Related papers: BioReason: Incentivizing Multimodal Biological Rea…

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma.…

With the emergence of advanced reasoning models like OpenAI o3 and DeepSeek-R1, large language models (LLMs) have demonstrated remarkable reasoning capabilities. However, their ability to perform rigorous logical reasoning remains an open…

Foundation models, first introduced in 2021, refer to large-scale pretrained models (e.g., large language models (LLMs) and vision-language models (VLMs)) that learn from extensive unlabeled datasets through unsupervised methods, enabling…

In recent years, large language models (LLMs) have driven major advances in language understanding, marking a significant step toward artificial general intelligence (AGI). With increasing demands for higher-level semantics and cross-modal…

Genes are fundamental for analyzing biological systems and many recent works proposed to utilize gene expression for various biological tasks by deep learning models. Despite their promising performance, it is hard for deep neural networks…

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…

We present BioLangFusion, a simple approach for integrating pre-trained DNA, mRNA, and protein language models into unified molecular representations. Motivated by the central dogma of molecular biology (information flow from gene to…

Scientific reasoning, the process through which humans apply logic, evidence, and critical thinking to explore and interpret scientific phenomena, is essential in advancing knowledge reasoning across diverse fields. However, despite…

Large Language Models (LLMs) have demonstrated strong generalization across a wide range of tasks. Reasoning with LLMs is central to solving multi-step problems and complex decision-making. To support efficient reasoning, recent studies…

The exponential growth of scientific knowledge has created significant barriers to cross-disciplinary knowledge discovery, synthesis and research collaboration. In response to this challenge, we present BioSage, a novel compound AI…

Despite their linguistic competence, Large Language Models (LLMs) often struggle to reason reliably and flexibly. To identify these shortcomings, we introduce the Non-Linear Reasoning (NLR) dataset, a collection of 55 unique, hand-designed…

There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transparency and explainability, which…

Transparency in AI healthcare decision-making is crucial. By incorporating rationales to explain reason for each predicted label, users could understand Large Language Models (LLMs)'s reasoning to make better decision. In this work, we…

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:…

Advancements in artificial intelligence for molecular science are necessitating a paradigm shift from purely data-driven predictions to knowledge-guided computational reasoning. Existing molecular models are predominantly proprietary,…

With the advancement of large language models (LLMs), their performance on multiple-choice question (MCQ) tasks has improved significantly. However, existing approaches face key limitations: answer choices are typically presented to LLMs…

Large Language Models (LLMs) have transformed natural language processing and hold growing promise for advancing science, healthcare, and decision-making. Yet their training paradigms remain dominated by affirmation-based inference, akin to…

Large Language Models (LLMs) and Large Multimodal Models (LMMs) demonstrate impressive problem-solving skills in many tasks and domains. However, their ability to reason with complex images in academic domains has not been systematically…

Existing long-context benchmarks for Large Language Models (LLMs) focus on evaluating comprehension of long inputs, while overlooking the evaluation of long reasoning abilities. To address this gap, we introduce LongReasonArena, a benchmark…

Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing…