Related papers: PhageBench: Can LLMs Understand Raw Bacteriophage …

In contrast to their remarkable performance on general knowledge QA, the true abilities of Large Language Models (LLMs) in tasks demanding deep, specialized reasoning, such as in protein biology, have yet to be thoroughly investigated.…

Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks. However, their ability to reliably reason from gene-level knowledge to functional understanding, a core…

Bacteriophages (phages) are key regulators of bacterial populations and hold great promise for applications such as phage therapy, biocontrol, and industrial fermentation. The success of these applications depends on accurately determining…

The modeling of bio-molecular system across molecular scales remains a central challenge in scientific research. Large language models (LLMs) are increasingly applied to bio-molecular discovery, yet systematic evaluation across multi-scale…

Recent studies have demonstrated the feasibility of modeling single-cell data as natural languages and the potential of leveraging powerful large language models (LLMs) for understanding cell biology. However, a comprehensive evaluation of…

Motivation: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their bacterial hosts and mediating gene transfer. Recently,…

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and…

Large language models (LLMs) have gained significant attention in chemistry. However, most existing datasets center on molecular-level property prediction and overlook the role of fine-grained functional group (FG) information.…

Large Language Models (LLMs), such as ChatGPT, have taken the world by storm and have passed certain forms of the Turing test. However, LLMs are not limited to human language and analyze sequential data, such as DNA, protein, and gene…

Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However,…

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

Large Language Models (LLMs) have demonstrated remarkable abilities in scientific reasoning, yet their reasoning capabilities in materials science remain underexplored. To fill this gap, we introduce MatSciBench, a comprehensive…

Large Language Models (LLMs) have demonstrated remarkable capabilities on general text; however, their proficiency in specialized scientific domains that require deep, interconnected knowledge remains largely uncharacterized. Metabolomics…

Large language models (LLMs) have become important tools in solving biological problems, offering improvements in accuracy and adaptability over conventional methods. Several benchmarks have been proposed to evaluate the performance of…

The applications of large language models (LLMs) in various biological domains have been explored recently, but their reasoning ability in complex biological systems, such as pathways, remains underexplored, which is crucial for predicting…

Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step…

Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has inaugurated a novel paradigm for language-interfaced problem…

Large language models (LLMs) like ChatGPT have shown significant advancements across diverse natural language understanding (NLU) tasks, including intelligent dialogue and autonomous agents. Yet, lacking widely acknowledged testing…

The paper introduces a framework for the evaluation of the encoding of factual scientific knowledge, designed to streamline the manual evaluation process typically conducted by domain experts. Inferring over and extracting information from…

Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new…