Kaize Ding
Publications
GlassMol: Interpretable Molecular Property Prediction with Concept Bottleneck Models
Machine learning accelerates molecular property prediction, yet state-of-the-art Large Language Models and Graph Neural Networks operate as black boxes. In drug discovery, where safety is critical, this opacity risks masking false correlations and excluding human expertise. Existing interpretability methods suffer from the effectiveness-trustworthiness trade-off: explanations may fail to reflect a model's true reasoning, degrade performance, or lack domain grounding. Concept Bottleneck Models (CBMs) offer a solution by projecting inputs to human-interpretable concepts before readout, ensuring that explanations are inherently faithful to the decision process. However, adapting CBMs to chemistry faces three challenges: the Relevance Gap (selecting task-relevant concepts from a large descriptor space), the Annotation Gap (obtaining concept supervision for molecular data), and the Capacity Gap (degrading performance due to bottleneck constraints). We introduce GlassMol, a model-agnostic CBM that addresses these gaps through automated concept curation and LLM-guided concept selection. Experiments across thirteen benchmarks demonstrate that \method generally matches or exceeds black-box baselines, suggesting that interpretability does not sacrifice performance and challenging the commonly assumed trade-off. Code is available at https://github.com/walleio/GlassMol.
RAPTOR: Ridge-Adaptive Logistic Probes
Probing studies what information is encoded in a frozen LLM's layer representations by training a lightweight predictor on top of them. Beyond analysis, probes are often used operationally in probe-then-steer pipelines: a learned concept vector is extracted from a probe and injected via additive activation steering by adding it to a layer representation during the forward pass. The effectiveness of this pipeline hinges on estimating concept vectors that are accurate, directionally stable under ablation, and inexpensive to obtain. Motivated by these desiderata, we propose RAPTOR (Ridge-Adaptive Logistic Probe), a simple L2-regularized logistic probe whose validation-tuned ridge strength yields concept vectors from normalized weights. Across extensive experiments on instruction-tuned LLMs and human-written concept datasets, RAPTOR matches or exceeds strong baselines in accuracy while achieving competitive directional stability and substantially lower training cost; these quantitative results are supported by qualitative downstream steering demonstrations. Finally, using the Convex Gaussian Min-max Theorem (CGMT), we provide a mechanistic characterization of ridge logistic regression in an idealized Gaussian teacher-student model in the high-dimensional few-shot regime, explaining how penalty strength mediates probe accuracy and concept-vector stability and yielding structural predictions that qualitatively align with trends observed on real LLM embeddings.