Vivek Natarajan
Vivek Natarajan is a Research Scientist at Google Health AI advancing biomedical AI to help scale world class healthcare to everyone. Vivek is particularly interested in building large language models and multimodal foundation models for biomedical applications and leads the Google Brain moonshot behind Med-PaLM, Google's flagship medical large language model. Med-PaLM has been featured in The Scientific American, The Economist, STAT News, CNBC, Forbes, New Scientist among others.
More here - https://sites.research.google/med-palm/
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Towards Conversational Diagnostic AI
Anil Palepu
Khaled Saab
Jan Freyberg
Ryutaro Tanno
Amy Wang
Brenna Li
Nenad Tomašev
Le Hou
Albert Webson
Kavita Kulkarni
Sara Mahdavi
Juro Gottweis
Joelle Barral
Kat Chou
Arxiv (2024) (to appear)
Preview abstract
At the heart of medicine lies the physician-patient dialogue, where skillful history-taking paves the way for accurate diagnosis, effective management, and enduring trust. Artificial Intelligence (AI) systems capable of diagnostic dialogue could increase accessibility, consistency, and quality of care. However, approximating clinicians' expertise is an outstanding grand challenge. Here, we introduce AMIE (Articulate Medical Intelligence Explorer), a Large Language Model (LLM) based AI system optimized for diagnostic dialogue.
AMIE uses a novel self-play based simulated environment with automated feedback mechanisms for scaling learning across diverse disease conditions, specialties, and contexts. We designed a framework for evaluating clinically-meaningful axes of performance including history-taking, diagnostic accuracy, management reasoning, communication skills, and empathy. We compared AMIE's performance to that of primary care physicians (PCPs) in a randomized, double-blind crossover study of text-based consultations with validated patient actors in the style of an Objective Structured Clinical Examination (OSCE). The study included 149 case scenarios from clinical providers in Canada, the UK, and India, 20 PCPs for comparison with AMIE, and evaluations by specialist physicians and patient actors. AMIE demonstrated greater diagnostic accuracy and superior performance on 28 of 32 axes according to specialist physicians and 24 of 26 axes according to patient actors. Our research has several limitations and should be interpreted with appropriate caution. Clinicians were limited to unfamiliar synchronous text-chat which permits large-scale LLM-patient interactions but is not representative of usual clinical practice. While further research is required before AMIE could be translated to real-world settings, the results represent a milestone towards conversational diagnostic AI.
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An intentional approach to managing bias in embedding models
Atilla P. Kiraly
Jungyeon Park
Rory Pilgrim
Charles Lau
Heather Cole-Lewis
Shravya Shetty
Leo Anthony Celi
The Lancet Digital Health, vol. 6 (2024), E126-E130
Preview abstract
Advances in machine learning for health care have brought concerns about bias from the research community; specifically, the introduction, perpetuation, or exacerbation of care disparities. Reinforcing these concerns is the finding that medical images often reveal signals about sensitive attributes in ways that are hard to pinpoint by both algorithms and people. This finding raises a question about how to best design general purpose pretrained embeddings (GPPEs, defined as embeddings meant to support a broad array of use cases) for building downstream models that are free from particular types of bias. The downstream model should be carefully evaluated for bias, and audited and improved as appropriate. However, in our view, well intentioned attempts to prevent the upstream components—GPPEs—from learning sensitive attributes can have unintended consequences on the downstream models. Despite producing a veneer of technical neutrality, the resultant end-to-end system might still be biased or poorly performing. We present reasons, by building on previously published data, to support the reasoning that GPPEs should ideally contain as much information as the original data contain, and highlight the perils of trying to remove sensitive attributes from a GPPE. We also emphasise that downstream prediction models trained for specific tasks and settings, whether developed using GPPEs or not, should be carefully designed and evaluated to avoid bias that makes models vulnerable to issues such as distributional shift. These evaluations should be done by a diverse team, including social scientists, on a diverse cohort representing the full breadth of the patient population for which the final model is intended.
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Towards Generalist Biomedical AI
Danny Driess
Andrew Carroll
Chuck Lau
Ryutaro Tanno
Ira Ktena
Anil Palepu
Basil Mustafa
Simon Kornblith
Philip Mansfield
Sushant Prakash
Renee Wong
Sunny Virmani
Sara Mahdavi
Bradley Green
Ewa Dominowska
Joelle Barral
Pete Florence
NEJM AI (2024)
Preview abstract
BACKGROUND: Medicine is inherently multimodal, requiring the simultaneous interpretation and integration of insights between many data modalities spanning text, imaging, genomics, and more. Generalist biomedical artificial intelligence systems that flexibly encode, integrate, and interpret these data might better enable impactful applications ranging from scientific discovery to care delivery.
METHODS: To catalyze development of these models, we curated MultiMedBench, a new multimodal biomedical benchmark. MultiMedBench encompasses 14 diverse tasks, such as medical question answering, mammography and dermatology image interpretation, radiology report generation and summarization, and genomic variant calling. We then introduced Med-PaLM Multimodal (Med-PaLM M), our proof of concept for a generalist biomedical AI system that flexibly encodes and interprets biomedical data including clinical language, imaging, and genomics with the same set of model weights. To further probe the capabilities and limitations of Med-PaLM M, we conducted a radiologist evaluation of model-generated (and human) chest x-ray reports.
RESULTS: We observed encouraging performance across model scales. Med-PaLM M reached performance competitive with or exceeding the state of the art on all MultiMedBench tasks, often surpassing specialist models by a wide margin. In a side-by-side ranking on 246 retrospective chest x-rays, clinicians expressed a pairwise preference for Med-PaLM Multimodal reports over those produced by radiologists in up to 40.50% of cases, suggesting potential clinical utility.
CONCLUSIONS: Although considerable work is needed to validate these models in real-world cases and understand if cross-modality generalization is possible, our results represent a milestone toward the development of generalist biomedical artificial intelligence systems.
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Preview abstract
Artificial Intelligence (AI) holds the promise of transforming healthcare by improving patient outcomes, increasing accessibility and efficiency, and decreasing the cost of care. Realizing this vision of a healthier world for everyone everywhere requires partnerships and trust between healthcare systems, clinicians, payers, technology companies, pharmaceutical companies, and governments to drive innovations in machine learning and artificial intelligence to patients. Google is one example of a technology company that is partnering with healthcare systems, clinicians, and researchers to develop technology solutions that will directly improve the lives of patients. In this chapter we share landmark trials of the use of AI in healthcare. We also describe the application of our novel system of organizing information to unify data in electronic health records (EHRs) and bring an integrated view of patient records to clinicians. We discuss our consumer focused innovation in dermatology to help guide search journeys for personalized information about skin conditions. Finally, we share a perspective on how to embed ethics and a concern for all patients into the development of AI.
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Robust and data-efficient generalization of self-supervised machine learning for diagnostic imaging
Laura Anne Culp
Jan Freyberg
Basil Mustafa
Sebastien Baur
Simon Kornblith
Ting Chen
Patricia MacWilliams
Sara Mahdavi
Megan Zoë Walker
Aaron Loh
Cameron Chen
Scott Mayer McKinney
Zach William Beaver
Fiona Keleher Ryan
Mozziyar Etemadi
Umesh Telang
Lily Hao Yi Peng
Geoffrey Everest Hinton
Mohammad Norouzi
Nature Biomedical Engineering (2023)
Preview abstract
Machine-learning models for medical tasks can match or surpass the performance of clinical experts. However, in settings differing from those of the training dataset, the performance of a model can deteriorate substantially. Here we report a representation-learning strategy for machine-learning models applied to medical-imaging tasks that mitigates such ‘out of distribution’ performance problem and that improves model robustness and training efficiency. The strategy, which we named REMEDIS (for ‘Robust and Efficient Medical Imaging with Self-supervision’), combines large-scale supervised transfer learning on natural images and intermediate contrastive self-supervised learning on medical images and requires minimal task-specific customization. We show the utility of REMEDIS in a range of diagnostic-imaging tasks covering six imaging domains and 15 test datasets, and by simulating three realistic out-of-distribution scenarios. REMEDIS improved in-distribution diagnostic accuracies up to 11.5% with respect to strong supervised baseline models, and in out-of-distribution settings required only 1–33% of the data for retraining to match the performance of supervised models retrained using all available data. REMEDIS may accelerate the development lifecycle of machine-learning models for medical imaging.
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Towards Accurate Differential Diagnosis with Large Language Models
Daniel McDuff
Anil Palepu
Amy Wang
Yash Sharma
Kavita Kulkarni
Le Hou
Sara Mahdavi
Sushant Prakash
Anupam Pathak
Shwetak Patel
Ewa Dominowska
Juro Gottweis
Joelle Barral
Kat Chou
Jake Sunshine
Arxiv (2023)
Preview abstract
An accurate differential diagnosis (DDx) is a cornerstone of medical care, often reached through an iterative process of interpretation that combines clinical history, physical examination, investigations and procedures. Interactive interfaces powered by Large Language Models (LLMs) present new opportunities to both assist and automate aspects of this process. In this study, we introduce an LLM optimized for diagnostic reasoning, and evaluate its ability to generate a DDx alone or as an aid to clinicians. 20 clinicians evaluated 302 challenging, real-world medical cases sourced from the New England Journal of Medicine (NEJM) case reports. Each case report was read by two clinicians, who were randomized to one of two assistive conditions: either assistance from search engines and standard medical resources, or LLM assistance in addition to these tools. All clinicians provided a baseline, unassisted DDx prior to using the respective assistive tools. Our LLM for DDx exhibited standalone performance that exceeded that of unassisted clinicians (top-10 accuracy 59.1% vs 33.6%, [p = 0.04]). Comparing the two assisted study arms, the DDx quality score was higher for clinicians assisted by our LLM (top-10 accuracy 51.7%) compared to clinicians without its assistance (36.1%) (McNemar's Test: 45.7, p < 0.01) and clinicians with search (44.4%) (4.75, p = 0.03). Further, clinicians assisted by our LLM arrived at more comprehensive differential lists than those without its assistance. Our study suggests that our LLM for DDx has potential to improve clinicians' diagnostic reasoning and accuracy in challenging cases, meriting further real-world evaluation for its ability to empower physicians and widen patients' access to specialist-level expertise.
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Enhancing diagnostic accuracy of medical AI systems via selective deferral to clinicians
Dj Dvijotham
Melih Barsbey
Sumedh Ghaisas
Robert Stanforth
Nick Pawlowski
Patricia Strachan
Zahra Ahmed
Yoram Bachrach
Laura Culp
Mayank Daswani
Jan Freyberg
Atilla Kiraly
Timo Kohlberger
Scott Mayer McKinney
Basil Mustafa
Krzysztof Geras
Jan Witowski
Zhi Zhen Qin
Jacob Creswell
Shravya Shetty
Terry Spitz
Taylan Cemgil
Nature Medicine (2023)
Preview abstract
AI systems trained using deep learning have been shown to achieve expert-level identification of diseases in multiple medical imaging settings1,2. While these results are impressive, they don’t accurately reflect the impact of deployment of such systems in a clinical context. Due to the safety-critical nature of this domain and the fact that AI systems are not perfect and can make inaccurate assessments, they are predominantly deployed as assistive tools for clinical experts3. Although clinicians routinely discuss the diagnostic nuances of medical images with each other, weighing human diagnostic confidence against that of an AI system remains a major unsolved barrier to collaborative decision-making4. Furthermore, it has been observed that diagnostic AI models have complementary strengths and weaknesses compared to clinical experts. Yet, complementarity and the assessment of relative confidence between the members of a diagnostic team has remained largely unexploited in how AI systems are currently used in medical settings5.
In this paper, we study the behavior of a team composed of diagnostic AI model(s) and clinician(s) in diagnosing disease. To go beyond the performance level of a standalone AI system, we develop a novel selective deferral algorithm that can learn to decide when to rely on a diagnostic AI model and when to defer to a clinical expert. Using this algorithm, we demonstrate that the composite AI+human system has enhanced accuracy (both sensitivity and specificity) relative to a human-only or an AI-only baseline. We decouple the development of the deferral AI model from training of the underlying diagnostic AI model(s). Development of the deferral AI model only requires i) the predictions of a model(s) on a tuning set of medical images (separate from the diagnostic AI models’ training data), ii) the diagnoses made by clinicians on these images and iii) the ground truth disease labels corresponding to those images.
Our extensive analysis shows that the selective deferral (SD) system exceeds the performance of either clinicians or AI alone in multiple clinical settings: breast and lung cancer screening. For breast cancer screening, double-reading with arbitration (two readers interpreting each mammogram invoking an arbitrator if needed) is a “gold standard” for performance, never previously exceeded using AI6. The SD system exceeds the accuracy of double-reading with arbitration in a large representative UK screening program (25% reduction in false positives despite equivalent true-positive detection and 66% reduction in the requirement for clinicians to read an image), as well as exceeding the performance of a standalone state-of-art AI system (40% reduction in false positives with equivalent detection of true positives). In a large US dataset the SD system exceeds the accuracy of single-reading by board-certified radiologists and a standalone state-of-art AI system (32% reduction in false positives despite equivalent detection of true positives and 55% reduction in the clinician workload required). The SD system further outperforms both clinical experts alone, and AI alone for the detection of lung cancer in low-dose Computed Tomography images from a large national screening study, with 11% reduction in false positives while maintaining sensitivity given 93% reduction in clinician workload required. Furthermore, the SD system allows controllable trade-offs between sensitivity and specificity and can be tuned to target either specificity or sensitivity as desired for a particular clinical application, or a combination of both.
The system generalizes to multiple distribution shifts, retaining superiority to both the AI system alone and human experts alone. We demonstrate that the SD system retains performance gains even on clinicians not present in the training data for the deferral AI. Furthermore, we test the SD system on a new population where the standalone AI system’s performance significantly degrades. We showcase the few-shot adaptation capability of the SD system by demonstrating that the SD system can obtain superiority to both the standalone AI system and the clinician on the new population after being trained on only 40 cases from the new population.
Our comprehensive assessment demonstrates that a selective deferral system could significantly improve clinical outcomes in multiple medical imaging applications, paving the way for higher performance clinical AI systems that can leverage the complementarity between clinical experts and medical AI tools.
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Large Language Models Encode Clinical Knowledge
Sara Mahdavi
Jason Wei
Hyung Won Chung
Nathan Scales
Ajay Tanwani
Heather Cole-Lewis
Perry Payne
Martin Seneviratne
Paul Gamble
Abubakr Abdelrazig Hassan Babiker
Nathanael Schaerli
Philip Mansfield
Dina Demner-Fushman
Katherine Chou
Juraj Gottweis
Nenad Tomašev
Alvin Rajkomar
Joelle Barral
Nature (2023)
Preview abstract
Large language models (LLMs) have demonstrated impressive capabilities, but the bar for clinical applications is high. Attempts to assess the clinical knowledge of models typically rely on automated evaluations based on limited benchmarks. Here, to address these limitations, we present MultiMedQA, a benchmark combining six existing medical question answering datasets spanning professional medicine, research and consumer queries and a new dataset of medical questions searched online, HealthSearchQA. We propose a human evaluation framework for model answers along multiple axes including factuality, comprehension, reasoning, possible harm and bias. In addition, we evaluate Pathways Language Model (PaLM, a 540-billion parameter LLM) and its instruction-tuned variant, Flan-PaLM on MultiMedQA. Using a combination of prompting strategies, Flan-PaLM achieves state-of-the-art accuracy on every MultiMedQA multiple-choice dataset (MedQA, MedMCQA, PubMedQA and Measuring Massive Multitask Language Understanding (MMLU) clinical topics), including 67.6% accuracy on MedQA (US Medical Licensing Exam-style questions), surpassing the prior state of the art by more than 17%. However, human evaluation reveals key gaps. To resolve this, we introduce instruction prompt tuning, a parameter-efficient approach for aligning LLMs to new domains using a few exemplars. The resulting model, Med-PaLM, performs encouragingly, but remains inferior to clinicians. We show that comprehension, knowledge recall and reasoning improve with model scale and instruction prompt tuning, suggesting the potential utility of LLMs in medicine. Our human evaluations reveal limitations of today’s models, reinforcing the importance of both evaluation frameworks and method development in creating safe, helpful LLMs for clinical applications.
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Towards Physician-Level Medical Question Answering with Large Language Models
Juro Gottweis
Le Hou
Kevin Clark
Heather Cole-Lewis
Amy Wang
Sami Lachgar
Philip Mansfield
Sushant Prakash
Bradley Green
Ewa Dominowska
Nenad Tomašev
Renee Wong
Sara Mahdavi
Joelle Barral
Arxiv (2023) (to appear)
Preview abstract
Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge.
Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach.
Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets.
We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations.
While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.
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Consensus, dissensus and synergy between clinicians and specialist foundation models in radiology report generation
Ryutaro Tanno
David Barrett
Sumedh Ghaisas
Sumanth Dathathri
Abi See
Johannes Welbl
Rhys May
Roy Lee
SiWai Man
Zahra Ahmed
Sara Mahdavi
Joelle Barral
Ali Eslami
Danielle Belgrave
Shravya Shetty
Po-Sen Huang
Ira Ktena
Arxiv (2023)
Preview abstract
Radiology reports are an instrumental part of modern medicine, informing key clinical decisions such as diagnosis and treatment. The worldwide shortage of radiologists, however, restricts access to expert care and imposes heavy workloads, contributing to avoidable errors and delays in report delivery. While recent progress in automated report generation with vision-language models offer clear potential in ameliorating the situation, the path to real-world adoption has been stymied by the challenge of evaluating the clinical quality of AI-generated reports. In this study, we build a state-of-the-art report generation system for chest radiographs, Flamingo-CXR, by fine-tuning a well-known vision-language foundation model on radiology data. To evaluate the quality of the AI-generated reports, a group of 16 certified radiologists provide detailed evaluations of AI-generated and human written reports for chest X-rays from an intensive care setting in the United States and an inpatient setting in India. At least one radiologist (out of two per case) preferred the AI report to the ground truth report in over 60% of cases for both datasets. Amongst the subset of AI-generated reports that contain errors, the most frequently cited reasons were related to the location and finding, whereas for human written reports, most mistakes were related to severity and finding. This disparity suggested potential complementarity between our AI system and human experts, prompting us to develop an assistive scenario in which Flamingo-CXR generates a first-draft report, which is subsequently revised by a clinician. This is the first demonstration of clinician-AI collaboration for report writing, and the resultant reports are assessed to be equivalent or preferred by at least one radiologist to reports written by experts alone in 80% of in-patient cases and 60% of intensive care cases.
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Diagnosing failures of fairness transfer across distribution shift in real-world medical settings
Sanmi Koyejo
Eva Schnider
Krista Opsahl-Ong
Alex Brown
Christina Chen
Silvia Chiappa
Proceedings of Neural Information Processing Systems 2022 (2022)
Preview abstract
Diagnosing and mitigating changes in model fairness under distribution shift is an important component of the safe deployment of machine learning in healthcare settings. Importantly, the success of any mitigation strategy strongly depends on the structure of the shift. Despite this, there has been little discussion of how to empirically assess the structure of a distribution shift that one is encountering in practice. In this work, we adopt a causal framing to motivate conditional independence tests as a key tool for characterizing distribution shifts. Using our approach in two medical applications, we show that this knowledge can help diagnose failures of fairness transfer, including cases where real-world shifts are more complex than is often assumed in the literature. Based on these results, we discuss potential remedies at each step of the machine learning pipeline.
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Does Your Dermatology Classifier Know What It Doesn't Know? Detecting the Long-Tail of Unseen Conditions
Aaron Loh
Basil Mustafa
Nick Pawlowski
Jan Freyberg
Zach William Beaver
Nam Vo
Peggy Bui
Samantha Winter
Patricia MacWilliams
Umesh Telang
Taylan Cemgil
Medical Imaging Analysis (2021)
Preview abstract
Supervised deep learning models have proven to be highly effective in classification of dermatological conditions. These models rely on the availability of abundant labeled training examples. However, in the real world, many dermatological conditions are individually too infrequent for per-condition classification with supervised learning. Although individually infrequent, these conditions may collectively be common and therefore are clinically significant in aggregate. To avoid models generating erroneous outputs on such examples, there remains a considerable unmet need for deep learning systems that can better detect such infrequent conditions. These infrequent `outlier' conditions are seen very rarely (or not at all) during training. In this paper, we frame this task as an out-of-distribution (OOD) detection problem. We set up a benchmark ensuring that outlier conditions are disjoint between model train, validation, and test sets. Unlike most traditional OOD benchmarks which detect dataset distribution shift, we aim at detecting semantic differences, often referred to as near-OOD detection which is a more difficult task. We propose a novel hierarchical outlier detection (HOD) approach, which assigns multiple abstention classes for each training outlier class and jointly performs a coarse classification of inliers \vs{} outliers, along with fine-grained classification of the individual classes. We demonstrate that the proposed HOD outperforms existing techniques for outlier exposure based OOD detection. We also use different state-of-the-art representation learning approaches (BiT-JFT, SimCLR, MICLe) to improve OOD performance and demonstrate the effectiveness of HOD loss for them.
Further, we explore different ensembling strategies for OOD detection and propose a diverse ensemble selection process for the best result. We also performed a subgroup analysis over conditions of varying risk levels and different skin types to investigate how OOD performance changes over each subgroup and demonstrated the gains of our framework in comparison to baselines. Furthermore, we go beyond traditional performance metrics and introduce a cost metric to approximate downstream clinical impact. We used this cost metric to compare the proposed method against the baseline, thereby making a stronger case for its effectiveness in real-world deployment scenarios.
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Supervised Transfer Learning at Scale for Medical Imaging
Aaron Loh
Basil Mustafa
Jan Freyberg
Patricia MacWilliams
Megan Wilson
Scott Mayer McKinney
Peggy Bui
Umesh Telang
ArXiV (2021)
Preview abstract
Transfer learning is a standard building block of successful medical imaging models, yet previous efforts suggest that at limited scale of pre-training data and model capacity, benefits of transfer learning to medical imaging are insubstantial. In this work, we explore whether scaling up pre-training can help improve transfer to medical tasks. In particular, we show that when using the Big Transfer recipe to further scale up pre-training, we can indeed considerably improve transfer performance across three popular yet diverse medical imaging tasks - interpretation of chest radiographs, breast cancer detection from mammograms and skin condition detection from smartphone images. Despite pre-training on unrelated source domains, we show that scaling up the model capacity and pre-training data yields performance improvements regardless of how much downstream medical data is available. In particular, we show suprisingly large improvements to zero-shot generalisation under distribution shift. Probing and quantifying other aspects of model performance relevant to medical imaging and healthcare, we demonstrate that these gains do not come at the expense of model calibration or fairness.
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Big Self-Supervised Models Advance Medical Image Classification
Basil Mustafa
Fiona Ryan
Zachary Beaver
Jan Freyberg
Jonathan Deaton
Aaron Loh
Simon Kornblith
Ting Chen
Mohammad Norouzi
International Conference on Computer Vision (2021)
Preview abstract
Self-supervised pretraining followed by supervised fine-tuning has seen success in image recognition, especially when labeled examples are scarce, but has received limited attention in medical image analysis. This paper studies the effectiveness of self-supervised learning as a pretraining strategy for medical image classification. We conduct experiments on two distinct tasks: dermatology skin condition classification from digital camera images and multi-label chest X-ray classification, and demonstrate that self-supervised learning on ImageNet, followed by additional self-supervised learning on unlabeled domain-specific medical images significantly improves the accuracy of medical image classifiers. We introduce a novel Multi-Instance Contrastive Learning (MICLe) method that uses multiple images of the underlying pathology per patient case, when available, to construct more informative positive pairs for self-supervised learning. Combining our contributions, we achieve an improvement of 6.7% in top-1 accuracy and an improvement of 1.1% in mean AUC on dermatology and chest X-ray classification respectively, outperforming strong supervised baselines pretrained on ImageNet. In addition, we show that big self-supervised models are robust to distribution shift and can learn efficiently with a small number of labeled medical images.
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A deep learning system for differential diagnosis of skin diseases
Clara Eng
David Way
Kang Lee
Peggy Bui
Kimberly Kanada
Guilherme de Oliveira Marinho
Jess Gallegos
Sara Gabriele
Vishakha Gupta
Nalini Singh
Lily Peng
Dennis Ai
Susan Huang
Carter Dunn
Nature Medicine (2020)
Preview abstract
Skin conditions affect 1.9 billion people. Because of a shortage of dermatologists, most cases are seen instead by general practitioners with lower diagnostic accuracy. We present a deep learning system (DLS) to provide a differential diagnosis of skin conditions using 16,114 de-identified cases (photographs and clinical data) from a teledermatology practice serving 17 sites. The DLS distinguishes between 26 common skin conditions, representing 80% of cases seen in primary care, while also providing a secondary prediction covering 419 skin conditions. On 963 validation cases, where a rotating panel of three board-certified dermatologists defined the reference standard, the DLS was non-inferior to six other dermatologists and superior to six primary care physicians (PCPs) and six nurse practitioners (NPs) (top-1 accuracy: 0.66 DLS, 0.63 dermatologists, 0.44 PCPs and 0.40 NPs). These results highlight the potential of the DLS to assist general practitioners in diagnosing skin conditions.
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Underspecification Presents Challenges for Credibility in Modern Machine Learning
Dan Moldovan
Babak Alipanahi
Alex Beutel
Christina Chen
Jon Deaton
Shaobo Hou
Ghassen Jerfel
Yian Ma
Akinori Mitani
Andrea Montanari
Christopher Nielsen
Thomas Osborne
Rajiv Raman
Kim Ramasamy
Martin Gamunu Seneviratne
Shannon Sequeira
Harini Suresh
Victor Veitch
Journal of Machine Learning Research (2020)
Preview abstract
ML models often exhibit unexpectedly poor behavior when they are deployed in real-world domains. We identify underspecification as a key reason for these failures. An ML pipeline is underspecified when it can return many predictors with equivalently strong held-out performance in the training domain. Underspecification is common in modern ML pipelines, such as those based on deep learning. Predictors returned by underspecified pipelines are often treated as equivalent based on their training domain performance, but we show here that such predictors can behave very differently in deployment domains. This ambiguity can lead to instability and poor model behavior in practice, and is a distinct failure mode from previously identified issues arising from structural mismatch between training and deployment domains. We show that this problem appears in a wide variety of practical ML pipelines, using examples from computer vision, medical imaging, natural language processing, clinical risk prediction based on electronic health records, and medical genomics. Our results show the need to explicitly account for underspecification in modeling pipelines that are intended for real-world deployment in any domain.
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Preview abstract
Class imbalance is a common problem in medical diagnosis, causing a standard classifier to be biased towards majority classes and ignore the importance of the rest. This is especially true for dermatology, a specialty with thousands of skin conditions but many of which rarely occur in the wild. Buoyed by recent advances, we explore meta-learning based few-shot learning approaches in skin condition recognition problem and propose an evaluation setup to fairly assess the real-world impact of such approaches. When compared to conventional class imbalance techniques, we find that the state-of-the-art few-shot learning methods are not as performant, but combining the two approaches using a novel ensemble leads to improvement in all-way classification, especially the rare classes. We conclude that the ensemble can be useful to address the class imbalance problem, yet progress here can further be accelerated by the use of real-world evaluation setups for benchmarking new methods.
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Preview abstract
Despite the recent success in applying supervised deep learning to medical imaging tasks, the problem of obtaining large, diverse and expert-annotated datasets required for development of high performant models remains particularly challenging. In this work, we explore the possibility of using Generative Adverserial Networks (GAN) to synthesize natural images with skin pathology. We propose DermGAN, an adaptation of the popular Pix2Pix architecture, to create synthetic images for a pre-specified skin condition, with varying size and location, and the underlying skin color. In a human turing test, we show that the synthetic images are not only visually similar to real images, but also embody the respective skin condition in dermatologists' eyes. Furthermore, when using synthetic images as a data augmentation technique for training a skin condition classifier, the model is non-inferior to the baseline model while demonstrating improved performance for rare conditions.
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