Dr-LLaVA: Visual Instruction Tuning with Symbolic Clinical Grounding

Authors: Sun, Shenghuan, Schubert, Alexander, Goldgof, Gregory M., Sun, Zhiqing, Hartvigsen, Thomas, Butte, Atul J., Alaa, Ahmed

Subject Terms: Computer Science - Artificial Intelligence, Computer Science - Computation and Language, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2405.19567

The Minimum Information about CLinical Artificial Intelligence Checklist for Generative Modeling Research (MI-CLAIM-GEN)

Authors: Miao, Brenda Y., Chen, Irene Y., Williams, Christopher YK, Davidson, Jaysón, Garcia-Agundez, Augusto, Sun, Shenghuan, Zack, Travis, Saria, Suchi, Arnaout, Rima, Quer, Giorgio, Sadaei, Hossein J., Torkamani, Ali, Beaulieu-Jones, Brett, Yu, Bin, Gianfrancesco, Milena, Butte, Atul J., Norgeot, Beau, Sushil, Madhumita

Subject Terms: Computer Science - Computation and Language, Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2403.02558

Identifying Reasons for Contraceptive Switching from Real-World Data Using Large Language Models

Authors: Miao, Brenda Y., Williams, Christopher YK, Chinedu-Eneh, Ebenezer, Zack, Travis, Alsentzer, Emily, Butte, Atul J., Chen, Irene Y.

Subject Terms: Computer Science - Computation and Language, Computer Science - Information Retrieval, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2402.03597

A comparative study of zero-shot inference with large language models and supervised modeling in breast cancer pathology classification

Authors: Sushil, Madhumita, Zack, Travis, Mandair, Divneet, Zheng, Zhiwei, Wali, Ahmed, Yu, Yan-Ning, Quan, Yuwei, Butte, Atul J.

Subject Terms: Computer Science - Computation and Language, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2401.13887

Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies

Authors: Huang, Yu-Ning, Love, Michael I., Ronkowski, Cynthia Flaire, Deshpande, Dhrithi, Schriml, Lynn M., Wong-Beringer, Annie, Mons, Barend, Corbett-Detig, Russell, Hunter, Christopher I, Moore, Jason H., Garmire, Lana X., Reddy, T. B. K., Hide, Winston A., Butte, Atul J., Robinson, Mark D., Mangul, Serghei

Subject Terms: Computer Science - Digital Libraries

Access URL: http://arxiv.org/abs/2401.02965

Large Language Models as Agents in the Clinic

Authors: Mehandru, Nikita, Miao, Brenda Y., Almaraz, Eduardo Rodriguez, Sushil, Madhumita, Butte, Atul J., Alaa, Ahmed

Subject Terms: Computer Science - Human-Computer Interaction, Computer Science - Multiagent Systems

Access URL: http://arxiv.org/abs/2309.10895

CORAL: Expert-Curated medical Oncology Reports to Advance Language Model Inference

Authors: Sushil, Madhumita, Kennedy, Vanessa E., Mandair, Divneet, Miao, Brenda Y., Zack, Travis, Butte, Atul J.

Subject Terms: Computer Science - Computation and Language

Access URL: http://arxiv.org/abs/2308.03853

Revealing the impact of social circumstances on the selection of cancer therapy through natural language processing of social work notes

Authors: Sun, Shenghuan, Zack, Travis, Williams, Christopher Y. K., Butte, Atul J., Sushil, Madhumita

Subject Terms: Computer Science - Computation and Language

Access URL: http://arxiv.org/abs/2306.09877

Cross-institution text mining to uncover clinical associations: a case study relating social factors and code status in intensive care medicine

Authors: Sushil, Madhumita, Butte, Atul J., Schuit, Ewoud, van Smeden, Maarten, Leeuwenberg, Artuur M.

Subject Terms: Computer Science - Computation and Language, Statistics - Methodology, 68T50, 68U35, 62-xx, 62P10, 92C60, 92D30, I.2.7, G.3

Access URL: http://arxiv.org/abs/2301.06570

Topic Modeling on Clinical Social Work Notes for Exploring Social Determinants of Health Factors

Authors: Sun, Shenghuan, Zack, Travis, Sushil, Madhumita, Butte, Atul J.

Subject Terms: Computer Science - Computation and Language

Access URL: http://arxiv.org/abs/2212.01462

New Threshold for Defining Mild Aortic Stenosis Derived From Velocity-Encoded MRI in 60,000 Individuals

Authors: Kany, Shinwan ^{a, b, c, d}, Rämö, Joel T. ^{a, c, e}, Playford, David ^{f, g}, Strange, Geoff ^{f, h, i}, Hou, Cody ^{a, j}, Jurgens, Sean J. ^{a, k}, Nauffal, Victor ^{a, l}, Cunningham, Jonathan W. ^{a, l}, Lau, Emily S. ^{a, m}, Butte, Atul J. ⁿ, Ho, Jennifer E. ^{a, o}, Olgin, Jeffrey E. ^p, Elmariah, Sammy ^p, Lindsay, Mark E. ^{a, c, m, q, r}, Chan, Yih-Kai ^s, Stewart, Simon ^{f, t}, Ellinor, Patrick T. ^{a, c, m, q, u}, Pirruccello, James P. ^{a, n, p, v, w, t, ∗}

Source: In Journal of the American College of Cardiology 8 April 2025 85(13):1387-1399

Developing a general-purpose clinical language inference model from a large corpus of clinical notes

Authors: Sushil, Madhumita, Ludwig, Dana, Butte, Atul J., Rudrapatna, Vivek A.

Subject Terms: Computer Science - Computation and Language

Access URL: http://arxiv.org/abs/2210.06566

Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies

Authors: Huang, Yu-Ning ^{1, 20}, Munteanu, Viorel ^{2, 3, 20}, Love, Michael I. ^{4, 5}, Ronkowski, Cynthia Flaire ¹, Deshpande, Dhrithi ¹, Wong-Beringer, Annie ⁶, Corbett-Detig, Russell ⁷, Dimian, Mihai ⁸, Moore, Jason H. ⁹, Garmire, Lana X. ¹⁰, Reddy, T.B.K. ¹¹, Butte, Atul J. ^{12, 13}, Robinson, Mark D. ¹⁴, Eskin, Eleazar ^{15, 16, 17}, Abedalthagafi, Malak S. ^{18, 21}, Mangul, Serghei ^{1, 2, 3, 19, 21, ∗}

Source: In Cell Genomics

The evolution of computational research in a data-centric world

Authors: Deshpande, Dhrithi ^{1, 17, ∗}, Chhugani, Karishma ^{1, 17}, Ramesh, Tejasvene ², Pellegrini, Matteo ³, Shifman, Sagiv ⁴, Abedalthagafi, Malak S. ^{5, 6}, Alqahtani, Saleh ^{7, 8}, Ye, Jimmie ⁹, Liu, Xiaole Shirley ¹⁰, Leek, Jeffrey T. ¹¹, Brazma, Alvis ¹², Ophoff, Roel A. ¹³, Rao, Gauri ¹, Butte, Atul J. ¹⁴, Moore, Jason H. ¹⁵, Katritch, Vsevolod ¹⁶, Mangul, Serghei ^{16, ∗∗}

Source: In Cell 22 August 2024 187(17):4449-4457

Ethical and regulatory challenges of large language models in medicine

Authors: Ong, Jasmine Chiat Ling ^{a, b, †}, Chang, Shelley Yin-Hsi ^{d, e, †}, William, Wasswa ^f, Butte, Atul J ^{g, h}, Shah, Nigam H ^{i, j}, Chew, Lita Sui Tjien ^{c, k, l}, Liu, Nan ^b, Doshi-Velez, Finale ^m, Lu, Wei ⁿ, Savulescu, Julian ^{o, p, q}, Ting, Daniel Shu Wei ^{b, r, s, *}

Source: In The Lancet Digital Health June 2024 6(6):e428-e432

Characterisation of digital therapeutic clinical trials: a systematic review with natural language processing

Authors: Miao, Brenda Y ^*, Sushil, Madhumita, Xu, Ava, Wang, Michelle, Arneson, Douglas, Berkley, Ellen, Subash, Meera, Vashisht, Rohit, Rudrapatna, Vivek, Butte, Atul J

Source: In The Lancet Digital Health March 2024 6(3):e222-e229

Cross-institution natural language processing for reliable clinical association studies: a methodological exploration

Authors: Sushil, Madhumita, Butte, Atul J., Schuit, Ewoud, van Smeden, Maarten, Leeuwenberg, Artuur M.

Source: In Journal of Clinical Epidemiology March 2024 167

Assessing the potential of GPT-4 to perpetuate racial and gender biases in health care: a model evaluation study

Authors: Zack, Travis ^†, Lehman, Eric ^†, Suzgun, Mirac, Rodriguez, Jorge A, Celi, Leo Anthony, Gichoya, Judy, Jurafsky, Dan, Szolovits, Peter, Bates, David W, Abdulnour, Raja-Elie E, Butte, Atul J, Alsentzer, Emily ^*

Source: In The Lancet Digital Health January 2024 6(1):e12-e22

Electrocardiogram Detection of Pulmonary Hypertension Using Deep Learning

Authors: ARAS, MANDAR A., ABREAU, SEAN, MILLS, HUNTER, RADHAKRISHNAN, LAKSHMI, KLEIN, LIVIU, MANTRI, NEHA, RUBIN, BENJAMIN, BARRIOS, JOSHUA, CHEHOUD, CHRISTEL, KOGAN, EMILY, GITTON, XAVIER, NNEWIHE, ANDERSON, QUINN, DEBORAH, BRIDGES, CHARLES, BUTTE, ATUL J., OLGIN, JEFFREY E., TISON, GEOFFREY H.

Source: In Journal of Cardiac Failure July 2023 29(7):1017-1028

Contextualising adverse events of special interest to characterise the baseline incidence rates in 24 million patients with COVID-19 across 26 databases: a multinational retrospective cohort study

Authors: Voss, Erica A., Shoaibi, Azza, Yin Hui Lai, Lana, Blacketer, Clair, Alshammari, Thamir, Makadia, Rupa, Haynes, Kevin, Sena, Anthony G., Rao, Gowtham, van Sandijk, Sebastiaan, Fraboulet, Clement, Boyer, Laurent, Le Carrour, Tanguy, Horban, Scott, Morales, Daniel R., Martínez Roldán, Jordi, Ramírez-Anguita, Juan Manuel, Mayer, Miguel A., de Wilde, Marcel, John, Luis H., Duarte-Salles, Talita, Roel, Elena, Pistillo, Andrea, Kolde, Raivo, Maljković, Filip, Denaxas, Spiros, Papez, Vaclav, Kahn, Michael G., Natarajan, Karthik, Reich, Christian, Secora, Alex, Minty, Evan P., Shah, Nigam H., Posada, Jose D., Garcia Morales, Maria Teresa, Bosca, Diego, Cadenas Juanino, Honorio, Diaz Holgado, Antonio, Pedrera Jiménez, Miguel, Serrano Balazote, Pablo, García Barrio, Noelia, Şen, Selçuk, Üresin, Ali Yağız, Erdogan, Baris, Belmans, Luc, Byttebier, Geert, Malbrain, Manu L.N.G., Dedman, Daniel J., Cuccu, Zara, Vashisht, Rohit, Butte, Atul J., Patel, Ayan, Dahm, Lisa, Han, Cora, Bu, Fan, Arshad, Faaizah, Ostropolets, Anna, Nyberg, Fredrik, Hripcsak, George, Suchard, Marc A., Prieto-Alhambra, Dani, Rijnbeek, Peter R., Schuemie, Martijn J., Ryan, Patrick B.

Source: In eClinicalMedicine April 2023 58