Jaehoon Yun, Jiwoong Sohn, Jungwoo Park, Hyunjae Kim, Xiangru Tang, Daniel Shao, Yong Hoe Koo, Ko Minhyeok, Qingyu Chen, Mark Gerstein, Michael Moor, Jaewoo Kang. Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing. 2025.

Multiple Instance Learning (MIL) is a cornerstone approach in computational pathology for distilling embeddings from gigapixel tissue images into patient-level representations to predict clinical outcomes. However, MIL is frequently challenged by the constraints of working with small, weakly-supervised clinical datasets. Unlike fields such as natural language processing and computer vision, which effectively use transfer learning to improve model quality in data-scarce environments, the transferability of MIL models remains largely unexplored. We conduct the first comprehensive investigation into transfer learning capabilities of pretrained MIL models, evaluating 11 MIL models across 19 pretraining tasks spanning tissue subtyping, cancer grading, and molecular subtype prediction. We observe a substantial performance boost with finetuning pretrained models over training from randomly initialized weights, even with domain differences between pretraining and target tasks. Pretraining on pan-cancer datasets enables consistent generalization across organs and task types compared to single-disease pretraining. Remarkably, this pan-cancer pretraining leads to better transfer than that of a state-of-the-art slide-level foundation model, while using only 6.5\% of the training data. These findings indicate that MIL architectures exhibit robust adaptability, offering insights into the benefits of leveraging pretrained models to enhance performance in computational pathology.

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. We further provide ChemCoTDataset, a pioneering 22,000-instance chemical reasoning dataset with expert-annotated chains of thought to facilitate LLM fine-tuning. By providing annotated trainable datasets, a reasoning taxonomy, and baseline evaluations, our work bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.