Publications

@inproceedings{khan2025multicancer,
  title = {Multi-cancer risk prediction using transformers trained on large-scale longitudinal {EHR} data},
  author = {Khan, Asif and Ritter, Daniel and Zheng, Chunlei and Forster, Duncan T. and Harsh, Moshir and Gazizov, Artem and Marks, Debora S. and Fillmore, Nathanael R. and Sander, Chris},
  booktitle = {NeurIPS 2025 Workshop on Learning from Time Series for Health},
  year = {2025},
  note = {Joint first authors: Asif Khan, Daniel Ritter},
  url = {https://openreview.net/forum?id=j24ly5CLZd}
}

@inproceedings{khan2025position,
  title = {Position: {AI}-driven risk stratification is essential for affordable early detection of cancer},
  author = {Khan, Asif and Forster, Duncan T. and Harsh, Moshir and Ritter, Daniel and Zheng, Chunlei and Orenbuch, Rose and Kuziez, Abdullah and Marks, Debora S. and Fillmore, Nathanael R. and Sander, Chris},
  booktitle = {GenAI for Health: Potential, Trust, and Policy Compliance (NeurIPS 2025 Workshop)},
  year = {2025},
  url = {https://openreview.net/forum?id=7PJYSePp2L}
}

@article{luque2025identifying,
  title = {Identifying tissue states by spatial protein patterns related to chemotherapy response in triple-negative breast cancer},
  author = {Luque, Luciana M. and Khan, Asif and Torrisi, Giovanni and Green, Tess D. and Hardman, David and Owczarek, Claudia and Phillips, Tom A. and Marks, Debora S. and Parsons, Maddy and Sander, Chris and Schumacher, Linus J.},
  journal = {bioRxiv},
  year = {2025},
  month = oct,
  doi = {10.1101/2025.10.06.680783},
  url = {https://www.biorxiv.org/content/10.1101/2025.10.06.680783v1}
}

@article{sun2025strategic,
  title = {Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence},
  author = {Sun, Yingying and Liu, Zhiwei and Sun, Rui and Qian, Liujia and Payne, Samuel H. and Bittremieux, Wout and Ralser, Markus and Li, Chen and Chen, Yi and Dong, Zhen and Perez-Riverol, Yasset and Khan, Asif and Sander, Chris and Aebersold, Ruedi and Vizcaíno, Juan Antonio and Krieger, Jonathan R. and Yao, Jianhua and Wen, Han and Zhang, Linfeng and Zhu, Yunping and Xuan, Yue and Sun, Benjamin Boyang and Qiao, Liang and Hermjakob, Henning and Tang, Haixu and Gao, Huanhuan and Deng, Yamin and Zhong, Qing and Chang, Cheng and Bandeira, Nuno and Li, Ming and Sun, Siqi and Yang, Yuedong and Omenn, Gilbert S. and Zhang, Yue and Xu, Ping and Fu, Yan and Liu, Xiaowen and Overall, Christopher M. and Wang, Yu and Deutsch, Eric W. and Chen, Luonan and Cox, Jürgen and Demichev, Vadim and He, Fuchu and Huang, Jiaxing and Jin, Huilin and Liu, Chao and Li, Nan and Luan, Zhongzhi and Song, Jiangning and Yu, Kaicheng and Wan, Wanggen and Wang, Tai and Zhang, Kang and Zhang, Le and Bell, Peter A. and Mann, Matthias and Zhang, Bing and Guo, Tiannan},
  year = {2025},
  journal = {Nature Methods},
  note = {Perspective. In press},
  archiveprefix = {arXiv},
  eprint = {2502.15867},
  doi = {10.48550/arXiv.2502.15867},
  url = {https://arxiv.org/abs/2502.15867}
}

@article{khan2025pancreatic,
  title = {Pancreatic cancer risk prediction using deep sequential modeling of longitudinal diagnostic and medication records},
  author = {Khan, Asif and Zheng, Chunlei and Ritter, Daniel and Marks, Debora S. and Do, Nhan V. and Fillmore, Nathanael R. and Sander, Chris},
  journal = {Cell Reports Medicine},
  year = {2025},
  doi = {10.1016/j.xcrm.2025.102359},
  note = {Joint first authors: Asif Khan, Chunlei Zheng, and Daniel Ritter},
  url = {https://www.sciencedirect.com/science/article/pii/S266637912500432X}
}

@inproceedings{khan2024batch,
  title = {Batch-effect invariant graph neural networks for predicting chemotherapy response in triple-negative breast cancer patients},
  author = {Khan, Asif and Torrisi, Giovanni and Luque, Luciana M. and Green, Tess D. and Owczarek, Claudia and Marks, Debora S. and Parsons, Maddy and Sander, Chris and Schumacher, Linus J.},
  booktitle = {ICML 2024 Workshop on Machine Learning for Life and Material Sciences},
  year = {2024},
  url = {https://openreview.net/forum?id=QBGP19dNkQ}
}

@phdthesis{khan2023geometry,
  title = {Geometry for deep representation learning},
  author = {Khan, Mohammad Asif},
  school = {University of Edinburgh},
  year = {2023},
  doi = {10.7488/era/3979}
}

@misc{khan2023contrastive,
  title = {Contrastive learning for non-local graphs with multi-resolution structural views},
  author = {Khan, Asif and Storkey, Amos},
  year = {2023},
  archiveprefix = {arXiv},
  eprint = {2308.10077},
  url = {https://arxiv.org/abs/2308.10077}
}

@inproceedings{khan2023adversarial,
  title = {Adversarial robustness of {VAEs} through the lens of local geometry},
  author = {Khan, Asif and Storkey, Amos},
  booktitle = {Proceedings of the 26th International Conference on Artificial Intelligence and Statistics},
  year = {2023},
  publisher = {PMLR},
  doi = {10.48550/arXiv.2208.03923}
}

@article{khan2023antibody,
  title = {Toward real-world automated antibody design with combinatorial Bayesian optimization},
  author = {Khan, Asif and Cowen-Rivers, Alexander I. and Grosnit, Antoine and Deik, Derrick-Goh-Xin and Robert, Philippe A. and Greiff, Victor and Smorodina, Eva and Rawat, Puneet and Akbar, Rahmad and Dreczkowski, Kamil and Tutunov, Rasul and Bou-Ammar, Dany and Wang, Jun and Storkey, Amos and Bou-Ammar, Haitham},
  journal = {Cell Reports Methods},
  year = {2023},
  doi = {10.1016/j.crmeth.2022.100374}
}

@inproceedings{cowen2022structured,
  title = {Structured {Q}-learning for antibody design},
  author = {Cowen-Rivers, Alexander I. and Gorinski, Philip J. and Sootla, Aivar and Khan, Asif and Furui, Long and Wang, Jun and Peters, Jan and Bou-Ammar, Haitham},
  booktitle = {NeurIPS 2022 Workshop on Reinforcement Learning for Real Life},
  year = {2022},
  url = {https://arxiv.org/abs/2209.04698}
}

@inproceedings{khan2022halo,
  title = {{HALO}: Hamiltonian latent operators for content and motion disentanglement in image sequences},
  author = {Khan, Asif and Storkey, Amos},
  booktitle = {Advances in Neural Information Processing Systems},
  year = {2022},
  url = {https://proceedings.neurips.cc/paper/2022/file/2f8ee6a3d766b426d2618e555b5aeb39-Paper-Conference.pdf}
}

@misc{khan2020unsupervised,
  title = {Unsupervised cross-domain speech-to-speech conversion with time-frequency consistency},
  author = {Khan, Mohammad Asif and Cardinaux, Fabien and Uhlich, Stefan and Ferras, Marc and Fischer, Asja},
  year = {2020},
  archiveprefix = {arXiv},
  eprint = {2005.07810},
  url = {https://arxiv.org/abs/2005.07810}
}

@incollection{khan2019soccer,
  title = {Utilizing temporal information in deep convolutional networks for efficient soccer ball detection and tracking},
  author = {Khan, Mohammad Asif and Kukleva, Anna and Farazi, Hafez and Behnke, Sven},
  booktitle = {RoboCup 2019: Robot World Cup XXIII},
  publisher = {Springer},
  year = {2019},
  doi = {10.1007/978-3-030-35699-6_9},
  note = {Equal contribution: Asif Khan and Anna Kukleva}
}

@incollection{khan2019literalkg,
  title = {Incorporating literals into knowledge graph embeddings},
  author = {Khan, Mohammad Asif and Kristiadi, Agustinus and Lukovnikov, Denis and Lehmann, Jens and Fischer, Asja},
  booktitle = {The Semantic Web -- {ISWC} 2019},
  publisher = {Springer},
  year = {2019},
  doi = {10.1007/978-3-030-30793-6_20},
  note = {Equal contribution: Asif Khan and Agustinus Kristiadi}
}

@article{agarwal2018learning,
  title = {Learning-based predictive dynamic spectrum access framework: a practical perspective for enhanced {QoE} of secondary users},
  author = {Agarwal, Anirudh and Gangopadhyay, Ranjan and Dubey, Shivangi and Debnath, Soumitra and Khan, Mohammad Asif},
  journal = {IET Communications},
  year = {2018},
  doi = {10.1049/iet-com.2017.1370}
}

@article{kulmanov2017deepgo,
  title = {{DeepGO}: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier},
  author = {Kulmanov, Maxat and Khan, Mohammed Asif and Hoehndorf, Robert},
  journal = {Bioinformatics},
  year = {2017},
  doi = {10.1093/bioinformatics/btx624}
}

@article{alshahrani2017neurosymbolic,
  title = {Neuro-symbolic representation learning on biological knowledge graphs},
  author = {Alshahrani, Mona and Khan, Mohammad Asif and Maddouri, Olfa and Kinjo, Akira R. and Queralt-Rosinach, N{\'u}ria and Hoehndorf, Robert},
  journal = {Bioinformatics},
  year = {2017},
  doi = {10.1093/bioinformatics/btx275}
}

@article{tanveer2016robust,
  title = {Robust energy-based least squares twin support vector machines},
  author = {Tanveer, Mohammad and Khan, Mohammad Asif and Ho, Shen-Shyang},
  journal = {Applied Intelligence},
  year = {2016},
  url = {https://link.springer.com/article/10.1007/s10489-015-0751-1}
}

@inproceedings{agarwal2016learning,
  title = {Learning based primary user activity prediction in cognitive radio networks for efficient dynamic spectrum access},
  author = {Agarwal, Anirudh and Dubey, Shivangi and Khan, Mohammad Asif and Gangopadhyay, Ranjan and Debnath, Soumitra},
  booktitle = {2016 International Conference on Signal Processing and Communications ({SPCOM})},
  year = {2016},
  url = {https://ieeexplore.ieee.org/document/7746632}
}