VECT-GAN: A variationally encoded generative model for overcoming data scarcity in pharmaceutical science

Data scarcity in pharmaceutical research has led to reliance on labour-intensive trial and error approaches for development rather than data driven methods. While Machine Learning offers a solution, existing datasets are often small and noisy, limiting their utility. To address this, we developed a Variationally Encoded Conditional Tabular Generative Adversarial Network (VECT GAN), a novel generative model specifically designed for augmenting small, noisy datasets. We introduce a pipeline where data is augmented before regression model development and demonstrate that this consistently and significantly improves performance over other state of the art tabular generative models. We apply this pipeline across six pharmaceutical datasets, and highlight its real-world applicability by developing novel polymers with medically desirable mucoadhesive properties, which we made and experimentally characterised. Additionally, we pre-train the model on the ChEMBL database of drug-like molecules, leveraging knowledge distillation to enhance its generalisability, making it readily available for use on pharmaceutical datasets containing small molecules, which is an extremely common pharmaceutical task. We demonstrate the power of synthetic data for regularising small tabular datasets, highlighting its potential to become standard practice in pharmaceutical model development, and make our method, including VECT GAN pretrained on ChEMBL available as a pip package.

Borrowing Treasures from Neighbors: In-Context Learning for Multimodal Learning with Missing Modalities and Data Scarcity

Multimodal machine learning with missing modalities is an increasingly relevant challenge arising in various applications such as healthcare. This paper extends the current research into missing modalities to the low-data regime, i.e., a downstream task has both missing modalities and limited sample size issues. This problem setting is particularly challenging and also practical as it is often expensive to get full-modality data and sufficient annotated training samples. We propose to use retrieval-augmented in-context learning to address these two crucial issues by unleashing the potential of a transformer's in-context learning ability. Diverging from existing methods, which primarily belong to the parametric paradigm and often require sufficient training samples, our work exploits the value of the available full-modality data, offering a novel perspective on resolving the challenge. The proposed data-dependent framework exhibits a higher degree of sample efficiency and is empirically demonstrated to enhance the classification model's performance on both full- and missing-modality data in the low-data regime across various multimodal learning tasks. When only 1% of the training data are available, our proposed method demonstrates an average improvement of 6.1% over a recent strong baseline across various datasets and missing states. Notably, our method also reduces the performance gap between full-modality and missing-modality data compared with the baseline.

HgbNet: predicting hemoglobin level/anemia degree from EHR data

Anemia is a prevalent medical condition that typically requires invasive blood tests for diagnosis and monitoring. Electronic health records (EHRs) have emerged as valuable data sources for numerous medical studies. EHR-based hemoglobin level/anemia degree prediction is non-invasive and rapid but still faces some challenges due to the fact that EHR data is typically an irregular multivariate time series containing a significant number of missing values and irregular time intervals. To address these issues, we introduce HgbNet, a machine learning-based prediction model that emulates clinicians' decision-making processes for hemoglobin level/anemia degree prediction. The model incorporates a NanDense layer with a missing indicator to handle missing values and employs attention mechanisms to account for both local irregularity and global irregularity. We evaluate the proposed method using two real-world datasets across two use cases. In our first use case, we predict hemoglobin level/anemia degree at moment T+1 by utilizing records from moments prior to T+1. In our second use case, we integrate all historical records with additional selected test results at moment T+1 to predict hemoglobin level/anemia degree at the same moment, T+1. HgbNet outperforms the best baseline results across all datasets and use cases. These findings demonstrate the feasibility of estimating hemoglobin levels and anemia degree from EHR data, positioning HgbNet as an effective non-invasive anemia diagnosis solution that could potentially enhance the quality of life for millions of affected individuals worldwide. To our knowledge, HgbNet is the first machine learning model leveraging EHR data for hemoglobin level/anemia degree prediction.