I’m interested in developing machine learning techniques that are inspired by questions in biology and medicine. Here are some papers that I have written. An asterisk (*) means equal contribution.
Featured papers:
- Exploring Patterns Enriched in a Dataset with Contrastive Principal Component Analysis [PDF, Code]
Abubakar Abid*, Martin Zhang*, Vivek Bagaria, James Zou.
Nature Communications, 2018
- Model-Based Estimation of Respiratory Parameters from Capnography, with Application to Diagnosing Obstructive Lung Disease [PDF]
Abubakar Abid, Rebecca Mieloszyk, George Verghese, Baruch Krauss, Thomas Heldt.
IEEE Transactions on Biomedical Engineering, 2017
- Interpretation of Neural Networks is Fragile [PDF, Code]
Abubakar Abid*, Amirata Ghorbani*, James Zou.
AAAI 2019
Other papers and presentations (17):
Constrained Unsupervised Learning
- Concrete Autoencoders for Differentiable Feature Selection and Reconstruction [PDF, Code]
Abubakar Abid*, Muhammad Fatih Balin*, James Zou.
International Conference on Machine Learning (ICML), 2019 - Contrastive Variational Autoencoder Enhances Salient Features [PDF, Code]
Abubakar Abid, James Zou.
ArXiv Preprint, 2019
Machine Learning with Time Series
- Learning a Warping Distance from Unlabeled Time Series Using Sequence Autoencoders [PDF]
Abubakar Abid, James Zou.
Neural Information Processing Systems (NIPS), 2018 - Contrastive Multivariate Singular Spectrum Analysis [PDF, Code]
Abdi-Hakin Dirie, Abubakar Abid, James Zou.
NIPS Spatiotemporal Workshop, 2018
Deep Learning and Genomics
- A Primer of Deep Learning in Genomics
James Zou, Mikael Huss, Abubakar Abid, Pejman Mohammadi, Ali Torkamani, Amalio Telenti.
Nature Genetics 2018 - Mutation-Convolution-Max Layers Enhance Deep Learning of DNA Motifs [PDF]
Abubakar Abid*, Amirata Ghorbani*, James Zou.
NIPS Workshop on Computational Biology, 2017 [Spotlight Talk]
Linear Regression with Shuffled Labels
- Stochastic Expectation-Maximization Approach to Shuffled Linear Regression [PDF, Slides, Code]
Abubakar Abid, James Zou.
Allerton Conference, 2018 - Linear Regression with Shuffled Labels [PDF]
Abubakar Abid, Ada Poon, James Zou.
Arxiv Preprint, 2017 - The Least-Squares Estimator for Shuffled Linear Regression is Intractable or Inconsistent (or Both) [PDF]
Abubakar Abid, James Zou.
Technical Note, 2018
Mathematical Modeling of Capnography
- An Enhanced Mechanistic Model for Capnography, with Application to CHF-COPD Discrimination [PDF]
Ekin Karasan, Abubakar Abid, Rebecca Mieloszyk, Baruch Krauss, Thomas Heldt, George Verghese.
IEEE Engineering in Medicine and Biology Conference, 2018 - Clinical Applications of Respiratory Modeling Via Quantitative Capnography
Thomas Heldt, Rebecca Mieloszyk, Abubakar Abid, George Verghese, Baruch Krauss.
IEEE Engineering in Medicine and Biology Conference, 2017 - Model-Based Estimation of Pulmonary Compliance and Resistance Parameters from Time-Based Capnography [PDF]
Abubakar Abid, Rebecca Mieloszyk, George Verghese, Baruch Krauss.
IEEE Engineering in Medicine and Biology Conference, 2015
Resident Medical Devices
- 3D Printed Gastric Resident Electronics
Yong Lin Kong, Xingyu Zou, Caitlin A. McCandler, Shen Ning, Ameya R. Kirtane, Jianlin Zhou, Abubakar Abid, et al.
Submitted to Advanced Materials Technologies in 2018 - Wireless Power Transfer to Millimeter-Sized Gastrointestinal Electronics Validated in a Swine Model [PDF]
Abubakar Abid, Jonathan M. O’Brien, Taylor Bensel, et al.
Scientific Reports, 2017 - Chronic Neural Probes for Brain-Computer Interfaces
Abubakar Abid, Aalap Dighe, Joel Voldman
MIT EECScon Undergraduate Research Conference, 2014. [2nd place award]
Miscellaneous
- Using AI for Fatwas: A Turing Test for Legal Reasoning [Slides]
Abubakar Abid*, Mehmet Efe Akengin*.
Cambridge Religion & Science Conference, 2018 - Toxin Detection Using Nanofabricated Silicon Nitride Microrings at Visible Wavelength
Farshid Ghasemi, Ali Eftekhar, Abubakar Abid, et al.
GT² Symposium at Georgia Tech, 2013. [3rd place award]