Chenghui Zhou

Chenghui Zhou, Barnabas Poczos

Variational autoencoder (VAE) is a popular method for drug discovery and various architectures and pipelines have been proposed to improve its performance. However, VAE approaches are known to suffer from poor manifold recovery when the data lie on a low-dimensional manifold embedded in a higher dimensional ambient space [Dai and Wipf, 2019]. The consequences of it in drug discovery are somewhat under-explored. In this paper, we explore applying a multi-stage VAE approach, that can improve manifold recovery on a synthetic dataset, to the field of drug discovery. We experimentally evaluate our multi-stage VAE approach using the ChEMBL dataset and demonstrate its ability to improve the property statistics of generated molecules substantially from pre-existing methods without incorporating property predictors into the training pipeline. We further fine-tune our models on two curated and much smaller molecule datasets that target different proteins. Our experiments show an increase in the number of active molecules generated by the multi-stage VAE in comparison to their one-stage equivalent. For each of the two tasks, our baselines include methods that use learned property predictors to incorporate target metrics directly into the training objective and we discuss complications that arise with this methodology.

Chenghui Zhou, Barnabas Poczos

Variational autoencoder (VAE) is a popular method for drug discovery and there had been a great deal of architectures and pipelines proposed to improve its performance. But the VAE model itself suffers from deficiencies such as poor manifold recovery when data lie on low-dimensional manifold embedded in higher dimensional ambient space and they manifest themselves in each applications differently. The consequences of it in drug discovery is somewhat under-explored. In this paper, we study how to improve the similarity of the data generated via VAE and the training dataset by improving manifold recovery via a 2-stage VAE where the second stage VAE is trained on the latent space of the first one. We experimentally evaluated our approach using the ChEMBL dataset as well as a polymer datasets. In both dataset, the 2-stage VAE method is able to improve the property statistics significantly from a pre-existing method.

Divya Tadimeti, Shawn Pan, Sameera Lanka et al.

Short-form text rewriting is a constrained variant of paraphrasing in which limited context and high semantic density leave little room for variation. While large language models perform well on general paraphrasing, small language models (SLMs) often struggle with semantic fidelity and hallucination robustness in short-form settings. In this work, we present an empirical study of adapting an SLM, Phi Silica, for short-form rewrite through dataset curation, prompt distillation, parameter-efficient fine-tuning, and evaluation. We curate a dataset of short presentation-style text from public slide decks and use GPT-5-chat both to generate rewrite supervision and to conduct LLM-as-a-judge evaluation. Our results show that finetuning improves semantic fidelity, reduces hallucinations, and increases preference win rate against GPT-5-chat rewrites. The findings suggest that targeted adaptation for SLMs can substantially narrow the gap to cloud models and provide practical guidance for adapting SLMs to precision-critical rewrite tasks.