In recent years, the rapid advancement of Artificial Intelligence (AI) technologies, particularly Large Language Models (LLMs), has revolutionized the paradigm of scientific discovery, establishing AI-for-Science (AI4Science) as a dynamic and evolving field. However, there is still a lack of an effective framework for the overall assessment of AI4Science, particularly from a holistic perspective on data quality and model capability. Therefore, in this study, we propose SciHorizon, a comprehensive assessment framework designed to benchmark the readiness of AI4Science from both scientific data and LLM perspectives. First, we introduce a generalizable framework for assessing AI-ready scientific data, encompassing four key dimensions: Quality, FAIRness, Explainability, and Compliance which are subdivided into 15 sub-dimensions. Drawing on data resource papers published between 2018 and 2023 in peer-reviewed journals, we present recommendation lists of AI-ready datasets for both Earth and Life Sciences, making a novel and original contribution to the field. Concurrently, to assess the capabilities of LLMs across multiple scientific disciplines, we establish 16 assessment dimensions based on five core indicators Knowledge, Understanding, Reasoning, Multimodality, and Values spanning Mathematics, Physics, Chemistry, Life Sciences, and Earth and Space Sciences. Using the developed benchmark datasets, we have conducted a comprehensive evaluation of over 20 representative open-source and closed source LLMs. All the results are publicly available and can be accessed online at www.scihorizon.cn/en.

The rapid advancement of large language models (LLMs) in biological-medical applications has highlighted a gap between their potential and the limited scale and often low quality of available open-source annotated textual datasets. In addition, the inherent complexity of the biomedical knowledge hierarchy significantly hampers efforts to bridge this gap.Can LLMs themselves play a pivotal role in overcoming this limitation? Motivated by this question, we investigate this challenge in the present study.We propose a framework that automates the distillation of high-quality textual training data from the extensive scientific literature. Our approach self-evaluates and generates questions that are more closely aligned with the biomedical domain, guided by the biomedical knowledge hierarchy through medical subject headings (MeSH). This comprehensive framework establishes an automated workflow, thereby eliminating the need for manual intervention. Furthermore, we conducted comprehensive experiments to evaluate the impact of our framework-generated data on downstream language models of varying sizes. Our approach substantially improves question-answering tasks compared to pre-trained models from the life sciences domain and powerful close-source models represented by GPT-4. Notably, the generated AI-Ready dataset enabled the Llama3-70B base model to outperform GPT-4 using MedPrompt with multiple times the number of parameters. Detailed case studies and ablation experiments underscore the significance of each component within our framework

Discovering gene-disease associations is crucial for understanding disease mechanisms, yet identifying these associations remains challenging due to the time and cost of biological experiments. Computational methods are increasingly vital for efficient and scalable gene-disease association prediction. Graph-based learning models, which leverage node features and network relationships, are commonly employed for biomolecular predictions. However, existing methods often struggle to effectively integrate node features, heterogeneous structures, and semantic information. To address these challenges, we propose COmprehensive MEtapath-based heterogeneous graph Transformer(COMET) for predicting gene-disease associations. COMET integrates diverse datasets to construct comprehensive heterogeneous networks, initializing node features with BioGPT. We define seven Metapaths and utilize a transformer framework to aggregate Metapath instances, capturing global contexts and long-distance dependencies. Through intra- and inter-metapath aggregation using attention mechanisms, COMET fuses latent vectors from multiple Metapaths to enhance GDA prediction accuracy. Our method demonstrates superior robustness compared to state-of-the-art approaches. Ablation studies and visualizations validate COMET's effectiveness, providing valuable insights for advancing human health research.