training stability and efficiency, including partial rollout with off-policy correction, adaptive length regularization, online speculative decoding, robust multi-task optimization, and trace-aware experience assembly for agentic tasks. At the architecture level, Intern-S2-Preview-397B extends time series modelling from efficient long-sequence understanding to numerical forecasting, while Memory Decoder is studied as a separate memory-augmented path for rapid scientific specialization without modifying the frozen 397B backbone. Evaluations across scientific, multimodal, agentic, and general-purpose benchmarks show that Intern-S2-Preview-397B achieves competitive or leading results in multiple settings. The time series modules improve scientific signal understanding and forecasting on SciTS, while the separate Intern-MemDec-4B extension improves the Biology-Instructions average score from 56.92 to 60.32 without modifying the frozen 397B backbone.

Understanding and designing biomolecules, such as proteins and small molecules, is central to advancing drug discovery, synthetic biology, and enzyme engineering. Recent breakthroughs in Artificial Intelligence (AI) have revolutionized biomolecular research, achieving remarkable accuracy in biomolecular prediction and design. However, a critical gap remains between AI's computational power and researchers' intuition, using natural language to align molecular complexity with human intentions. Large Language Models (LLMs) have shown potential to interpret human intentions, yet their application to biomolecular research remains nascent due to challenges including specialized knowledge requirements, multimodal data integration, and semantic alignment between natural language and biomolecules. To address these limitations, we present InstructBioMol, a novel LLM designed to bridge natural language and biomolecules through a comprehensive any-to-any alignment of natural language, molecules, and proteins. This model can integrate multimodal biomolecules as input, and enable researchers to articulate design goals in natural language, providing biomolecular outputs that meet precise biological needs. Experimental results demonstrate InstructBioMol can understand and design biomolecules following human instructions. Notably, it can generate drug molecules with a 10% improvement in binding affinity and design enzymes that achieve an ESP Score of 70.4, making it the only method to surpass the enzyme-substrate interaction threshold of 60.0 recommended by the ESP developer. This highlights its potential to transform real-world biomolecular research.

Jailbreak attacks bypass the guardrails of large language models to produce harmful outputs. In this paper, we ask whether the model outputs produced by existing jailbreaks are actually useful. For example, when jailbreaking a model to give instructions for building a bomb, does the jailbreak yield good instructions? Since the utility of most unsafe answers (e.g., bomb instructions) is hard to evaluate rigorously, we build new jailbreak evaluation sets with known ground truth answers, by aligning models to refuse questions related to benign and easy-to-evaluate topics (e.g., biology or math). Our evaluation of eight representative jailbreaks across five utility benchmarks reveals a consistent drop in model utility in jailbroken responses, which we term the jailbreak tax. For example, while all jailbreaks we tested bypass guardrails in models aligned to refuse to answer math, this comes at the expense of a drop of up to 92% in accuracy. Overall, our work proposes the jailbreak tax as a new important metric in AI safety, and introduces benchmarks to evaluate existing and future jailbreaks. We make the benchmark available at https://github.com/ethz-spylab/jailbreak-tax

The push toward large language models for biology (BioLM) has created a need for training corpora that can endow models with a genuine understanding of biology. However, existing biological resources, such as molecular databases, protein repositories, genomic annotations, single-cell atlases, and pathway databases, are scattered across heterogeneous formats and remain unorganized into a cohesive corpus for language model training. We present TheBioCollection, a 52.6B-token pre-training-scale corpus that converts these disparate resources into a unified, training-ready form spanning small molecules, proteins, genomic sequences, cells, and pathways. Beyond consolidating existing data, TheBioCollection enriches each record with tool-computed biological properties and introduces new instruction tasks for capabilities that current corpora barely cover. We pair the corpus with TheBioCollection-Eval, a matched suite probing recognition, generation, and prediction across molecular, protein, genomic, cellular, and cross-domain settings. Holding the base Gravity-16B-A3B architecture fixed, training on TheBioCollection more than doubles its overall score on TheBioCollection-Eval with gains in every domain, while leaving general linguistic ability nearly intact.

Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular biology", capturing intricate gene expression patterns at the single-cell level. However, interacting with this "language" through conventional tools is often inefficient and unintuitive, posing challenges for researchers. To address these limitations, we present InstructCell, a multi-modal AI copilot that leverages natural language as a medium for more direct and flexible single-cell analysis. We construct a comprehensive multi-modal instruction dataset that pairs text-based instructions with scRNA-seq profiles from diverse tissues and species. Building on this, we develop a multi-modal cell language architecture capable of simultaneously interpreting and processing both modalities. InstructCell empowers researchers to accomplish critical tasks-such as cell type annotation, conditional pseudo-cell generation, and drug sensitivity prediction-using straightforward natural language commands. Extensive evaluations demonstrate that InstructCell consistently meets or exceeds the performance of existing single-cell foundation models, while adapting to diverse experimental conditions. More importantly, InstructCell provides an accessible and intuitive tool for exploring complex single-cell data, lowering technical barriers and enabling deeper biological insights.