Publications

Preprints

• Reasoning in Token Economies: Budget-Aware Evaluation of LLM Reasoning Strategies (Under submission)
  Junlin Wang, Siddhartha Jain, Dejiao Zhang, Baishakhi Ray, Varun Kumar, Ben Athiwaratkun
  


• Lightweight reranking for language model generations (Under submission)
  Siddhartha Jain, Xiaofei Ma, Anoop Deoras, Bing Xiang
  [preprint]

• Information Condensing Active Learning
  Siddhartha Jain, Ge Liu, David Gifford
  [preprint] [code]

Accepted/Published papers

• Code-Aware Prompting: A study of Coverage Guided Test Generation in Regression Setting using LLM
  Gabriel Ryan, Siddhartha Jain, Mingyue Shang, Shiqi Wang, Xiaofei Ma, Murali Krishna Ramanathan, Baishakhi Ray
  FSE, 2024
  [preprint]


• Multi-lingual Evaluation of Code Generation Models
  Ben Athiwaratkun, Sanjay Krishna Gouda, Zijian Wang, Xiaopeng Li, Yuchen Tian, Ming Tan, Wasi Uddin Ahmad, Shiqi Wang, Qing Sun, Mingyue Shang, Sujan Kumar Gonugondla, Hantian Ding, Varun Kumar, Nathan Fulton, Arash Farahani, Siddhartha Jain, Robert Giaquinto, Haifeng Qian, Murali Krishna Ramanathan, Ramesh Nallapati, Baishakhi Ray, Parminder Bhatia, Sudipta Sengupta, Dan Roth, Bing Xiang
  ICLR, 2022
  [preprint]


• Overinterpretation reveals image classification model pathologies
  Brandon Carter, Siddhartha Jain, Jonas Mueller, David Gifford
  Neurips, 2021
  [preprint]


• Machine learning optimization of peptides for presentation by class II MHCs
  Zheng Dai, Brooke Huisman, Haoyang Zeng, Brandon Carter, Siddhartha Jain, Michael Birnbaum, David Gifford
  Bioinformatics, 2020
  [preprint]


• Robust computational design and evaluation of peptide vaccines for cellular immunity with application to SARS-CoV-2
  Ge Liu, Brandon Carter, Trenton Bricken, Siddhartha Jain, Mathias Viard, Mary Carrington, David Gifford
  Cell Systems, 2020
  [preprint] [code]


• Machine Learning Optimization of MHC Class II Presented Peptides
  Haoyang Zeng, Brandon Carter, Siddhartha Jain, Brooke Huisman, Michael Birnbaum, David Gifford
  Machine Learning in Computational Biology, 2019
  


• Maximizing Overall Diversity for Improved Uncertainty Estimates in Deep Ensembles
  Siddhartha Jain*, Ge Liu*, Jonas Mueller, David Gifford
  AAAI 2020
  [paper]


• Transcriptional regulatory model of fibrosis progression in the human lung
  John McDonough, Farida Ahangari, Qin Li, Siddhartha Jain, Stijn E. Stijn E. Verleden, Jose Herazo-Maya, Milica Vukmirovic, Giuseppe DeIuliis, Argyrios Tzouvelekis, Naoya Tanabe, Fanny Chu, Xiting Yan, Johny Verschakelen, Robert Homer, Dimitris V Manatakis, Junke Zhang, Jun Ding, Karen Maes, Laurens De Sadeleer, Robin Vos, Arne Neyrinck, Panayiotis Benos, Ziv Bar-Joseph, Dean Tantin, James Hogg, Bart V Vanaudenaerde, Wim Wuyts, Naftali Kaminski
  JCI Insights
  [paper]


• Approximate Mutual Information-based Acquisition for General Models in Bayesian Optimization
  Siddhartha Jain, Nathan Hunt, David Gifford
  NeurIPS Workshop on Bayesian Deep Learning, 2018
  


• Maximizing Overall Diversity to Control Out-of-Distribution Behavior of Deep Ensembles
  Siddhartha Jain*, Ge Liu*, Jonas Mueller, David Gifford
  NeurIPS Workshop on Bayesian Deep Learning, 2018
  


• What made you do this? Understanding black-box decisions with sufficient input subsets
  Brandon Carter*, Jonas Mueller*, Siddhartha Jain, David Gifford
  AISTATS, 2019
  [paper]


• Using Neural Networks for Reducing the Dimensions of Single-Cell RNA-Seq Data.
  Chieh Lin, Siddhartha Jain, Hannah Kim, Ziv Bar-Joseph
  Nucleic Acids Research
  [paper]


• Transcriptome analyses identify key cellular factors associated with HIV-1 associated neuropathogenesis in infected men.
  Narasimhan J. Venkatachari, Siddhartha Jain, Leah Walker, Shalmali Bilavaker-Mehla, Ansuman Chattopadhyay, Ziv Bar-Joseph, Charles Rinaldo, Ann Ragin, Eric Seaberg, Andrew Levine, James Becker, Eileen Martin, Ned Sacktor, Velpandi Ayyavoo
  AIDS journal
  [paper]


• Reconstructing the temporal progression of HIV-1 immune response pathways.
  Siddhartha Jain, Joel Arrais, Narasimhan J. Venkatachari, Velpandi Ayyavoo, Ziv Bar-Joseph.
  International Symposium on Molecular Biology (ISMB), 2016
  [Supporting Website, paper]


• Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch.
  Narasimhan J Venkatachari, Jennifer M Zerbato, Siddhartha Jain, Allison E Mancini, Ansuman Chattopadhyay, Nicolas Sluis-Cremer, Ziv Bar-Joseph, Velpandi Ayyavoo.
  Retrovirology, 2015
  [paper]


• Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu
  Siddhartha Jain, Anthony Gitter, Ziv Bar-Joseph.
  PLOS Computational Biology. 10:12, 2014 and
  Society for Laboratory Automation & Screening (SLAS), 2015
  [Supporting Website, paper]


• Large Neighborhood Search for the Dial-a-Ride Problem.
  Siddhartha Jain, Pascal Van Hentenryck.
  17th International Conference on Principles and Practices of Constraint Programming (CP), 2011 [pdf]


• A General Nogood-Learning Framework for Pseudo-Boolean Multi-Valued SAT.
  Siddhartha Jain, Ashish Sabharwal, Meinolf Sellmann.
  25th Conference on Artificial Intelligence (AAAI), 2011 [pdf]


• A Complete Multi-valued SAT Solver.
  Siddhartha Jain, Eoin O'Mahony, Meinolf Sellmann.
  16th International Conference on Principles and Practices of Constraint Programming (CP), 2010 [pdf]


• Upper Bounds on the Number of Solutions of Binary Integer Programs.
  Siddhartha Jain, Serdar Kadioglu, Meinolf Sellmann.
  7th International Conference on Integration of AI and OR Techniques in Constraint Programming (CPAIOR), 2010 [pdf]