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RESEARCH

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Thesis

• Artificial Intelligence Methods for Improved Diagnosis of Autism Spectrum Disorder
  M Varma, 2020
  Undergraduate Honors Thesis, Department of Computer Science
  Advised by Dr. Dennis P. Wall and Dr. James Landay
  » David M. Kennedy Thesis Prize for Best Engineering Thesis
  » Ben Wegbreit Prize for Best Thesis in Computer Science
  » Firestone Medal for Excellence in Undergraduate Research

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Patents

• Intelligent traffic alerting and control system
  M Varma, 2015
  US Patent 9035797

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Publications

(* indicates equal contribution)

2023

• ViLLA: Fine‑grained vision‑language representation learning from real‑world data
  M Varma, JB Delbrouck, S Hooper, A Chaudhari, C Langlotz
  International Conference on Computer Vision (ICCV), 2023

• Toward expanding the scope of radiology report summarization to multiple anatomies and modalities
  Z Chen*, M Varma*, X Wan, C Langlotz, JB Delbrouck*
  Association for Computational Linguistics (ACL), 2023

• Graph representations and algorithms in biomedicine
  B Chrisman, M Varma, S Maleki, M Brbic, C Joslyn, M Zitnik
  Pacific Symposium of Biocomputing, 2023

2022

• ViLMedic: A framework for research at the intersection of vision and language in medical AI
  JB Delbrouck, K Saab, M Varma, S Eyuboglu, P Chambon, J Dunnmon, J Zambrano, A Chaudhari, C Langlotz
  Association for Computational Linguistics (ACL), 2022

• Improved digital therapy for developmental pediatrics using domain-specific artificial intelligence
  P Washington, H Kalantarian, J Kent, A Husic, A Kline, E Leblanc, C Hou, OC Mutlu, K Dunlap, Y Penev, M Varma, NT Stockham, B Chrisman, K Paskov, MW Sun, JY Jung, C Voss, N Haber, DP Wall
  JMIR Pediatrics and Parenting, 2022

• Domino: Discovering systematic errors with cross-modal embeddings
  S Eyuboglu*, M Varma*, K Saab*, JB Delbrouck, C Lee-Messer, J Dunnmon, J Zou, C Ré
  International Conference on Learning Representations (ICLR), 2022
  Oral Presentation (Top 1.5% of Submissions)

• Identification of social engagement indicators associated with autism spectrum disorder using a game-based mobile app
  M Varma, P Washington, B Chrisman, A Kline, E Leblanc, K Paskov, N Stockham, JY Jung, MW Sun, DP Wall
  Journal of Medical Internet Research, 2022

2021

• Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers
  BS Chrisman, KM Paskov, N Stockham, JY Jung, M Varma, PY Washington, C Tataru, S Iwai, TZ DeSantis, M David, DP Wall
  BMC Bioinformatics, 2021

• Cross-domain data integration for named entity disambiguation in biomedical text
  M Varma, L Orr, S Wu, M Leszczynski, X Ling, C Ré
  Findings of EMNLP, 2021

• A maximum flow-based network approach for identification of stable noncoding biomarkers associated with the multigenic neurological condition, autism
  M Varma, KM Paskov, BS Chrisman, MW Sun, JY Jung, NT Stockham, PY Washington, DP Wall
  BMC BioData Mining, 2021

• Estimating sequencing error rates using families
  K Paskov, JY Jung, B Chrisman, NT Stockham, P Washington, M Varma, MW Sun, DP Wall
  BMC BioData Mining, 2021

• Crowdsourced privacy-preserved feature tagging of short home videos for machine learning ASD detection
  P Washington, Q Tariq, E Leblanc, B Chrisman, K Dunlap, A Kline, H Kalantarian, Y Penev, K Paskov, C Voss, N Stockham, M Varma, A Husic, J Kent, N Haber, T Winograd, DP Wall
  Scientific Reports, 2021

• Indels in SARS-CoV-2 occur at template-switching hotspots
  BS Chrisman, K Paskov, NT Stockham, K Tabatabaei, JY Jung, P Washington, M Varma, MW Sun, S Maleki, DP Wall
  BMC BioData Mining, 2021

• Selection of trustworthy crowd workers for telemedical diagnosis of pediatric autism spectrum disorder
  P Washington, E Leblanc, K Dunlap, Y Penev, M Varma, JY Jung, B Chrisman, MW Sun, N Stockham, KM Paskov, H Kalantarian, C Voss, N Haber, DP Wall
  Pacific Symposium of Biocomputing, 2021

2020

• Feature replacement methods enable reliable home video analysis for machine learning detection of autism
  E Leblanc, P Washington, M Varma, K Dunlap, Y Penev, A Kline, DP Wall
  Scientific Reports, 2020

• Game theoretic centrality: a novel approach to prioritize disease candidate genes by combining biological networks with the Shapley value
  MW Sun, S Moretti, KM Paskov, NT Stockham, M Varma, BS Chrisman, PY Washington, JY Jung, DP Wall
  BMC Bioinformatics, 2020

• Precision telemedicine through crowdsourced machine learning: testing variability of crowd workers for video-based autism feature recognition
  P Washington, E Leblanc, K Dunlap, Y Penev, A Kline, K Paskov, MW Sun, B Chrisman, N Stockham, M Varma, C Voss, N Haber, DP Wall
  Journal of Personalized Medicine, 2020

• Feature selection and dimension reduction of social autism data
  P Washington, KM Paskov, H Kalantarian, N Stockham, C Voss, A Kline, R Patnaik, B Chrisman, M Varma, Q Tariq, K Dunlap, J Schwartz, N Haber, DP Wall
  Pacific Symposium of Biocomputing, 2020

2019

• Data-driven diagnostics and the potential of mobile artificial intelligence for digital therapeutic phenotyping in computational psychiatry
  P Washington, N Park, P Srivastava, C Voss, A Kline, M Varma, Q Tariq, H Kalantarian, J Schwartz, R Patnaik, N Haber, DP Wall
  Biological Psychiatry, 2019

• Automated abnormality detection in lower extremity radiographs using deep learning
  M Varma, M Lu, R Gardner, J Dunnmon, N Khandwala, P Rajpurkar, J Long, C Beaulieu, K Shpanskaya, L Fei-Fei, MP Lungren, BN Patel.
  Nature: Machine Intelligence, 2019

• Coalitional game theory facilitates identification of non-coding variants associated with autism
  MW Sun, A Gupta, M Varma, KM Paskov, JY Jung, NT Stockham, DP Wall
  Biomedical Informatics Insights, 2019

• Validity of online screening for autism: crowdsourcing study comparing paid and unpaid diagnostic tasks
  P Washington, H Kalantarian, Q Tariq, J Schwartz, K Dunlap, B Chrisman, M Varma, M Ning, A Kline, N Stockham, K Paskov, C Voss, N Haber, DP Wall
  Journal of Medical Internet Research, 2019

• Outgroup machine learning approach identifies single nucleotide variants in noncoding DNA associated with Autism Spectrum Disorder
  M Varma, KM Paskov, JY Jung, B Chrisman, NT Stockham, P Washington, DP Wall
  Pacific Symposium on Biocomputing, 2019
  Oral Presentation

2018

• Analysis of sex and recurrence ratios in simplex and multiplex Autism Spectrum Disorder implicates sex-specific alleles as inheritance mechanism
  B Chrisman, M Varma, P Washington, K Paskov, N Stockham, JY Jung, DP Wall
  IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018
   

2017

• Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes
  L Diaz-Beltran, FJ Esteban, M Varma, A Ozturk, M David, DP Wall
  BMC Genomics, 2017

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Workshop Papers & Preprints

• Diagnostically lossless compression of medical images
  R van der Sluijs*, M Varma*, J Prince, C Langlotz, A Chaudhari
  Workshop on Neural Compression @ ICML, 2023

• Overview of the RadSum23 shared task on multi‑modal and multi‑anatomical radiology report summarization
  JB Delbrouck, M Varma, P Chambon, C Langlotz
  Workshop on Biomedical Natural Language Processing @ ACL, 2023
  Oral Presentation

• Toward expanding the scope of radiology report summarization to multiple anatomies and modalities
  JB Delbrouck, M Varma, C Langlotz
  Extended Abstract, Machine Learning for Health (ML4H) Symposium, 2022

• Determining question-answer plausibility in crowdsourced datasets using multi-task learning
  R Gardner, M Varma, C Zhu, R Krishna
  Workshop on Noisy User-generated Text (W-NUT) @ EMNLP, 2020