arXiv subjects

Shiyun Wa

Publications and source records attributed to Shiyun Wa.

3 recordsLinked to original sources

arXiv2026

Elite-Weighted Supervised Fine-tuning for Goal-Directed Molecular Optimization

Goal-directed optimization is essential for steering molecular generators to propose candidates with desired properties. However, it is often implemented with policy-gradient reinforcement learning, which requires a generation-trajectory log-probability whose form depends on the model architecture and generation procedure. This makes an optimizer difficult to reuse across architectures and conditional generative designs. Supervised fine-tuning needs none of that machinery, but its update is driven by a fixed dataset, so the reward never enters the update. We introduce Elite-Weighted Supervised Fine-tuning (EW-SFT), which uses reward to guide elite selection of high-scoring molecules, and updates the model by its own pretraining loss on that set. Ablations show that reward information is passed primarily through elite selection, rather than through continuous weighting within the selected set. Because the update consumes only scored molecules and the model's native loss, the same rule applies across autoregressive, masked-diffusion, and discrete-flow generators, and across de novo, motif-extension, and linker-design tasks. Under a fixed budget of 3D shape alignment oracle calls on two kinase reference compounds, EW-SFT consistently outperforms the corresponding native optimizers. It further improves goal-directed optimization under a 2D similarity oracle on four held-out references and achieves comparable performance on a sample-efficiency benchmark without a trajectory-level RL formulation. These results demonstrate that EW-SFT is a unified and effective optimizer across molecular generators, design constraints, references, and oracles.

cs.LG↗

arXiv2026

Advancing Ligand-based Virtual Screening and Molecular Generation with Pretrained Molecular Embedding Distance

Molecular similarity plays a central role in ligand-based drug discovery, such as virtual screening, analog searching, and goal-directed molecular generation. However, traditional similarity measures, ranging from fingerprint-based Tanimoto coefficients to 3D shape overlays, are often computationally expensive at scale or rely on hand-crafted molecular descriptors. Meanwhile, many deep learning approaches to similarity-aware design still depend on similarity-specific supervision or costly data curation, limiting their generality across targets. In this work, we propose pretrained embedding distance (PED) as an effective alternative, computed directly from pretrained molecular models without task-specific training. Experimental results show that PED exhibits distinct correlations with traditional similarity metrics, and performs effectively in both ranking molecules for virtual screening and guiding molecular generation via reward design. These findings suggest that pretrained molecular embeddings capture rich structural information and can serve as a promising and scalable similarity measurement for modern AI-aided drug discovery.

cs.LG↗

arXiv2023

Stable and Interpretable Deep Learning for Tabular Data: Introducing InterpreTabNet with the Novel InterpreStability Metric

As Artificial Intelligence (AI) integrates deeper into diverse sectors, the quest for powerful models has intensified. While significant strides have been made in boosting model capabilities and their applicability across domains, a glaring challenge persists: many of these state-of-the-art models remain as black boxes. This opacity not only complicates the explanation of model decisions to end-users but also obstructs insights into intermediate processes for model designers. To address these challenges, we introduce InterpreTabNet, a model designed to enhance both classification accuracy and interpretability by leveraging the TabNet architecture with an improved attentive module. This design ensures robust gradient propagation and computational stability. Additionally, we present a novel evaluation metric, InterpreStability, which quantifies the stability of a model's interpretability. The proposed model and metric mark a significant stride forward in explainable models' research, setting a standard for transparency and interpretability in AI model design and application across diverse sectors. InterpreTabNet surpasses other leading solutions in tabular data analysis across varied application scenarios, paving the way for further research into creating deep-learning models that are both highly accurate and inherently explainable. The introduction of the InterpreStability metric ensures that the interpretability of future models can be measured and compared in a consistent and rigorous manner. Collectively, these contributions have the potential to promote the design principles and development of next-generation interpretable AI models, widening the adoption of interpretable AI solutions in critical decision-making environments.

cs.LG↗