Related papers: Interleaved Tool-Call Reasoning for Protein Functi…

Traditional agentic workflows rely on external prompts to manage interactions with tools and the environment, which limits the autonomy of reasoning models. We position \emph{Large Agent Models (LAMs)} that internalize the generation of…

Large Language Models (LLMs) demonstrate enhanced capabilities and reliability by reasoning more, evolving from Chain-of-Thought prompting to product-level solutions like OpenAI o1. Despite various efforts to improve LLM 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…

While reasoning models (e.g., DeepSeek R1) trained with reinforcement learning (RL), excel in textual reasoning, they struggle in scenarios requiring structured problem-solving, such as geometric reasoning, concise computation, or complex…

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…

Large language models (LLMs) sometimes demonstrate poor performance on knowledge-intensive tasks, commonsense reasoning is one of them. Researchers typically address these issues by retrieving related knowledge from knowledge graphs or…

Supervised fine-tuning (SFT) has emerged as one of the most effective ways to improve the performance of large language models (LLMs) in downstream tasks. However, SFT can have difficulty generalizing when the underlying data distribution…

Reinforcement learning (RL) has emerged as a central paradigm for training large language models (LLMs) in reasoning tasks. Yet recent studies question RL's ability to incentivize reasoning capacity beyond the base model. This raises a key…

Large language models (LLMs) have demonstrated remarkable capabilities in function calling for autonomous agents, yet current mechanisms lack explicit reasoning transparency during parameter generation, particularly for complex functions…

Large Language Models (LLMs) have revolutionized natural language processing, yet they struggle with inconsistent reasoning, particularly in novel domains and complex logical sequences. This research introduces Proof of Thought, a framework…

As robots are expected to perform increasingly diverse tasks, they must understand not only low-level actions but also the higher-level structure that determines how a task should unfold. Existing vision-language-action (VLA) models…

Large Language Models (LLMs) have transformed AI but often struggle with tasks that require domain-specific reasoning and logical alignment. Traditional fine-tuning methods do not leverage the vast amount of symbolic domain-knowledge…

Large language models have achieved strong performance on medical reasoning benchmarks, yet their deployment in clinical settings demands rigorous verification to ensure factual accuracy. While reward models offer a scalable approach for…

This paper proposes a detailed prompting flow, termed Table-Logic, to investigate the performance contrasts between bigger and smaller language models (LMs) utilizing step-by-step reasoning methods in the TableQA task. The method processes…

This work enhances the ability of large language models (LLMs) to perform complex reasoning in 3D scenes. Recent work has addressed the 3D situated reasoning task by invoking tool usage through large language models. Large language models…

Large Language Models (LLMs) have emerged as one of the most significant technological advancements in artificial intelligence in recent years. Their ability to understand, generate, and reason with natural language has transformed how we…

Large language models (LLMs) have demonstrated strong performance in a wide-range of language tasks without requiring task-specific fine-tuning. However, they remain prone to hallucinations and inconsistencies, and often struggle with…

Large Language Models (LLMs) achieve impressive performance in a wide range of tasks, even if they are often trained with the only objective of chatting fluently with users. Among other skills, LLMs show emergent abilities in mathematical…

Motivation: We explored how explainable artificial intelligence (XAI) can help to shed light into the inner workings of neural networks for protein function prediction, by extending the widely used XAI method of integrated gradients such…

Protein design is a fundamental challenge in biotechnology, aiming to design novel sequences with specific functions within the vast space of possible proteins. Recent advances in deep generative models have enabled function-based protein…