Ameet Soni

Ameet Soni

Associate Professor
Associate Dean of the Faculty for Diversity, Recruitment, and Retention
Computer Science Department
Swarthmore College

phone: (610) 957-6288
office: 212 East Parrish

I am currently an Associate Professor of Computer Science at Swarthmore College. I received my Ph.D. in Computer Science in August 2011 from the University of Wisconsin where I was advised by Professor Jude Shavlik. My general research interests are in the areas of machine learning and computational biology and medicine.

Current Semester

I will be on leave from 2021-24 serving in the Provost Office as Associate Dean of the Faculty for Diversity, Recruitment, and Retention.

Previous Courses:

Research Interests

Please see my 2017 Faculty Lecture for an overview of my research as well as my 2022 talk on teaching Ethics in AI.


Transcription factor binding: transcription factors govern the regulation of genes - that is, determine when a gene is on or off. Understanding which transcription factors bind to which areas of the genome and in which cells helps understand the function of target genes. Our lab utilizes deep neural networks to predict the binding affinity of specific transcription factors to a given portion of DNA to identify these relationships without the need for expensive in vivo experiments.

Brain image analysis: Recently, my group has been researching several different computational problems in the area of MRI braining imaging. Initial results in this area include improved approaches for performing image segmentation in brain images using probabilistic graphical models (conditional random fields). Ongoing work aims to apply deep learning approaches - including convolutional neural networks - to improve early diagnosis of Alzheimer's disease.

Statistical relational learning: Real world data is inherently noisy and relational (i.e., elements are dependent on one another). Traditional machine learning algorithms fail to account for these realities. In collaboration with Prof. Sriraam Natarajan at Indiana University, I have done work with Relational Dependency Networks to model problems in complex domains. Examples including relational extraction problems from text (e.g., identify the CEO of a company from a newswire article) and diagnosis of Parkinson's disease from medical records.

Protein Structure Prediction: Previously, I worked on ACMI (Automated Crystallographic Map Interpretation). The task of determining protein structures has been a central one to the biological community for several decades. The most popular method for producing protein structures is by interpreting an electron-density map - a three-dimensional image of a molecule produced through X-ray crystallography. This process, however, remains a resource- intensive and time-consuming task, stunting basic biological research. Thus, the main objective of the project is: The result of our group's efforts is ACMI, a probabilistic technique for determining protein structures. Prior to ACMI, techniques failed when trying to interpret low-quality images. With ACMI, crystallographers can now obtain complete and accurate structures from these difficult proteins instead of scrapping the project or dedicating months of effort.

Selected Publications

[Complete List]

Asterick's (*) indicate supervised students.

A Module for Introducing Ethics in AI: Detecting Bias in Language Models.
Ameet Soni and Krista Karbowski Thomason.
In Proceedings of the 10th Symposium on Educational Advances in Artificial Intelligence (EAAI), . [slides]

Dugesia japonica is the best suited of three planarian species for high-throughput toxicology screening.
Danielle Ireland, Veronica Bochenek, *Daniel Chaiken*, Christina Rabeler, *Sumi Onoe*, Ameet Soni and Eva-Maria S. Collins.
In Chemosphere, vol. 253, pp. 126718, . [cached]

Deep Residual Nets for Improved Alzheimer’s Diagnosis.
*Aly Valliani* and Ameet Soni.
In Proceedings of the 8th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), . [poster]

Identifying Parkinson’s Patients: A Functional Gradient Boosting Approach.
Devendra Singh Dhami, Ameet Soni, David Page and Sriraam Natarajan.
In Artificial Intelligence in Medicine (AIME), .

Learning relational dependency networks for relation extraction.
Ameet Soni, Dileep Viswanathan, Jude W. Shavlik and Sriraam Natarajan.
In Proceedings of the 26th International Conference on Inductive Logic Programming (ILP), . [slides]

A Comparison of weak supervision methods for knowledge base construction.
Ameet Soni, Dileep Viswanathan, Pachaiyappan, Niranjan and Sriraam Natarajan.
In 5th Workshop on Automated Knowledge Base Construction (AKBC) at NAACL, . [poster]

A comprehensive analysis of classification algorithms for cancer prediction from gene expression.
*Raehoon Jeong* and Ameet Soni.
In Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), pp. 525–526, . [poster]

A support program for introductory CS courses that improves student performance and retains students from underrepresented groups.
Newhall, Tia, Meeden, Lisa, Danner, Andrew, Ameet Soni, Ruiz, Frances and Wicentowski, Richard.
In Proceedings of the 45th ACM Technical Symposium on Computer Science Education (SIGCSE), pp. 433–438, .

A graphical model approach to ATLAS-free mining of MRI images.
*Chris S. Magnano*, Ameet Soni, Sriraam Natarajan and Kunapuli, Gautam.
In Proceedings of the 2014 SIAM International Conference on Data Mining (SDM), pp. 974–982, . [poster]

Probabilistic ensembles for improved inference in protein-structure determination.
Ameet Soni and Jude W. Shavlik.
In Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), pp. 264–273, . Invited for journal publication. [slides] [cached]

Guiding belief propagation using domain knowledge for protein-structure determination.
Ameet Soni, Craig A. Bingman and Jude W. Shavlik.
In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB), pp. 285–294, . Best Paper Award. [slides] [cached]

Creating protein models from electron-density maps using particle-filtering methods.
Frank DiMaio, Kondrashov, Dmitry A., Bitto, Eduard, Ameet Soni, Craig A. Bingman, George N. Phillips Jr. and Jude W. Shavlik.
In Bioinformatics, Oxford Univ Press, vol. 23, no. 21, pp. 2851–2858, . PMCID: PMC2567142
[pdf] [doi]

Improved methods for template-matching in electron-density maps using spherical harmonics.
Frank DiMaio, Ameet Soni, George N. Phillips Jr. and Jude W. Shavlik.
In IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 258–265, . Invited for journal publication. [code/data]

Research Students

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