Publications

Ravandi, C. B., Mowrey, W. R., Chatterjee, A., Khanshan, F., Haddadi, P., Mobarec, J. C., Lambden, S., Eliassi-Rad, T., Ricchiuto, P., & Risa, G. (2026). Clinical trial and ontology-derived positive and negative benchmark datasets for drug repurposing across rare diseases. bioRxiv , 2026.06.15.732135.

Chatterjee, A., Ikica, B., Ravandi, B., & Palowitch, J. (2025). Transfer learning for temporal link prediction. 2025 International Joint Conference on Neural Networks (IJCNN) , 1–8.

Chatterjee, A., Ravandi, B., Haddadi, P., Philip, N. H., Abdelmessih, M., Mowrey, W. R., Ricchiuto, P., Liang, Y., Ding, W., Mobarec, J. C., & Eliassi-Rad, T. (2025). Topology-driven negative sampling enhances generalizability in protein–protein interaction prediction. Bioinformatics, 41 (5), btaf148.

Ravandi, B., Mowrey, W. R., Chatterjee, A., Haddadi, P., Abdelmessih, M., Ding, W., Lambden, S., Ughetto, M., Barrett, I., Diethe, T., Del Angel, G., Eliassi-Rad, T., & Ricchiuto, P. (2024). Representation learning of human disease mechanisms for a foundation model in rare and common diseases. bioRxiv , 2024.11.19.624381.

Shafi, Z., Chatterjee, A., & Eliassi-Rad, T. (2024). Generating human understandable explanations for node embeddings. arXiv , 2406.07642.

Sunil, S., Rajeev, R. S., Chatterjee, A., Pilitsis, J., Mukherjee, A., & Paluh, J. L. (2024). SIENNA: Lightweight generalizable machine learning platform for brain tumor diagnostics. medRxiv , 2024.04.03.24305210.

Chatterjee, A., Walters, R., Shafi, Z., Ahmed, O. S., Sebek, M., Gysi, D., Yu, R., Eliassi-Rad, T., Barabási, A.-L., & Menichetti, G. (2023). Improving the generalizability of protein-ligand binding predictions with AI-Bind. Nature Communications, 14 (1), 1989.

Chatterjee, A., Walters, R., Menichetti, G., & Eliassi-Rad, T. (2023). Inductive link prediction in static and temporal graphs for isolated nodes. Temporal Graph Learning Workshop @ NeurIPS 2023 .

Chatterjee, A., Walters, R., Menichetti, G., & Eliassi-Rad, T. (2023). Disentangling node attributes from graph topology for improved generalizability in link prediction. arXiv , 2307.08877.

Shafi, Z., Miller, B. A., Chatterjee, A., Eliassi-Rad, T., & Caceres, R. S. (2023). GRASP: Accelerating shortest path attacks via graph attention. arXiv , 2310.07980.

Pacza, T., Martins, M. L., Rockaya, M., Müller, K., Chatterjee, A., Barabási, A.-L., & Baranyi, J. (2022). MilkyBase, a database of human milk composition as a function of maternal-, infant- and measurement conditions. Scientific Data, 9 , 557.