# ChemVA: Interactive Visual Analysis of Chemical Compound Similarity in Virtual Screening

arXiv: https://arxiv.org/abs/2008.13150 · HTML: https://mlsanity.com/paper/2008.13150/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 30 Aug 2020.

## Built on by (most cited first, 6 of 6)

- [SAME: Stabilized Mixture-of-Experts for Multimodal Continual Instruction Tuning](https://mlsanity.com/paper/2602.01990/) (2026)
- [Using Molecular Embeddings in QSAR Modeling: Does it Make a Difference?](https://mlsanity.com/paper/2104.02604/) (2021)
- [Prism: A Plug-in Reproducible Infrastructure for Scalable Multimodal Continual Instruction Tuning](https://mlsanity.com/paper/2605.26110/) (2026)
- [CRAM: Centroid-Routing and Adaptive MoE for Multimodal Continual Instruction Tuning](https://mlsanity.com/paper/2606.02502/) (2026)
- [ProtoAda: Prototype-Guided Adaptive Adapter Expansion and Geometric Consolidation for Multimodal Continual Instruction Tuning](https://mlsanity.com/paper/2606.02576/) (2026)
- [LatentFlow: Visual Analytics for Latent Space Analysis in Molecular Graph Neural Networks](https://mlsanity.com/paper/2607.21941/) (2026)

## Abstract (arXiv)

In the modern drug discovery process, medicinal chemists deal with the complexity of analysis of large ensembles of candidate molecules. Computational tools, such as dimensionality reduction (DR) and classification, are commonly used to efficiently process the multidimensional space of features. These underlying calculations often hinder interpretability of results and prevent experts from assessing the impact of individual molecular features on the resulting representations. To provide a solution for scrutinizing such complex data, we introduce ChemVA, an interactive application for the visual exploration of large molecular ensembles and their features. Our tool consists of multiple coordinated views: Hexagonal view, Detail view, 3D view, Table view, and a newly proposed Difference view designed for the comparison of DR projections. These views display DR projections combined with biological activity, selected molecular features, and confidence scores for each of these projections. This conjunction of views allows the user to drill down through the dataset and to efficiently select candidate compounds. Our approach was evaluated on two case studies of finding structurally similar ligands with similar binding affinity to a target protein, as well as on an external qualitative evaluation. The results suggest that our system allows effective visual inspection and comparison of different high-dimensional molecular representations. Furthermore, ChemVA assists in the identification of candidate compounds while providing information on the certainty behind different molecular representations.