Automating Exploratory Proteomics Research via Language Models

With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advancement requires both specialized general models grounded in real-world scientific data and iterative, exploratory frameworks that mirror human scientific methodologies. In this paper, we present PROTEUS, a fully automated system for scientific discovery from raw proteomics data. PROTEUS uses large language models (LLMs) to perform hierarchical planning, execute specialized bioinformatics tools, and iteratively refine analysis workflows to generate high-quality scientific hypotheses. The system takes proteomics datasets as input and produces a comprehensive set of research objectives, analysis results, and novel biological hypotheses without human intervention. We evaluated PROTEUS on 12 proteomics datasets collected from various biological samples (e.g. immune cells, tumors) and different sample types (single-cell and bulk), generating 191 scientific hypotheses. These were assessed using both automatic LLM-based scoring on 5 metrics and detailed reviews from human experts. Results demonstrate that PROTEUS consistently produces reliable, logically coherent results that align well with existing literature while also proposing novel, evaluable hypotheses. The system's flexible architecture facilitates seamless integration of diverse analysis tools and adaptation to different proteomics data types. By automating complex proteomics analysis workflows and hypothesis generation, PROTEUS has the potential to considerably accelerate the pace of scientific discovery in proteomics research, enabling researchers to efficiently explore large-scale datasets and uncover biological insights.

Curriculum-Driven Edubot: A Framework for Developing Language Learning Chatbots Through Synthesizing Conversational Data

Chatbots have become popular in educational settings, revolutionizing how students interact with material and how teachers teach. We present Curriculum-Driven EduBot, a framework for developing a chatbot that combines the interactive features of chatbots with the systematic material of English textbooks to assist students in enhancing their conversational skills. We begin by extracting pertinent topics from textbooks and then using large language models to generate dialogues related to these topics. We then fine-tune an open-source LLM using our generated conversational data to create our curriculum-driven chatbot. User studies demonstrate that our chatbot outperforms ChatGPT in leading curriculum-based dialogues and adapting its dialogue to match the user's English proficiency level. By combining traditional textbook methodologies with conversational AI, our approach offers learners an interactive tool that aligns with their curriculum and provides user-tailored conversation practice. This facilitates meaningful student-bot dialogues and enriches the overall learning experience within the curriculum's pedagogical framework.

Reformulating Sequential Recommendation: Learning Dynamic User Interest with Content-enriched Language Modeling

Recommender systems are essential for online applications, and sequential recommendation has enjoyed significant prevalence due to its expressive ability to capture dynamic user interests. However, previous sequential modeling methods still have limitations in capturing contextual information. The primary reason for this issue is that language models often lack an understanding of domain-specific knowledge and item-related textual content. To address this issue, we adopt a new sequential recommendation paradigm and propose LANCER, which leverages the semantic understanding capabilities of pre-trained language models to generate personalized recommendations. Our approach bridges the gap between language models and recommender systems, resulting in more human-like recommendations. We demonstrate the effectiveness of our approach through experiments on several benchmark datasets, showing promising results and providing valuable insights into the influence of our model on sequential recommendation tasks. Furthermore, our experimental codes are publicly available.