Research

Selected scholarly works created using Ada:

  1. Govindarajan VS, Biester L. Dark & Stormy: Modeling Humor in Sentences from the Bulwer-Lytton Fiction Contest. In: Liakata M, Moreira VP, Zhang J, Jurgens D, editors. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers). San Diego, California, United States: Association for Computational Linguistics; 2026. p. 501–10. doi:10.18653/v1/2026.acl-short.42
  2. Scott E, Biester L. Global Bias in Question Answering for Large Language Models. Abstract presented at the International Conference on Computational Social Science; 2026.
  3. Luster CB, Morie KP, Legido J, Mayes LC, Potenza MN, Zhai ZW. Alexithymia mediates white-matter microstructure and substance use escalation in trauma-exposed individuals. Journal of Affective Disorders. November 2026;413:122185. doi:10.1016/j.jad.2026.122185
  4. Ross V, Cataldo F, Chodrow PS. Growing Hypergraphs with Homophily. arXiv; 2026. Available at: http://arxiv.org/abs/2607.16046 doi:10.48550/arXiv.2607.16046
  5. Caplan P, Milliken O, Pouler T, Tong Z, McDermott C, Millay S. A Lagrangian method for solving the sphericalshallow water equations using power diagrams. Journal of Computational Physics. July 2026;557:114833. doi:10.1016/j.jcp.2026.114833
  6. Thompson W, Tian M, Huynh L, Wiedemann A, Modisette V, Chodrow PS, Brooks HZ. Learning Social Influence with Unobserved Attention. arXiv; 2026. Available at: http://arxiv.org/abs/2610.12616 doi:10.48550/arXiv.2610.12616
  7. Mirshahidi P, Frighetto G, Orth J, Vaccari A, Dombrovski M. Expansion-Assisted Hybridization Chain Reaction-smFISH and Immunohistochemistry in Drosophila Brain. Journal of Visualized Experiments (JoVE). June 2026;(232):e71400. doi:10.3791/71400
  8. Frighetto G, Dombrovski M, Palacios Castillo LM, Meera P, Mirshahidi PS, Mirshahidi PS, Sanfilippo P, Vaccari A, Kandimalla P, Hartenstein V, Kurmangaliyev YZ, Zipursky SL, Frye MA. Electrical synapses mediate visual orientation behavior. Current Biology. October 2026. doi:10.1016/j.cub.2026.09.060
  9. Biester L. Sports and Women’s Sports: Gender Bias in Text Generation with Olympic Data. In: Chiruzzo L, Ritter A, Wang L, editors. Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 2: Short Papers). Albuquerque, New Mexico: Association for Computational Linguistics; 2025. p. 195–205. doi:10.18653/v1/2025.naacl-short.17
  10. Linderman MD, Banerjee S, Chang C, Liem J, Cruz Loaiza S, Pezza A, Gelb BD, Bashir A. Leveraging simulation, deep learning, and variation graphs for structural variant genotyping in short-read genome sequencing. Abstract presented at the Cold Spring Harbor Laboratory Meeting on Genome Informatics; 2025.
  11. Caplan P, Millay S. Evaluating a Voronoi-based Lagrangian method for solving the spherical shallow water equations. Abstract presented at the AGU Fall Meeting; 2025.
  12. Dombrovski M, Zang Y, Frighetto G, Vaccari A, Jang HJ, Mirshahidi PS, Xie F, Sanfilippo P, Hina BW, Rehan A, Hussein RH, Mirshahidi PS, Lee C, Morris A, Frye MA, Reyn CR von, Kurmangaliyev YZ, Card GM, Zipursky SL. Molecular gradients shape synaptic specificity of a visuomotor transformation. Nature. August 2025;644(8076):453–62. doi:10.1038/s41586-025-09037-4
  13. Linderman MD, Wallace J, Heyde A van der, Wieman E, Brey D, Shi Y, Hansen P, Shamsi Z, Gelb BD, Bashir A. NPSV-deep: A deep learning method for genotyping structural variants in short read genome sequencing data. Bioinformatics. March 2024;40(3):btae129. doi:10.1093/bioinformatics/btae129
  14. Armstrong EE, Bissell KL, Fatima HS, Heikkinen MA, Jessup A, Junaid MO, Lee DH, Lieb EC, Liem JT, Martin EM, Moreno M, Otgonbayar K, Romans BW, Royar K, Adler MB, Needle DB, Harkess A, Kelley JL, Mooney JA, Mychajliw AM. Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae. G3 Genes-Genomes-Genetics. April 2024;14(4):jkae034. doi:10.1093/g3journal/jkae034
  15. Dombrovski M, Vaccari A, Kurmangaliyev YZ, Card GM, Zipursky SL. Circuit mechanisms and molecular determinants of a visuomotor transformation. Abstract presented at the Cold Spring Harbor Laboratory Meeting on Neuronal Circuits; 2024.
  16. Dombrovski M, Zang Y, Vaccari A, Jang HJ, Mirshahidi PS, Sanfilippo P, Frye MA, Reyn CR von, Kurmangaliyev YZ, Card GM, Zipursky SL, Frighetto G. Gradients of recognition molecules regulate synaptic gradients at a visuomotor interface. Abstract presented at the Cold Spring Harbor Laboratory Meeting on Molecular Mechanisms of Neuronal Connectivity; 2024.
  17. Vaccari A, Dombrovski M. FlySeg: an Automated Volumetric Instance Segmentation Algorithm for Dense Cell Populations in Drosophila Melanogaster Nervous System. In: 2023 57th Asilomar Conference on Signals, Systems, and Computers. 2023. p. 1474–8. Available at: https://ieeexplore.ieee.org/document/10476819 doi:10.1109/IEEECONF59524.2023.10476819
  18. Dombrovski M, Vaccari A, Kurmangaliyev YZ, Card GM, Zipursky SL. Within-cell-type synaptic specificity underlying a visuomotor transformation. Abstract presented at the Cold Spring Harbor Laboratory Meeting on the Neurobiology of Drosophila; 2023.
  19. Dombrovski M, Vaccari A, Kurmangaliyev YZ, Card GM, Zipursky SL. Investigating the determinants of within-cell-type synaptic specificity. Abstract presented at the Janelia meeting on The Role of Adhesion Complexes, Cell Recognition, and Neural Activity during Circuit Assembly; 2023.
  20. Linderman MD, Brey D, Hansen P, Shi Y, Heyde A van der, Wallace J, Wieman E, Shamsi Z, Liu J, Gelb BD, Bashir A. Deep metric learning for structural variant genotyping in genome sequencing data. Abstract presented at the Cold Spring Harbor Laboratory Meeting on Biological Data Science; 2022.
  21. Caplan PC. Parallel four-dimensional anisotropic mesh adaptation. In: Proceedings of the 2022 SIAM International Meshing Roundtable. 2022. Available at: https://internationalmeshingroundtable.com/assets/papers/2022/09-Caplan-compressed.pdf
  22. Linderman M, Paudyal C, Shakeel M, Kelley W, Bashir A, Gelb BD. Supporting data for "NPSV: A simulation-driven approach to genotyping structural variants in whole genome sequencing data". GigaScience Database. July 2021;10(7). doi:10.5524/100908
  23. Linderman MD, Paudyal C, Shakeel M, Kelley W, Bashir A, Gelb BD. NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data. GigaScience. July 2021;10(7):giab046. doi:10.1093/gigascience/giab046
  24. Linderman MD, Brey D, Heyde A van der, Kelley W, Paudyal C, Shakeel M, Wallace J, Wieman E, Shamsi Z, Liu J, Gelb BD, Bashir A. Machine-learning approaches to structural variant genotyping in whole genome sequencing data. Abstract presented at the Cold Spring Harbor Laboratory Meeting on Genome Informatics; 2021.
  25. Koster C, Foley J. Middlebury at TREC News ’21 Exploring Learning to Rank Model Variants. In: Soboroff I, Ellis A, editors. Proceedings of the Thirtieth Text REtrieval Conference, TREC 2021, online, November 15-19, 2021. National Institute of Standards and Technology (NIST); 2021. (NIST Special Publication). Available at: https://trec.nist.gov/pubs/trec30/papers/middlebury-N.pdf
  26. Yuen A. Negotiating peacekeeping consent: Information and peace outcomes. Journal of Peace Research. March 2020;57(2):297–311. doi:10.1177/0022343319861424
  27. Linderman MD, Paudyal C, Shakeel M, Kelley W, Gelb BD. Non-parametric genotyping of structural variants in short-read whole genome sequencing data. Abstract presented at the 70th Annual Meeting of The American Society of Human Genetics; 2020.