arXiv subjects

Katherine Chou

Publications and source records attributed to Katherine Chou.

27 records · Page 2Linked to original sources

arXiv2023

ELIXR: Towards a general purpose X-ray artificial intelligence system through alignment of large language models and radiology vision encoders

In this work, we present an approach, which we call Embeddings for Language/Image-aligned X-Rays, or ELIXR, that leverages a language-aligned image encoder combined or grafted onto a fixed LLM, PaLM 2, to perform a broad range of chest X-ray tasks. We train this lightweight adapter architecture using images paired with corresponding free-text radiology reports from the MIMIC-CXR dataset. ELIXR achieved state-of-the-art performance on zero-shot chest X-ray (CXR) classification (mean AUC of 0.850 across 13 findings), data-efficient CXR classification (mean AUCs of 0.893 and 0.898 across five findings (atelectasis, cardiomegaly, consolidation, pleural effusion, and pulmonary edema) for 1% (~2,200 images) and 10% (~22,000 images) training data), and semantic search (0.76 normalized discounted cumulative gain (NDCG) across nineteen queries, including perfect retrieval on twelve of them). Compared to existing data-efficient methods including supervised contrastive learning (SupCon), ELIXR required two orders of magnitude less data to reach similar performance. ELIXR also showed promise on CXR vision-language tasks, demonstrating overall accuracies of 58.7% and 62.5% on visual question answering and report quality assurance tasks, respectively. These results suggest that ELIXR is a robust and versatile approach to CXR AI.

cs.CV↗

arXiv2022

Large Language Models Encode Clinical Knowledge

Large language models (LLMs) have demonstrated impressive capabilities in natural language understanding and generation, but the quality bar for medical and clinical applications is high. Today, attempts to assess models' clinical knowledge typically rely on automated evaluations on limited benchmarks. There is no standard to evaluate model predictions and reasoning across a breadth of tasks. To address this, we present MultiMedQA, a benchmark combining six existing open question answering datasets spanning professional medical exams, research, and consumer queries; and HealthSearchQA, a new free-response dataset of medical questions searched online. We propose a framework for human evaluation of model answers along multiple axes including factuality, precision, possible harm, and bias. In addition, we evaluate 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, MMLU clinical topics), including 67.6% accuracy on MedQA (US Medical License Exam questions), surpassing prior state-of-the-art by over 17%. However, human evaluation reveals key gaps in Flan-PaLM responses. 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, recall of knowledge, and medical reasoning improve with model scale and instruction prompt tuning, suggesting the potential utility of LLMs in medicine. Our human evaluations reveal important limitations of today's models, reinforcing the importance of both evaluation frameworks and method development in creating safe, helpful LLM models for clinical applications.

cs.CL↗

arXiv2022

Enabling faster and more reliable sonographic assessment of gestational age through machine learning

Fetal ultrasounds are an essential part of prenatal care and can be used to estimate gestational age (GA). Accurate GA assessment is important for providing appropriate prenatal care throughout pregnancy and identifying complications such as fetal growth disorders. Since derivation of GA from manual fetal biometry measurements (head, abdomen, femur) are operator-dependent and time-consuming, there have been a number of research efforts focused on using artificial intelligence (AI) models to estimate GA using standard biometry images, but there is still room to improve the accuracy and reliability of these AI systems for widescale adoption. To improve GA estimates, without significant change to provider workflows, we leverage AI to interpret standard plane ultrasound images as well as 'fly-to' ultrasound videos, which are 5-10s videos automatically recorded as part of the standard of care before the still image is captured. We developed and validated three AI models: an image model using standard plane images, a video model using fly-to videos, and an ensemble model (combining both image and video). All three were statistically superior to standard fetal biometry-based GA estimates derived by expert sonographers, the ensemble model has the lowest mean absolute error (MAE) compared to the clinical standard fetal biometry (mean difference: -1.51 $\pm$ 3.96 days, 95% CI [-1.9, -1.1]) on a test set that consisted of 404 participants. We showed that our models outperform standard biometry by a more substantial margin on fetuses that were small for GA. Our AI models have the potential to empower trained operators to estimate GA with higher accuracy while reducing the amount of time required and user variability in measurement acquisition.

cs.LG↗

arXiv2022

AI system for fetal ultrasound in low-resource settings

Despite considerable progress in maternal healthcare, maternal and perinatal deaths remain high in low-to-middle income countries. Fetal ultrasound is an important component of antenatal care, but shortage of adequately trained healthcare workers has limited its adoption. We developed and validated an artificial intelligence (AI) system that uses novice-acquired "blind sweep" ultrasound videos to estimate gestational age (GA) and fetal malpresentation. We further addressed obstacles that may be encountered in low-resourced settings. Using a simplified sweep protocol with real-time AI feedback on sweep quality, we have demonstrated the generalization of model performance to minimally trained novice ultrasound operators using low cost ultrasound devices with on-device AI integration. The GA model was non-inferior to standard fetal biometry estimates with as few as two sweeps, and the fetal malpresentation model had high AUC-ROCs across operators and devices. Our AI models have the potential to assist in upleveling the capabilities of lightly trained ultrasound operators in low resource settings.

cs.LG↗

arXiv2021

Vaccine Search Patterns Provide Insights into Vaccination Intent

Despite ample supply of COVID-19 vaccines, the proportion of fully vaccinated individuals remains suboptimal across much of the US. Rapid vaccination of additional people will prevent new infections among both the unvaccinated and the vaccinated, thus saving lives. With the rapid rollout of vaccination efforts this year, the internet has become a dominant source of information about COVID-19 vaccines, their safety and efficacy, and their availability. We sought to evaluate whether trends in internet searches related to COVID-19 vaccination - as reflected by Google's Vaccine Search Insights (VSI) index - could be used as a marker of population-level interest in receiving a vaccination. We found that between January and August of 2021: 1) Google's weekly VSI index was associated with the number of new vaccinations administered in the subsequent three weeks, and 2) the average VSI index in earlier months was strongly correlated (up to r = 0.89) with vaccination rates many months later. Given these results, we illustrate an approach by which data on search interest may be combined with other available data to inform local public health outreach and vaccination efforts. These results suggest that the VSI index may be useful as a leading indicator of population-level interest in or intent to obtain a COVID-19 vaccine, especially early in the vaccine deployment efforts. These results may be relevant to current efforts to administer COVID-19 vaccines to unvaccinated individuals, to newly eligible children, and to those eligible to receive a booster shot. More broadly, these results highlight the opportunities for anonymized and aggregated internet search data, available in near real-time, to inform the response to public health emergencies.

cs.SI↗

arXiv2021

Deep learning for detecting pulmonary tuberculosis via chest radiography: an international study across 10 countries

Tuberculosis (TB) is a top-10 cause of death worldwide. Though the WHO recommends chest radiographs (CXRs) for TB screening, the limited availability of CXR interpretation is a barrier. We trained a deep learning system (DLS) to detect active pulmonary TB using CXRs from 9 countries across Africa, Asia, and Europe, and utilized large-scale CXR pretraining, attention pooling, and noisy student semi-supervised learning. Evaluation was on (1) a combined test set spanning China, India, US, and Zambia, and (2) an independent mining population in South Africa. Given WHO targets of 90% sensitivity and 70% specificity, the DLS's operating point was prespecified to favor sensitivity over specificity. On the combined test set, the DLS's ROC curve was above all 9 India-based radiologists, with an AUC of 0.90 (95%CI 0.87-0.92). The DLS's sensitivity (88%) was higher than the India-based radiologists (75% mean sensitivity), p<0.001 for superiority; and its specificity (79%) was non-inferior to the radiologists (84% mean specificity), p=0.004. Similar trends were observed within HIV positive and sputum smear positive sub-groups, and in the South Africa test set. We found that 5 US-based radiologists (where TB isn't endemic) were more sensitive and less specific than the India-based radiologists (where TB is endemic). The DLS also remained non-inferior to the US-based radiologists. In simulations, using the DLS as a prioritization tool for confirmatory testing reduced the cost per positive case detected by 40-80% compared to using confirmatory testing alone. To conclude, our DLS generalized to 5 countries, and merits prospective evaluation to assist cost-effective screening efforts in radiologist-limited settings. Operating point flexibility may permit customization of the DLS to account for site-specific factors such as TB prevalence, demographics, clinical resources, and customary practice patterns.

eess.IV↗

arXiv2021

Impacts of Social Distancing Policies on Mobility and COVID-19 Case Growth in the US

Social distancing remains an important strategy to combat the COVID-19 pandemic in the United States. However, the impacts of specific state-level policies on mobility and subsequent COVID-19 case trajectories have not been completely quantified. Using anonymized and aggregated mobility data from opted-in Google users, we found that state-level emergency declarations resulted in a 9.9% reduction in time spent away from places of residence. Implementation of one or more social distancing policies resulted in an additional 24.5% reduction in mobility the following week, and subsequent shelter-in-place mandates yielded an additional 29.0% reduction. Decreases in mobility were associated with substantial reductions in case growth 2 to 4 weeks later. For example, a 10% reduction in mobility was associated with a 17.5% reduction in case growth 2 weeks later. Given the continued reliance on social distancing policies to limit the spread of COVID-19, these results may be helpful to public health officials trying to balance infection control with the economic and social consequences of these policies.

q-bio.PE↗

arXiv2018

Speech recognition for medical conversations

In this work we explored building automatic speech recognition models for transcribing doctor patient conversation. We collected a large scale dataset of clinical conversations ($14,000$ hr), designed the task to represent the real word scenario, and explored several alignment approaches to iteratively improve data quality. We explored both CTC and LAS systems for building speech recognition models. The LAS was more resilient to noisy data and CTC required more data clean up. A detailed analysis is provided for understanding the performance for clinical tasks. Our analysis showed the speech recognition models performed well on important medical utterances, while errors occurred in causal conversations. Overall we believe the resulting models can provide reasonable quality in practice.

cs.CL↗

arXiv2018

Scalable and accurate deep learning for electronic health records

Predictive modeling with electronic health record (EHR) data is anticipated to drive personalized medicine and improve healthcare quality. Constructing predictive statistical models typically requires extraction of curated predictor variables from normalized EHR data, a labor-intensive process that discards the vast majority of information in each patient's record. We propose a representation of patients' entire, raw EHR records based on the Fast Healthcare Interoperability Resources (FHIR) format. We demonstrate that deep learning methods using this representation are capable of accurately predicting multiple medical events from multiple centers without site-specific data harmonization. We validated our approach using de-identified EHR data from two U.S. academic medical centers with 216,221 adult patients hospitalized for at least 24 hours. In the sequential format we propose, this volume of EHR data unrolled into a total of 46,864,534,945 data points, including clinical notes. Deep learning models achieved high accuracy for tasks such as predicting in-hospital mortality (AUROC across sites 0.93-0.94), 30-day unplanned readmission (AUROC 0.75-0.76), prolonged length of stay (AUROC 0.85-0.86), and all of a patient's final discharge diagnoses (frequency-weighted AUROC 0.90). These models outperformed state-of-the-art traditional predictive models in all cases. We also present a case-study of a neural-network attribution system, which illustrates how clinicians can gain some transparency into the predictions. We believe that this approach can be used to create accurate and scalable predictions for a variety of clinical scenarios, complete with explanations that directly highlight evidence in the patient's chart.

cs.CY↗