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Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM…

The rapid evolution of large language models (LLMs) has expanded their capabilities from basic dialogue to advanced scientific reasoning. However, existing benchmarks in biology often fail to assess a critical skill required of researchers:…

Data science plays a critical role in biomedical research, but it requires professionals with expertise in coding and medical data analysis. Large language models (LLMs) have shown great potential in supporting medical tasks and performing…

Research on long non-coding RNAs (lncRNAs) has garnered significant attention due to their critical roles in gene regulation and disease mechanisms. However, the complexity and diversity of lncRNA sequences, along with the limited knowledge…

Large Language Models (LLMs) have demonstrated impressive capabilities in natural language processing tasks, such as text generation and semantic understanding. However, their performance on numerical reasoning tasks, such as basic…

Large Language Models (LLMs) are increasingly excelling and outpacing human performance on many tasks. However, to improve LLM reasoning, researchers either rely on ad-hoc generated datasets or formal mathematical proof systems such as the…

Large language models (LLMs) have shown strong performance on mathematical reasoning under well-defined conditions. However, real-world engineering problems involve uncertainty, context, and open-ended settings that extend beyond symbolic…

Assessing the capacity of Large Language Models (LLMs) to plan and reason within the constraints of interactive environments is crucial for developing capable AI agents. We introduce $\textbf{LLM-BabyBench}$, a new benchmark suite designed…

For Large Language Models (LLMs) to be reliably deployed in both everyday and high-stakes domains, knowing when not to answer is equally critical as answering correctly. Real-world user queries, which can be underspecified, ill-posed, or…

Most of the existing Large Language Model (LLM) benchmarks on scientific problem reasoning focus on problems grounded in high-school subjects and are confined to elementary algebraic operations. To systematically examine the reasoning…

Protein-Text Question Answering (QA) is crucial for interpreting biological sequences through natural language. The integration of Large Language Models (LLMs) with Retrieval-Augmented Generation (RAG) that efficiently leverages biological…

Reasoning about hypotheses and updating knowledge through empirical observations are central to scientific discovery. In this work, we applied logic-based machine learning methods to drive biological discovery by guiding experimentation.…

Materials characterization is fundamental to acquiring materials information, revealing the processing-microstructure-property relationships that guide material design and optimization. While multimodal large language models (MLLMs) have…

Large language models (LLMs) have shown remarkable improvements in reasoning and many existing benchmarks have been addressed by models such as o1 and o3 either fully or partially. However, a majority of these benchmarks emphasize deductive…

With the increasing use of large language models (LLMs), ensuring reliable performance in diverse, real-world environments is essential. Despite their remarkable achievements, LLMs often struggle with adversarial inputs, significantly…

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis,…

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. However, we possess only a limited systematic understanding of the…

The rapid advancement of large language models (LLMs) has accelerated their integration into clinical decision support, particularly in prescription review. To enable systematic and fine-grained evaluation, we developed RxBench, a…

Deep neural networks and other sophisticated machine learning models are widely applied to biomedical signal data because they can detect complex patterns and compute accurate predictions. However, the difficulty of interpreting such models…

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…