Research
scDataset
ICML 2026A PyTorch data loader for datasets too large for memory. It reads blocks of contiguous samples and fetches several minibatches at once, so training gets shuffled data without one random read per sample.
Hierarchical cross-entropy loss
Nature Computational Science 6, 243–249When labels form a hierarchy, standard cross-entropy treats a prediction that is more specific than the label as simply wrong. This loss scores each class together with its subclasses, so any prediction inside the label's subtree counts.
Compositional sparsity
ICML 2025, Position Paper TrackDeep networks learn functions of many variables without the exponential cost the curse of dimensionality predicts. We argue the reason is that the functions worth learning are built from pieces that each depend on a few inputs.
Monotonicity of centrality measures
Social Network Analysis and Mining 14, 183When you add an edge to an undirected network, one of its endpoints can lose rank. We prove that the two can never both lose it, for closeness, betweenness and distance-decay centralities.
Provenance of LLM-generated code
Journal of Systems and Software 245, 113147Code models sometimes reproduce snippets from their training data without saying where they come from. We find the source by shortlisting candidates with vector search and re-ranking them with code fingerprints.
Papers
- 2026Efficient and Scalable Provenance Tracking for LLM-Generated Code SnippetsA. Gurioli, D. D'Ascenzo, F. Pennino, M. Gabbrielli, S. ZacchiroliJournal of Systems and Software 245, 113147DOIarXiv
@article{Gurioli2027, title = {Efficient and Scalable Provenance Tracking for {LLM}-Generated Code Snippets}, author = {Gurioli, Andrea and D'Ascenzo, Davide and Pennino, Federico and Gabbrielli, Maurizio and Zacchiroli, Stefano}, journal = {Journal of Systems and Software}, volume = {245}, pages = {113147}, year = {2027}, month = mar, publisher = {Elsevier}, issn = {0164-1212}, doi = {10.1016/j.jss.2026.113147}, url = {https://doi.org/10.1016/j.jss.2026.113147} } - 2026Score Distributions, Not Cells: Evaluating Single-Cell Perturbations Under Class OverlapY. Marrakchi*, D. D'Ascenzo*, S. Cultrera di MontesanoarXiv preprintarXiv
@misc{marrakchi2026scoredistributionscellsevaluating, title={Score Distributions, Not Cells: Evaluating Single-Cell Perturbations Under Class Overlap}, author={Youssef Marrakchi and Davide D'Ascenzo and Sebastiano Cultrera di Montesano}, year={2026}, eprint={2607.04595}, archivePrefix={arXiv}, primaryClass={cs.LG}, url={https://arxiv.org/abs/2607.04595}, } - 2026scDataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell OmicsD. D'Ascenzo, S. Cultrera di MontesanoICML 2026PMLRarXivCodeDocs
@InProceedings{pmlr-v306-d-ascenzo26a, title = {sc{D}ataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell Omics}, author = {D'Ascenzo, Davide and Cultrera di Montesano, Sebastiano}, booktitle = {Proceedings of the 43rd International Conference on Machine Learning}, pages = {22246--22262}, year = {2026}, editor = {Zhang, Tong and Dudik, Miroslav and Jaggi, Martin and Agarwal, Alekh and Li, Sharon and Schuurmans, Dale and Zhu, Jerry and Berkenkamp, Felix and Dong, Hanze and Bietti, Alberto}, volume = {306}, series = {Proceedings of Machine Learning Research}, month = {06--11 Jul}, publisher = {PMLR}, pdf = {https://raw.githubusercontent.com/mlresearch/v306/main/assets/d-ascenzo26a/d-ascenzo26a.pdf}, url = {https://proceedings.mlr.press/v306/d-ascenzo26a.html}, } - 2026When Labels Have Structure: Improving Image Classification with Hierarchy-Aware Cross-EntropyA. Chan, D. D'Ascenzo, S. Cultrera di MontesanoarXiv preprintarXiv
@misc{chan2026labelsstructureimprovingimage, title={When Labels Have Structure: Improving Image Classification with Hierarchy-Aware Cross-Entropy}, author={April Chan and Davide D'Ascenzo and Sebastiano Cultrera di Montesano}, year={2026}, eprint={2605.06274}, archivePrefix={arXiv}, primaryClass={cs.LG}, url={https://arxiv.org/abs/2605.06274}, } - 2026Improving atlas-scale single-cell annotation models with hierarchical cross-entropy lossS. Cultrera di Montesano*, D. D'Ascenzo*, S. Raghavan, A. P. Amini, P. S. Winter, L. CrawfordNature Computational Science 6, 243–249DOIbioRxiv
@Article{CultreradiMontesano2026, author="Cultrera di Montesano, Sebastiano and D'Ascenzo, Davide and Raghavan, Srivatsan and Amini, Ava P. and Winter, Peter S. and Crawford, Lorin", title="Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss", journal="Nature Computational Science", year="2026", month="Mar", day="01", volume="6", number="3", pages="243--249", issn="2662-8457", doi="10.1038/s43588-025-00945-z", url="https://doi.org/10.1038/s43588-025-00945-z" } - 2025Theory and Tools for Structure-Aware Machine Learning on Biological DataD. D'AscenzoPhD thesis, Politecnico di Torino and Università degli Studi di MilanoPDF
@phdthesis{DAscenzo2025, title = {Theory and Tools for Structure-Aware Machine Learning on Biological Data}, author = {D'Ascenzo, Davide}, school = {Politecnico di Torino and Universit{\`a} degli Studi di Milano}, type = {{PhD} thesis, Doctoral Program in Artificial Intelligence}, year = {2025}, url = {https://tesidottorato.depositolegale.it/bitstream/20.500.14242/361991/1/conv_phd_thesis.pdf} } - 2025Position: A Theory of Deep Learning Must Include Compositional SparsityD. A. Danhofer*, D. D'Ascenzo*, R. Dubach*, T. A. Poggio*ICML 2025, Position Paper TrackPMLRarXiv
@InProceedings{pmlr-v267-danhofer25a, title = {Position: A Theory of Deep Learning Must Include Compositional Sparsity}, author = {Danhofer, David A. and D'Ascenzo, Davide and Dubach, Rafael and Poggio, Tomaso A}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, pages = {81199--81210}, year = {2025}, editor = {Singh, Aarti and Fazel, Maryam and Hsu, Daniel and Lacoste-Julien, Simon and Berkenkamp, Felix and Maharaj, Tegan and Wagstaff, Kiri and Zhu, Jerry}, volume = {267}, series = {Proceedings of Machine Learning Research}, month = {13--19 Jul}, publisher = {PMLR}, pdf = {https://raw.githubusercontent.com/mlresearch/v267/main/assets/danhofer25a/danhofer25a.pdf}, url = {https://proceedings.mlr.press/v267/danhofer25a.html}, } - 2024Score and rank semi-monotonicity for closeness, betweenness, and distance-decay centralitiesP. Boldi*, D. D'Ascenzo*, F. Furia*, S. Vigna*Social Network Analysis and Mining 14, 183DOI
@Article{Boldi2024, author="Boldi, Paolo and D'Ascenzo, Davide and Furia, Flavio and Vigna, Sebastiano", title="Score and rank semi-monotonicity for closeness, betweenness, and distance--decay centralities", journal="Social Network Analysis and Mining", year="2024", month="Sep", day="06", volume="14", number="1", pages="183", issn="1869-5469", doi="10.1007/s13278-024-01285-y", url="https://doi.org/10.1007/s13278-024-01285-y" } - 2024Score and Rank Semi-monotonicity for Closeness, Betweenness and Harmonic CentralityP. Boldi*, D. D'Ascenzo*, F. Furia*, S. Vigna*Complex Networks & Their Applications XIIDOI
@InProceedings{10.1007/978-3-031-53472-0_9, author="Boldi, Paolo and D'Ascenzo, Davide and Furia, Flavio and Vigna, Sebastiano", editor="Cherifi, Hocine and Rocha, Luis M. and Cherifi, Chantal and Donduran, Murat", title="Score and Rank Semi-monotonicity for Closeness, Betweenness and Harmonic Centrality", booktitle="Complex Networks {\&} Their Applications XII", year="2024", publisher="Springer Nature Switzerland", address="Cham", pages="102--113", isbn="978-3-031-53472-0" }
Talks
- 2026scDataset: Scalable data loading for deep learning on large-scale single-cell omicsEWSC Symposium 2026, Eric and Wendy Schmidt Center, Broad Institute
- 2025Infrastructure and modeling challenges in single-cell omicsEric and Wendy Schmidt Center, Broad InstituteVideo
- 2025Research in the era of LLMsCenter for Complexity & Biosystems, University of Milan
- 2025scDataset: Scalable data loading for deep learning on large-scale single-cell omicsscverse conference 2025, Tahoe Therapeutics
- 2022Hands-on Graph Neural Networks with PyTorchCenter for Complexity & Biosystems, University of Milan
