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Since the introduction of Large Language Models (LLMs), they have been widely adopted for various tasks such as text summarization, question answering, speech-to-text translation, and more. In recent times, the use of LLMs for code…

Large language models (LLMs) are beginning to reshape how chemists plan and run reactions in organic synthesis. Trained on millions of reported transformations, these text-based models can propose synthetic routes, forecast reaction…

We propose an intuitive LLM prompting framework (AgentKit) for multifunctional agents. AgentKit offers a unified framework for explicitly constructing a complex "thought process" from simple natural language prompts. The basic building…

Large Language Model (LLM)-based agents are increasingly employed to automate complex software engineering tasks, such as program repair and issue resolution. These agents operate by autonomously generating natural language thoughts,…

Large language models (LLMs) have recently attracted considerable interest for their ability to perform complex reasoning tasks, such as chain-of-thought (CoT) reasoning. However, most of the existing approaches to enhance this ability rely…

Automated theorem proving is fundamental to formal methods, and the recent trend is to integrate large language models (LLMs) and proof assistants to form effective proof agents. While existing proof agents show promising performance, they…

Parameter-efficient methods are able to use a single frozen pre-trained large language model (LLM) to perform many tasks by learning task-specific soft prompts that modulate model behavior when concatenated to the input text. However, these…

Deploying large language model (LLM)-driven conversational agents in enterprise settings requires prompts that are simultaneously correct at launch and resilient to the non-deterministic behavioral drift that characterizes production LLM…

Deep learning in \emph{de novo} protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries without explicitly reasoning about which residues or…

Scaling LLM-based embodied agents from text-only environments to complex multimodal settings remains a major challenge. Recent work identifies a perception-reasoning-decision gap in standalone Vision-Language Models (VLMs), which often…

The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…

This paper presents an integrated framework that combines traditional network optimization models with large language models (LLMs) to deliver interactive, explainable, and role-aware decision support for supply chain planning. The proposed…

Planning is a crucial element of both human intelligence and contemporary large language models (LLMs). In this paper, we initiate a theoretical investigation into the emergence of planning capabilities in Transformer-based LLMs via their…

Large Language Models (LLMs) have become increasingly capable of handling diverse tasks with the aid of well-crafted prompts and integration of external tools, but as task complexity rises, the workflow involving LLMs can be complicated and…

Protein language models (PLMs) have enabled advances in structure prediction and de novo protein design, yet they frequently collapse into pathological repetition during generation. Unlike in text, where repetition merely reduces…

Predictive Process Monitoring is a branch of process mining that aims to predict the outcome of an ongoing process. Recently, it leveraged machine-and-deep learning architectures. In this paper, we extend our prior LLM-based Predictive…

Large language models (LLMs) increasingly solve complex reasoning tasks via long chain-of-thought, but their forward-only autoregressive generation process is fragile; early token errors can cascade, which creates a clear need for…

Designing therapeutic peptides with tailored properties is hindered by the vastness of sequence space, limited experimental data, and poor interpretability of current generative models. To address these challenges, we introduce PepThink-R1,…

Chain-of-thought (CoT) reasoning has enabled large language models (LLMs) to utilize additional computation through intermediate tokens to solve complex tasks. However, we posit that typical reasoning traces contain many redundant tokens,…

Curriculum learning is a training mechanism in reinforcement learning (RL) that facilitates the achievement of complex policies by progressively increasing the task difficulty during training. However, designing effective curricula for a…