Publications
Some of our recent publications are included below. You can find a more comprehensive, up to date list at Google Scholar.
SynCoGen: synthesizable 3D molecule generation via joint reaction and coordinate modeling
Rekesh, A., Cretu, M., Shevchuk, D., Liò, P., Batey, R.A., Tyers, M., Koziarski, M., Liu, C.H.
ICLR. 2026.
Link to paper
Rekesh, A., Cretu, M., Shevchuk, D., Liò, P., Batey, R.A., Tyers, M., Koziarski, M., Liu, C.H.
ICLR. 2026.
Link to paper
Scalable and cost-efficient de novo template-based molecular generation
Gaiński, P., Boussif, O., Shevchuk, D., Rekesh, A., Parviz, A., Tyers, M., Batey, R.A., Koziarski, M.
NeurIPS. 2025.
Link to paper
Gaiński, P., Boussif, O., Shevchuk, D., Rekesh, A., Parviz, A., Tyers, M., Batey, R.A., Koziarski, M.
NeurIPS. 2025.
Link to paper
Deep-learning-based virtual screening of antibacterial compounds
Scalia, G., Rutherford, S. T., Lu, Z., Buchholz, K. R., Skelton, N., Chuang, K., ... & Biancalani, T.
Nature Biotechnology. 2025.
Link to paper
Scalia, G., Rutherford, S. T., Lu, Z., Buchholz, K. R., Skelton, N., Chuang, K., ... & Biancalani, T.
Nature Biotechnology. 2025.
Link to paper
Learning decision trees as amortized structure inference
Mahfoud, M., Boukachab, G., Koziarski, M., Hernandez-Garcia, A., Bauer, S., Bengio, Y., Malkin, N.
ICLR Frontiers in Probabilistic Inference Workshop. 2025.
Link to paper
Mahfoud, M., Boukachab, G., Koziarski, M., Hernandez-Garcia, A., Bauer, S., Bengio, Y., Malkin, N.
ICLR Frontiers in Probabilistic Inference Workshop. 2025.
Link to paper
Diverse and feasible retrosynthesis using GFlowNets
Gaiński, P., Koziarski, M., Maziarz, K., Segler, M., Tabor, J. and Śmieja, M.
Information Sciences. 2025.
Link to paper
Gaiński, P., Koziarski, M., Maziarz, K., Segler, M., Tabor, J. and Śmieja, M.
Information Sciences. 2025.
Link to paper
Action abstractions for amortized sampling
Boussif, O., Ezzine, L.N., Viviano, J.D., Koziarski, M., Jain, M., Malkin, N., Bengio, E., Assouel, R., Bengio, Y.
ICLR. 2025.
Link to paper
Boussif, O., Ezzine, L.N., Viviano, J.D., Koziarski, M., Jain, M., Malkin, N., Bengio, E., Assouel, R., Bengio, Y.
ICLR. 2025.
Link to paper
RGFN: synthesizable molecular generation using GFlowNets
Koziarski, M., Rekesh, A., Shevchuk, D., van der Sloot, A., Gaiński, P., Bengio, Y., Liu, C.H., Tyers, M. and Batey, R.A.
NeurIPS. 2024.
Link to paper
Koziarski, M., Rekesh, A., Shevchuk, D., van der Sloot, A., Gaiński, P., Bengio, Y., Liu, C.H., Tyers, M. and Batey, R.A.
NeurIPS. 2024.
Link to paper
Cell morphology-guided small molecule generation with GFlowNets
Lu, S.Z., Lu, Z., Hajiramezanali, E., Biancalani, T., Bengio, Y., Scalia, G. and Koziarski, M.
ICML AI for Science Workshop. 2024.
Link to paper
Lu, S.Z., Lu, Z., Hajiramezanali, E., Biancalani, T., Bengio, Y., Scalia, G. and Koziarski, M.
ICML AI for Science Workshop. 2024.
Link to paper
Towards equilibrium molecular conformation generation with GFlowNets
Volokhova, A., Koziarski, M., Hernández-García, A., Liu, C.H., Miret, S., Lemos, P., Thiede, L., Yan, Z., Aspuru-Guzik, A. and Bengio, Y.
Digital Discovery. 2024.
Link to paper
Volokhova, A., Koziarski, M., Hernández-García, A., Liu, C.H., Miret, S., Lemos, P., Thiede, L., Yan, Z., Aspuru-Guzik, A. and Bengio, Y.
Digital Discovery. 2024.
Link to paper
Towards foundational models for molecular learning on large-scale multi-task datasets
Beaini, D., Huang, S., Cunha, J. A., Li, Z., Moisescu-Pareja, G., Dymov, O., ... & Masters, D.
ICLR. 2024.
Link to paper
Beaini, D., Huang, S., Cunha, J. A., Li, Z., Moisescu-Pareja, G., Dymov, O., ... & Masters, D.
ICLR. 2024.
Link to paper
ChiENN: embracing molecular chirality with graph neural networks
Gaiński, P., Koziarski, M., Tabor, J. and Śmieja, M.
ECML. 2023.
Link to paper
Gaiński, P., Koziarski, M., Tabor, J. and Śmieja, M.
ECML. 2023.
Link to paper