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4. Supporting Human-AI Collaboration in Auditing LLMs with LLMs

Author

Rastogi, Charvi, Ribeiro, Marco Tulio, King, Nicholas, and Amershi, Saleema

Subjects
Computer Science - Human-Computer Interaction, Computer Science - Artificial Intelligence, Computer Science - Computation and Language
Abstract

Large language models are becoming increasingly pervasive and ubiquitous in society via deployment in sociotechnical systems. Yet these language models, be it for classification or generation, have been shown to be biased and behave irresponsibly, causing harm to people at scale. It is crucial to audit these language models rigorously. Existing auditing tools leverage either or both humans and AI to find failures. In this work, we draw upon literature in human-AI collaboration and sensemaking, and conduct interviews with research experts in safe and fair AI, to build upon the auditing tool: AdaTest (Ribeiro and Lundberg, 2022), which is powered by a generative large language model (LLM). Through the design process we highlight the importance of sensemaking and human-AI communication to leverage complementary strengths of humans and generative models in collaborative auditing. To evaluate the effectiveness of the augmented tool, AdaTest++, we conduct user studies with participants auditing two commercial language models: OpenAI's GPT-3 and Azure's sentiment analysis model. Qualitative analysis shows that AdaTest++ effectively leverages human strengths such as schematization, hypothesis formation and testing. Further, with our tool, participants identified a variety of failures modes, covering 26 different topics over 2 tasks, that have been shown before in formal audits and also those previously under-reported., Comment: 21 pages, 3 figures

Published
2023

5. A single-dose intranasal live-attenuated codon deoptimized vaccine provides broad protection against SARS-CoV-2 and its variants

Author

Liu, Xiang, Ng, Wern Hann, Zusinaite, Eva, Freitas, Joseph, Taylor, Adam, Yerragunta, Venugopal, Aavula, Shukra Madhaha, Gorriparthi, Sambaiah, Ponsekaran, Santhakumar, Bonda, Rama Lakshmi, Mani, Priyanka, Nimmagadda, Sridevi V., Wang, Sainan, Lello, Laura Sandra, Zaid, Ali, Dua, Ujjwal, Taft-Benz, Sharon A., Anderson, Elizabeth, Baxter, Victoria K., Sarkar, Sanjay, Ling, Zheng L., Ashhurst, Thomas M., Cheng, Samuel M. S., Pattnaik, Priyabrata, Kanakasapapathy, Anand Kumar, Baric, Ralph S., Burt, Felicity J., Peiris, Malik, Heise, Mark T., King, Nicholas J. C., Merits, Andres, Lingala, Rajendra, and Mahalingam, Suresh

Published
2024
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6. Capabilities of GPT-4 on Medical Challenge Problems

Author

Nori, Harsha, King, Nicholas, McKinney, Scott Mayer, Carignan, Dean, and Horvitz, Eric

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence
Abstract

Large language models (LLMs) have demonstrated remarkable capabilities in natural language understanding and generation across various domains, including medicine. We present a comprehensive evaluation of GPT-4, a state-of-the-art LLM, on medical competency examinations and benchmark datasets. GPT-4 is a general-purpose model that is not specialized for medical problems through training or engineered to solve clinical tasks. Our analysis covers two sets of official practice materials for the USMLE, a three-step examination program used to assess clinical competency and grant licensure in the United States. We also evaluate performance on the MultiMedQA suite of benchmark datasets. Beyond measuring model performance, experiments were conducted to investigate the influence of test questions containing both text and images on model performance, probe for memorization of content during training, and study probability calibration, which is of critical importance in high-stakes applications like medicine. Our results show that GPT-4, without any specialized prompt crafting, exceeds the passing score on USMLE by over 20 points and outperforms earlier general-purpose models (GPT-3.5) as well as models specifically fine-tuned on medical knowledge (Med-PaLM, a prompt-tuned version of Flan-PaLM 540B). In addition, GPT-4 is significantly better calibrated than GPT-3.5, demonstrating a much-improved ability to predict the likelihood that its answers are correct. We also explore the behavior of the model qualitatively through a case study that shows the ability of GPT-4 to explain medical reasoning, personalize explanations to students, and interactively craft new counterfactual scenarios around a medical case. Implications of the findings are discussed for potential uses of GPT-4 in medical education, assessment, and clinical practice, with appropriate attention to challenges of accuracy and safety., Comment: 35 pages, 15 figures; added GPT-4-base model results and discussion

Published
2023

15. Federal Circuit Clarifies Printed Matter Doctrine In Claim Interpretation Of Electronic Communications

Author

King, Nicholas S.

Subjects
United States. Court of Appeals for the Federal Circuit -- Cases, Telecommunication -- Cases, Appellate procedure -- Cases, Patent infringement -- Cases, Company legal issue, Communications technology, Business, international
Abstract

In IOEngine, LLC v. Ingenico Inc.1, the U.S. Court of Appeals for the Federal Circuit (CAFC) reversed in part the U.S. Patent Trial and Appeal Board's (PTAB) Final Written Decisions [...]

Published
2024

18. A unique human cord blood CD8+CD45RA+CD27+CD161+ T‐cell subset identified by flow cytometric data analysis using Seurat

Author

Reyes, Julen Gabirel Araneta, primary, Ni, Duan, additional, Santner‐Nanan, Brigitte, additional, Pinget, Gabriela Veronica, additional, Kraftova, Lucie, additional, Ashhurst, Thomas Myles, additional, Marsh‐Wakefield, Felix, additional, Wishart, Claire Leana, additional, Tan, Jian, additional, Hsu, Peter, additional, King, Nicholas Jonathan Cole, additional, Macia, Laurence, additional, and Nanan, Ralph, additional

Published
2024
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24. SARS-CoV-2 infection results in immune responses in the respiratory tract and peripheral blood that suggest mechanisms of disease severity

Author

Zhang, Wuji, Chua, Brendon Y., Selva, Kevin J., Kedzierski, Lukasz, Ashhurst, Thomas M., Haycroft, Ebene R., Shoffner-Beck, Suzanne K., Hensen, Luca, Boyd, David F., James, Fiona, Mouhtouris, Effie, Kwong, Jason C., Chua, Kyra Y. L., Drewett, George, Copaescu, Ana, Dobson, Julie E., Rowntree, Louise C., Habel, Jennifer R., Allen, Lilith F., Koay, Hui-Fern, Neil, Jessica A., Gartner, Matthew J., Lee, Christina Y., Andersson, Patiyan, Khan, Sadid F., Blakeway, Luke, Wisniewski, Jessica, McMahon, James H., Vine, Erica E., Cunningham, Anthony L., Audsley, Jennifer, Thevarajan, Irani, Seemann, Torsten, Sherry, Norelle L., Amanat, Fatima, Krammer, Florian, Londrigan, Sarah L., Wakim, Linda M., King, Nicholas J. C., Godfrey, Dale I., Mackay, Laura K., Thomas, Paul G., Nicholson, Suellen, Arnold, Kelly B., Chung, Amy W., Holmes, Natasha E., Smibert, Olivia C., Trubiano, Jason A., Gordon, Claire L., Nguyen, Thi H. O., and Kedzierska, Katherine

Published
2022
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25. Ocular tropism of SARS-CoV-2 in animal models with retinal inflammation via neuronal invasion following intranasal inoculation

Author

Jeong, Gi Uk, Kwon, Hyung-Jun, Ng, Wern Hann, Liu, Xiang, Moon, Hyun Woo, Yoon, Gun Young, Shin, Hye Jin, Lee, In-Chul, Ling, Zheng Lung, Spiteri, Alanna G., King, Nicholas J. C., Taylor, Adam, Chae, Ji Soo, Kim, Chonsaeng, Ahn, Dae-Gyun, Kim, Kyun-Do, Ryu, Young Bae, Kim, Seong-Jun, Mahalingam, Suresh, and Kwon, Young-Chan

Published
2022
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27. Phase-Encoded Hyperpolarized Nanodiamond for Magnetic Resonance Imaging

Author

Waddington, David E. J., Boele, Thomas, Rej, Ewa, McCamey, Dane R., King, Nicholas J. C., Gaebel, Torsten, and Reilly, David J.

Subjects
Physics - Medical Physics, Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Instrumentation and Detectors
Abstract

Surface-functionalized nanomaterials can act as theranostic agents that detect disease and track biological processes using hyperpolarized magnetic resonance imaging (MRI). Candidate materials are sparse however, requiring spinful nuclei with long spin-lattice relaxation (T1) and spin-dephasing times (T2), together with a reservoir of electrons to impart hyperpolarization. Here, we demonstrate the versatility of the nanodiamond material system for hyperpolarized 13C MRI, making use of its intrinsic paramagnetic defect centers, hours-long nuclear T1 times, and T2 times suitable for spatially resolving millimeter-scale structures. Combining these properties, we enable a new imaging modality that exploits the phase-contrast between spins encoded with a hyperpolarization that is aligned, or anti-aligned with the external magnetic field. The use of phase-encoded hyperpolarization allows nanodiamonds to be tagged and distinguished in an MRI based on their spin-orientation alone, and could permit the action of specific bio-functionalized complexes to be directly compared and imaged., Comment: Supplemental Material available via email

Published
2017

28. A unique human cord blood CD8+CD45RA+CD27+CD161+ T‐cell subset identified by flow cytometric data analysis using Seurat.

Author

Reyes, Julen Gabirel Araneta, Ni, Duan, Santner‐Nanan, Brigitte, Pinget, Gabriela Veronica, Kraftova, Lucie, Ashhurst, Thomas Myles, Marsh‐Wakefield, Felix, Wishart, Claire Leana, Tan, Jian, Hsu, Peter, King, Nicholas Jonathan Cole, Macia, Laurence, and Nanan, Ralph

Subjects
MONONUCLEAR leukocytes, CORD blood, BLOOD cells, T cells, PACKAGING waste
Abstract

Advances in single‐cell level analytical techniques, especially cytometric approaches, have led to profound innovation in biomedical research, particularly in the field of clinical immunology. This has resulted in an expansion of high‐dimensional data, posing great challenges for comprehensive and unbiased analysis. Conventional manual analysis is thus becoming untenable to handle these challenges. Furthermore, most newly developed computational methods lack flexibility and interoperability, hampering their accessibility and usability. Here, we adapted Seurat, an R package originally developed for single‐cell RNA sequencing (scRNA‐seq) analysis, for high‐dimensional flow cytometric data analysis. Based on a 20‐marker antibody panel and analyses of T‐cell profiles in both adult blood and cord blood (CB), we showcased the robust capacity of Seurat in flow cytometric data analysis, which was further validated by Spectre, another high‐dimensional cytometric data analysis package, and conventional manual analysis. Importantly, we identified a unique CD8+ T‐cell population defined as CD8+CD45RA+CD27+CD161+ T cell that was predominantly present in CB. We characterised its IFN‐γ‐producing and potential cytotoxic properties using flow cytometry experiments and scRNA‐seq analysis from a published dataset. Collectively, we identified a unique human CB CD8+CD45RA+CD27+CD161+ T‐cell subset and demonstrated that Seurat, a widely used package for scRNA‐seq analysis, possesses great potential to be repurposed for cytometric data analysis. This facilitates an unbiased and thorough interpretation of complicated high‐dimensional data using a single analytical pipeline and opens a novel avenue for data‐driven investigation in clinical immunology. [ABSTRACT FROM AUTHOR]

Published
2024
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29. Interleukin‐6 and interferon‐alpha differentially regulate microglia function.

Author

Verdillo, Rovin, Spiteri, Alanna, Viengkhou, Barney, Wishart, Claire, King, Nicholas J. C., and Hofer, Markus J.

Subjects
PHAGOCYTOSIS, MICROGLIA, DRUG target, TRANSCRIPTOMES
Abstract

Previous reports have shown that IL‐6 and IFN‐⍺ induce distinct transcriptomic and morphological changes in microglia. Here, we demonstrate that IL‐6 increases tissue surveillance, migration and phagocytosis in primary murine microglia, whereas IFN‐⍺ inhibits these functions. Our results provide a crucial link between transcriptome and function. It holds the potential to serve as the foundation for future studies aimed at identifying therapeutic targets for cytokine‐mediated neuroinflammatory diseases. [ABSTRACT FROM AUTHOR]

Published
2024
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35. Faecal microbial transfer and complex carbohydrates mediate protection against COPD

Author

Budden, Kurtis F, primary, Shukla, Shakti D, additional, Bowerman, Kate L, additional, Vaughan, Annalicia, additional, Gellatly, Shaan L, additional, Wood, David L A, additional, Lachner, Nancy, additional, Idrees, Sobia, additional, Rehman, Saima Firdous, additional, Faiz, Alen, additional, Patel, Vyoma K, additional, Donovan, Chantal, additional, Alemao, Charlotte A, additional, Shen, Sj, additional, Amorim, Nadia, additional, Majumder, Rajib, additional, Vanka, Kanth S, additional, Mason, Jazz, additional, Haw, Tatt Jhong, additional, Tillet, Bree, additional, Fricker, Michael, additional, Keely, Simon, additional, Hansbro, Nicole, additional, Belz, Gabrielle T, additional, Horvat, Jay, additional, Ashhurst, Thomas, additional, van Vreden, Caryn, additional, McGuire, Helen, additional, Fazekas de St Groth, Barbara, additional, King, Nicholas J C, additional, Crossett, Ben, additional, Cordwell, Stuart J, additional, Bonaguro, Lorenzo, additional, Schultze, Joachim L, additional, Hamilton‐Williams, Emma E, additional, Mann, Elizabeth, additional, Forster, Samuel C, additional, Cooper, Matthew A, additional, Segal, Leopoldo N, additional, Chotirmall, Sanjay H, additional, Collins, Peter, additional, Bowman, Rayleen, additional, Fong, Kwun M, additional, Yang, Ian A, additional, Wark, Peter A B, additional, Dennis, Paul G, additional, Hugenholtz, Philip, additional, and Hansbro, Philip M, additional

Published
2024
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36. A unique human cord blood CD8 + CD45RA + CD27 + CD161 + T cell subset identified by flow cytometric data analysis using Seurat

Author

Ni, Duan, primary, Reyes, Julen Gabirel Araneta, additional, Santner-Nanan, Brigitte, additional, Pinget, Gabriela Veronica, additional, Kraftova, Lucie, additional, Ashhurst, Thomas M., additional, Marsh-Wakefield, Felix, additional, Wishart, Claire Leana, additional, Tan, Jian, additional, Hsu, Peter, additional, King, Nicholas Jonathan Cole, additional, Macia, Laurence, additional, and Nanan, Ralph, additional

Published
2024
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39. Integrated immune dynamics define correlates of COVID-19 severity and antibody responses

Author

Koutsakos, Marios, Rowntree, Louise C., Hensen, Luca, Chua, Brendon Y., van de Sandt, Carolien E., Habel, Jennifer R., Zhang, Wuji, Jia, Xiaoxiao, Kedzierski, Lukasz, Ashhurst, Thomas M., Putri, Givanna H., Marsh-Wakefield, Felix, Read, Mark N., Edwards, Davis N., Clemens, E. Bridie, Wong, Chinn Yi, Mordant, Francesca L., Juno, Jennifer A., Amanat, Fatima, Audsley, Jennifer, Holmes, Natasha E., Gordon, Claire L., Smibert, Olivia C., Trubiano, Jason A., Hughes, Carly M., Catton, Mike, Denholm, Justin T., Tong, Steven Y.C., Doolan, Denise L., Kotsimbos, Tom C., Jackson, David C., Krammer, Florian, Godfrey, Dale I., Chung, Amy W., King, Nicholas J.C., Lewin, Sharon R., Wheatley, Adam K., Kent, Stephen J., Subbarao, Kanta, McMahon, James, Thevarajan, Irani, Nguyen, Thi H.O., Cheng, Allen C., and Kedzierska, Katherine

Published
2021
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40. A Difference-in-Differences Approach to Assess the Effect of a Heat Action Plan on Heat-Related Mortality, and Differences in Effectiveness According to Sex, Age, and Socioeconomic Status (Montreal, Quebec)

Author

Benmarhnia, Tarik, Bailey, Zinzi, Kaiser, David, Auger, Nathalie, King, Nicholas, and Kaufman, Jay S

Subjects
Aging, Behavioral and Social Science, Basic Behavioral and Social Science, Good Health and Well Being, Adult, Age Factors, Aged, Aged, 80 and over, Female, Health Planning, Heat Stress Disorders, Humans, Male, Middle Aged, Program Evaluation, Quebec, Sex Factors, Socioeconomic Factors, Environmental Sciences, Medical and Health Sciences, Toxicology
Abstract

BackgroundThe impact of heat waves on mortality and health inequalities is well documented. Very few studies have assessed the effectiveness of heat action plans (HAPs) on health, and none has used quasi-experimental methods to estimate causal effects of such programs.ObjectivesWe developed a quasi-experimental method to estimate the causal effects associated with HAPs that allows the identification of heterogeneity across subpopulations, and to apply this method specifically to the case of the Montreal (Quebec, Canada) HAP.MethodsA difference-in-differences approach was undertaken using Montreal death registry data for the summers of 2000-2007 to assess the effectiveness of the Montreal HAP, implemented in 2004, on mortality. To study equity in the effect of HAP implementation, we assessed whether the program effects were heterogeneous across sex (male vs. female), age (≥ 65 years vs. < 65 years), and neighborhood education levels (first vs. third tertile). We conducted sensitivity analyses to assess the validity of the estimated causal effect of the HAP program.ResultsWe found evidence that the HAP contributed to reducing mortality on hot days, and that the mortality reduction attributable to the program was greater for elderly people and people living in low-education neighborhoods.ConclusionThese findings show promise for programs aimed at reducing the impact of extreme temperatures and health inequities. We propose a new quasi-experimental approach that can be easily applied to evaluate the impact of any program or intervention triggered when daily thresholds are reached. Citation: Benmarhnia T, Bailey Z, Kaiser D, Auger N, King N, Kaufman J. 2016. A difference-in-differences approach to assess the effect of a heat action plan on heat-related mortality, and differences in effectiveness according to sex, age, and socioeconomic status (Montreal, Quebec). Environ Health Perspect 124:1694-1699; http://dx.doi.org/10.1289/EHP203.

Published
2016

42. Dimensionality Reduction for Clustering and Cluster Tracking of Cytometry Data

Author

Putri, Givanna H., Read, Mark N., Koprinska, Irena, Ashhurst, Thomas M., King, Nicholas J. C., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Tetko, Igor V., editor, Kůrková, Věra, editor, Karpov, Pavel, editor, and Theis, Fabian, editor

Published
2019
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46. Lockdown texts

Author

Fitzgerald, Des, Ashcroft, Richard, Hollin, Greg, Karkazis, Katrina, King, Nicholas B., Landecker, Hannah, Langlitz, Nicolas, Lentzos, Filippa, Meyers, Todd, Niewöhner, Jörg, Novas, Carlos, Pollock, Anne, Rose, Nikolas, Silverman, Chloe, Stevens, Hallam, Subramaniam, Banu, Wahlberg, Ayo, and Wilson, Elizabeth A.

Published
2020
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47. Ebola, 1995/2014

Author

King, Nicholas B

Abstract

Nicholas B. King looks back at the dialectics of confidence and paranoia in the Ebola outbreaks of 1995 and 2014.

Published
2015

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