4 papers
Representation Alignment as a Bottleneck in LLM-Based Retrosynthesis Planning
Hyunwoo Yoo, Cassie Huang, Haebin Shin +2
While LLMs show promise in general reasoning, symbolic planning in chemistry remains a bottleneck. Direct ''SMILES-to-PDDL'' attempts fail because they force models to juggle chemi…
Abundance-Aware Set Transformer for Microbiome Sample Embedding
Hyunwoo Yoo, Gail Rosen
Microbiome sample representation to input into LLMs is essential for downstream tasks such as phenotype prediction and environmental classification. While prior studies have explor…
Predicting Microbial Ontology and Pathogen Risk from Environmental Metadata with Large Language Models
Hyunwoo Yoo, Gail L. Rosen
Traditional machine learning models struggle to generalize in microbiome studies where only metadata is available, especially in small-sample settings or across studies with hetero…
Exploring Adversarial Robustness in Classification tasks using DNA Language Models
Hyunwoo Yoo, Haebin Shin, Kaidi Xu +1
DNA Language Models, such as GROVER, DNABERT2 and the Nucleotide Transformer, operate on DNA sequences that inherently contain sequencing errors, mutations, and laboratory-induced…