Graph-based Molecular In-context Learning Grounded on Morgan Fingerprints

Aug 1, 2025·

Ali Al-Lawati

Jason Lucas

Zhiwei Zhang

Prasenjit Mitra

Suhang Wang

· 1 min read

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Abstract

In-context learning (ICL) effectively conditions large language models (LLMs) for molecular tasks, such as property prediction and molecule captioning, by embedding carefully selected demonstration examples into the input prompt. This approach eliminates the computational overhead of extensive pre-training and fine-tuning. However, current prompt retrieval methods for molecular tasks rely on molecule feature similarity, such as Morgan fingerprints, which do not adequately capture the global molecular and atom-binding relationships. As a result, these methods fail to represent the full complexity of molecular structures during inference. Moreover, medium-sized LLMs, which offer simpler deployment requirements in specialized systems, have remained largely unexplored in the molecular ICL literature. To address these gaps, we propose a self-supervised learning technique, GAMIC (Graph-Aligned Molecular In-Context learning), which aligns global molecular structures, represented by graph neural networks (GNNs), with textual captions (descriptions) while leveraging local feature similarity through Morgan fingerprints. In addition, we introduce a Maximum Marginal Relevance (MMR) based diversity heuristic during retrieval to optimize input prompt demonstration samples. Our experimental findings using diverse benchmark datasets show GAMIC outperforms simple Morgan-based ICL retrieval methods across all tasks by up to 45%.

Type

Conference paper

Publication

In Findings of the Association for Computational Linguistics, Empirical Methods in Natural Language Processing

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Last updated on Nov 8, 2025

Authors

Ali Al-Lawati

Authors

Jason Lucas

Ph.D. Candidate in Informatics

I am a PhD candidate in Informatics in the College of IST at Penn State University, where I conduct research at the PIKE Research Lab under the guidance of Dr. Dongwon Lee. I specialize in AI/ML research focused on Information Integrity, Safe and Ethical AI, including combating harmful content across multiple languages and modalities. My research spans low-resource multilingual NLP, generative AI, and adversarial machine learning, with work extending across 79 languages. I have published 12 papers with 260+ citations in premier venues including ACL, EMNLP, IEEE, and NAACL.

My doctoral research focuses on bridging the digital language divide through transfer learning, classification (NLU), generation (NLG), adversarial attacks, and developing end-to-end AI pipelines using RAG and Agentic AI workflows for combating multilingual threats. Drawing from my Grenadian background and knowledge of local Creole languages, I bring a global perspective to AI challenges, working to democratize state-of-the-art AI capabilities for underserved linguistic communities worldwide. My mission is to develop robust multilingual multimodal systems and mitigate evolving security vulnerabilities while enhancing access to human language technology through cutting-edge solutions.

As an NSF LinDiv Fellow, I conduct transdisciplinary research advancing human-AI language interaction for social good. I actively mentor 5+ research interns and teach Applied Generative AI courses. Through industry experience at Lawrence Livermore National Lab, Interaction LLC, and Coalfire, I bridge academic research with practical applications in combating evolving security threats and enhancing global AI accessibility. I see multilingual advances and interdisciplinary collaboration as a competitive advantage, not a communication challenge. Beyond research, I stay active through dance, fitness, martial arts, and community service.