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@inproceedings{DBLP:conf/mlcb/AlzaidDM23, author = {Ethar Alzaid and Muhammad Dawood and Fayyaz Minhas}, editor = {David A. Knowles and Sara Mostafavi}, title = {A Transductive Approach to Survival Ranking for Cancer Risk Stratification}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {101--109}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/alzaid24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/AlzaidDM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/BajwaRKSI23, author = {Ayesha Bajwa and Ruchir Rastogi and Pooja Kathail and Richard W. Shuai and Nilah Ioannidis}, editor = {David A. Knowles and Sara Mostafavi}, title = {Characterizing uncertainty in predictions of genomic sequence-to-activity models}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {279--297}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/bajwa24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/BajwaRKSI23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/HongDH23, author = {Juneki Hong and Dezhong Deng and David A. Hendrix}, editor = {David A. Knowles and Sara Mostafavi}, title = {Improving transformer secondary structure predictions with secondary structure "fixing" task}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {267--278}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/hong24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/HongDH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/IsaevK23, author = {Keren Isaev and David A. Knowles}, editor = {David A. Knowles and Sara Mostafavi}, title = {Investigating {RNA} splicing as a source of cellular diversity using a binomial mixture model}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {163--175}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/isaev24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/IsaevK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/KenariAL23, author = {Neda Shokraneh Kenari and Megan Andrews and Max W. Libbrecht}, editor = {David A. Knowles and Sara Mostafavi}, title = {Model-based imputation enables improved resolution for identifying differential chromatin contacts in single-cell Hi-C data}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {176--193}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/shokraneh-kenari24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/KenariAL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/LiuK23, author = {Renming Liu and Arjun Krishnan}, editor = {David A. Knowles and Sara Mostafavi}, title = {Open Biomedical Network Benchmark: {A} Python Toolkit for Benchmarking Datasets with Biomedical Networks}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {23--59}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/liu24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/LiuK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/MajhaS023, author = {Arushi G. K. Majha and Ian Stott and Andreas Bender}, editor = {David A. Knowles and Sara Mostafavi}, title = {On Modelability and Generalizability: Are Machine Learning Models for Drug Synergy Exploiting Artefacts and Biases in Available Data?}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {123--134}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/majha24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/MajhaS023.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/MartensY23, author = {Kaspar M{\"{a}}rtens and Christopher Yau}, editor = {David A. Knowles and Sara Mostafavi}, title = {Disentangling shared and private latent factors in multimodal Variational Autoencoders}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {60--75}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/martens24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/MartensY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/NathansenKRNB23, author = {Andrea Nathansen and Kevin Klein and Bernhard Y. Renard and Melania Nowicka and Jakub M. Bartoszewicz}, editor = {David A. Knowles and Sara Mostafavi}, title = {Evaluating Tuning Strategies for Sequence Generation with Protein Language Models}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {76--89}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/nathansen24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/NathansenKRNB23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/RobsonI23, author = {Eyes S. Robson and Nilah Ioannidis}, editor = {David A. Knowles and Sara Mostafavi}, title = {GUANinE v1.0: Benchmark Datasets for Genomic {AI} Sequence-to-Function Models}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {250--266}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/robson24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/RobsonI23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/SimsC23, author = {Zachary S. Sims and Young Hwan Chang}, editor = {David A. Knowles and Sara Mostafavi}, title = {A Masked Image Modeling Approach to CyCIF Panel Reduction and Marker Imputation}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {1--9}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/sims24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/SimsC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/SzatkownikFCYJ23, author = {Antoine Szatkownik and Cyril Furtlehner and Guillaume Charpiat and Burak Yelmen and Flora Jay}, editor = {David A. Knowles and Sara Mostafavi}, title = {Towards creating longer genetic sequences with GANs: Generation in principal component space}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {110--122}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/szatkownik24a.html}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/SzatkownikFCYJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/TuHWKRL23, author = {Xinming Tu and Jan{-}Christian H{\"{u}}tter and Zitong Jerry Wang and Takamasa Kudo and Aviv Regev and Romain Lopez}, editor = {David A. Knowles and Sara Mostafavi}, title = {A Supervised Contrastive Framework for Learning Disentangled Representations of Cellular Perturbation Data}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {90--100}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/tu24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/TuHWKRL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/VisaniGPN23, author = {Gian Marco Visani and William Galvin and Michael N. Pun and Armita Nourmohammad}, editor = {David A. Knowles and Sara Mostafavi}, title = {H-Packer: Holographic Rotationally Equivariant Convolutional Neural Network for Protein Side-Chain Packing}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {230--249}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/visani24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/VisaniGPN23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/WuBLBLH23, author = {You Wu and Omid Bazgir and Yongju Lee and Tommaso Biancalani and James Lu and Ehsan Hajiramezanali}, editor = {David A. Knowles and Sara Mostafavi}, title = {Multitask-Guided Self-Supervised Tabular Learning for Patient-Specific Survival Prediction}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {10--22}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/wu24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/WuBLBLH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/WuYDBXESC023, author = {Kevin E. Wu and Kathryn Yost and Bence Daniel and Julia A. Belk and Yu Xia and Takeshi Egawa and Ansuman Satpathy and Howard Chang and James Zou}, editor = {David A. Knowles and Sara Mostafavi}, title = {{TCR-BERT:} learning the grammar of T-cell receptors for flexible antigen-binding analyses}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {194--229}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/wu24b.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/WuYDBXESC023.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/YuWMT023, author = {Jennifer Yu and Zhenqin Wu and Aaron T. Mayer and Alexandro Trevino and James Zou}, editor = {David A. Knowles and Sara Mostafavi}, title = {A Multi-Granularity Approach to Similarity Search in Multiplexed Immunofluorescence Images}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {135--147}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/yu24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/YuWMT023.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/mlcb/ZhangLBDC23, author = {Chenwei Zhang and Jordan Lovrod and Boyan Beronov and Khanh Dao Duc and Anne Condon}, editor = {David A. Knowles and Sara Mostafavi}, title = {ViDa: Visualizing {DNA} hybridization trajectories with biophysics-informed deep graph embeddings}, booktitle = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, pages = {148--162}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/zhang24a.html}, timestamp = {Mon, 13 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/ZhangLBDC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@proceedings{DBLP:conf/mlcb/2023, editor = {David A. Knowles and Sara Mostafavi}, title = {Machine Learning in Computational Biology, November 30 - December 1, 2023, Seattle, WA, {USA}}, series = {Proceedings of Machine Learning Research}, volume = {240}, publisher = {{PMLR}}, year = {2023}, url = {https://proceedings.mlr.press/v240/}, timestamp = {Fri, 10 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/mlcb/2023.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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