BIOME-Bench: A Benchmark for Biomolecular Interaction Inference and Multi-Omics Pathway Mechanism Elucidation from Scientific Literature

Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional redundancy, and limited sensitivity to molecular states and interventions. Although recent work has explored using large language models (LLMs) to improve PE-based interpretation, the lack of a standardized benchmark for end-to-end multi-omics pathway mechanism elucidation has largely confined evaluation to small, manually curated datasets or ad hoc case studies, hindering reproducible progress. To address this issue, we introduce BIOME-Bench, constructed via a rigorous four-stage workflow, to evaluate two core capabilities of LLMs in multi-omics analysis: Biomolecular Interaction Inference and end-to-end Multi-Omics Pathway Mechanism Elucidation. We develop evaluation protocols for both tasks and conduct comprehensive experiments across multiple strong contemporary models. Experimental results demonstrate that existing models still exhibit substantial deficiencies in multi-omics analysis, struggling to reliably distinguish fine-grained biomolecular relation types and to generate faithful, robust pathway-level mechanistic explanations.

YAYI 2: Multilingual Open-Source Large Language Models

As the latest advancements in natural language processing, large language models (LLMs) have achieved human-level language understanding and generation abilities in many real-world tasks, and even have been regarded as a potential path to the artificial general intelligence. To better facilitate research on LLMs, many open-source LLMs, such as Llama 2 and Falcon, have recently been proposed and gained comparable performances to proprietary models. However, these models are primarily designed for English scenarios and exhibit poor performances in Chinese contexts. In this technical report, we propose YAYI 2, including both base and chat models, with 30 billion parameters. YAYI 2 is pre-trained from scratch on a multilingual corpus which contains 2.65 trillion tokens filtered by our pre-training data processing pipeline. The base model is aligned with human values through supervised fine-tuning with millions of instructions and reinforcement learning from human feedback. Extensive experiments on multiple benchmarks, such as MMLU and CMMLU, consistently demonstrate that the proposed YAYI 2 outperforms other similar sized open-source models.