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.

Deep Learning-based MRI Reconstruction with Artificial Fourier Transform (AFT)-Net

The deep complex-valued neural network provides a powerful way to leverage complex number operations and representations, which has succeeded in several phase-based applications. However, most previously published networks have not fully accessed the impact of complex-valued networks in the frequency domain. Here, we introduced a unified complex-valued deep learning framework - artificial Fourier transform network (AFT-Net) - which combined domain-manifold learning and complex-valued neural networks. The AFT-Net can be readily used to solve the image inverse problems in domain-transform, especially for accelerated magnetic resonance imaging (MRI) reconstruction and other applications. While conventional methods only accept magnitude images, the proposed method takes raw k-space data in the frequency domain as inputs, allowing a mapping between the k-space domain and the image domain to be determined through cross-domain learning. We show that AFT-Net achieves superior accelerated MRI reconstruction and is comparable to existing approaches. Also, our approach can be applied to different tasks like denoised MRS reconstruction and different datasets with various contrasts. The AFT-Net presented here is a valuable preprocessing component for different preclinical studies and provides an innovative alternative for solving inverse problems in imaging and spectroscopy.