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Researcher profile

Marzyeh Ghassemi

Marzyeh Ghassemi contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine Learningcs.CYArtificial IntelligenceComputation and LanguageComputer Visioneess.IVApplicationsCryptography and SecurityDatabasesDigital LibrariesInformation RetrievalQuantitative Methods

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Published work

19 published item(s)

preprint2026arXiv

Croissant Baker: Metadata Generation for Discoverable, Governable, and Reusable ML Datasets

Croissant has emerged as the metadata standard for machine learning datasets, providing a structured, JSON-LD-based format that makes dataset discovery, automated ingestion, and reproducible analysis machine-checkable across ML platforms. Adoption has accelerated, and NeurIPS now requires Croissant metadata in every submission to its dataset tracks. Yet in practice Croissant generation usually starts with uploading data to a public platform, a path infeasible for governed and large local repositories that hold much of the high-value data ML increasingly relies on. We release Croissant Baker, a local-first, open-source command-line tool that generates validated Croissant metadata directly from a dataset directory through a modular handler registry. We evaluate Croissant Baker on over 140 datasets, scaling to MIMIC-IV at 886 million rows and 374 Parquet files. On held-out comparisons against producer-authored or standards-derived ground truth, Croissant Baker reaches 97-100% agreement across multiple domains.

0 citations0 reviewsNo code linkedOpen access
preprint2024arXiv

In the Name of Fairness: Assessing the Bias in Clinical Record De-identification

Data sharing is crucial for open science and reproducible research, but the legal sharing of clinical data requires the removal of protected health information from electronic health records. This process, known as de-identification, is often achieved through the use of machine learning algorithms by many commercial and open-source systems. While these systems have shown compelling results on average, the variation in their performance across different demographic groups has not been thoroughly examined. In this work, we investigate the bias of de-identification systems on names in clinical notes via a large-scale empirical analysis. To achieve this, we create 16 name sets that vary along four demographic dimensions: gender, race, name popularity, and the decade of popularity. We insert these names into 100 manually curated clinical templates and evaluate the performance of nine public and private de-identification methods. Our findings reveal that there are statistically significant performance gaps along a majority of the demographic dimensions in most methods. We further illustrate that de-identification quality is affected by polysemy in names, gender context, and clinical note characteristics. To mitigate the identified gaps, we propose a simple and method-agnostic solution by fine-tuning de-identification methods with clinical context and diverse names. Overall, it is imperative to address the bias in existing methods immediately so that downstream stakeholders can build high-quality systems to serve all demographic parties fairly.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Improving Dialogue Breakdown Detection with Semi-Supervised Learning

Building user trust in dialogue agents requires smooth and consistent dialogue exchanges. However, agents can easily lose conversational context and generate irrelevant utterances. These situations are called dialogue breakdown, where agent utterances prevent users from continuing the conversation. Building systems to detect dialogue breakdown allows agents to recover appropriately or avoid breakdown entirely. In this paper we investigate the use of semi-supervised learning methods to improve dialogue breakdown detection, including continued pre-training on the Reddit dataset and a manifold-based data augmentation method. We demonstrate the effectiveness of these methods on the Dialogue Breakdown Detection Challenge (DBDC) English shared task. Our submissions to the 2020 DBDC5 shared task place first, beating baselines and other submissions by over 12\% accuracy. In ablations on DBDC4 data from 2019, our semi-supervised learning methods improve the performance of a baseline BERT model by 2\% accuracy. These methods are applicable generally to any dialogue task and provide a simple way to improve model performance.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

A comparison of approaches to improve worst-case predictive model performance over patient subpopulations

Predictive models for clinical outcomes that are accurate on average in a patient population may underperform drastically for some subpopulations, potentially introducing or reinforcing inequities in care access and quality. Model training approaches that aim to maximize worst-case model performance across subpopulations, such as distributionally robust optimization (DRO), attempt to address this problem without introducing additional harms. We conduct a large-scale empirical study of DRO and several variations of standard learning procedures to identify approaches for model development and selection that consistently improve disaggregated and worst-case performance over subpopulations compared to standard approaches for learning predictive models from electronic health records data. In the course of our evaluation, we introduce an extension to DRO approaches that allows for specification of the metric used to assess worst-case performance. We conduct the analysis for models that predict in-hospital mortality, prolonged length of stay, and 30-day readmission for inpatient admissions, and predict in-hospital mortality using intensive care data. We find that, with relatively few exceptions, no approach performs better, for each patient subpopulation examined, than standard learning procedures using the entire training dataset. These results imply that when it is of interest to improve model performance for patient subpopulations beyond what can be achieved with standard practices, it may be necessary to do so via data collection techniques that increase the effective sample size or reduce the level of noise in the prediction problem.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Counterfactually Guided Off-policy Transfer in Clinical Settings

Domain shift, encountered when using a trained model for a new patient population, creates significant challenges for sequential decision making in healthcare since the target domain may be both data-scarce and confounded. In this paper, we propose a method for off-policy transfer by modeling the underlying generative process with a causal mechanism. We use informative priors from the source domain to augment counterfactual trajectories in the target in a principled manner. We demonstrate how this addresses data-scarcity in the presence of unobserved confounding. The causal parametrization of our sampling procedure guarantees that counterfactual quantities can be estimated from scarce observational target data, maintaining intuitive stability properties. Policy learning in the target domain is further regularized via the source policy through KL-divergence. Through evaluation on a simulated sepsis treatment task, our counterfactual policy transfer procedure significantly improves the performance of a learned treatment policy when assumptions of "no-unobserved confounding" are relaxed.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

If Influence Functions are the Answer, Then What is the Question?

Influence functions efficiently estimate the effect of removing a single training data point on a model's learned parameters. While influence estimates align well with leave-one-out retraining for linear models, recent works have shown this alignment is often poor in neural networks. In this work, we investigate the specific factors that cause this discrepancy by decomposing it into five separate terms. We study the contributions of each term on a variety of architectures and datasets and how they vary with factors such as network width and training time. While practical influence function estimates may be a poor match to leave-one-out retraining for nonlinear networks, we show they are often a good approximation to a different object we term the proximal Bregman response function (PBRF). Since the PBRF can still be used to answer many of the questions motivating influence functions, such as identifying influential or mislabeled examples, our results suggest that current algorithms for influence function estimation give more informative results than previous error analyses would suggest.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Improving the Fairness of Chest X-ray Classifiers

Deep learning models have reached or surpassed human-level performance in the field of medical imaging, especially in disease diagnosis using chest x-rays. However, prior work has found that such classifiers can exhibit biases in the form of gaps in predictive performance across protected groups. In this paper, we question whether striving to achieve zero disparities in predictive performance (i.e. group fairness) is the appropriate fairness definition in the clinical setting, over minimax fairness, which focuses on maximizing the performance of the worst-case group. We benchmark the performance of nine methods in improving classifier fairness across these two definitions. We find, consistent with prior work on non-clinical data, that methods which strive to achieve better worst-group performance do not outperform simple data balancing. We also find that methods which achieve group fairness do so by worsening performance for all groups. In light of these results, we discuss the utility of fairness definitions in the clinical setting, advocating for an investigation of the bias-inducing mechanisms in the underlying data generating process whenever possible.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Is Fairness Only Metric Deep? Evaluating and Addressing Subgroup Gaps in Deep Metric Learning

Deep metric learning (DML) enables learning with less supervision through its emphasis on the similarity structure of representations. There has been much work on improving generalization of DML in settings like zero-shot retrieval, but little is known about its implications for fairness. In this paper, we are the first to evaluate state-of-the-art DML methods trained on imbalanced data, and to show the negative impact these representations have on minority subgroup performance when used for downstream tasks. In this work, we first define fairness in DML through an analysis of three properties of the representation space -- inter-class alignment, intra-class alignment, and uniformity -- and propose finDML, the fairness in non-balanced DML benchmark to characterize representation fairness. Utilizing finDML, we find bias in DML representations to propagate to common downstream classification tasks. Surprisingly, this bias is propagated even when training data in the downstream task is re-balanced. To address this problem, we present Partial Attribute De-correlation (PARADE) to de-correlate feature representations from sensitive attributes and reduce performance gaps between subgroups in both embedding space and downstream metrics.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Learning Optimal Predictive Checklists

Checklists are simple decision aids that are often used to promote safety and reliability in clinical applications. In this paper, we present a method to learn checklists for clinical decision support. We represent predictive checklists as discrete linear classifiers with binary features and unit weights. We then learn globally optimal predictive checklists from data by solving an integer programming problem. Our method allows users to customize checklists to obey complex constraints, including constraints to enforce group fairness and to binarize real-valued features at training time. In addition, it pairs models with an optimality gap that can inform model development and determine the feasibility of learning sufficiently accurate checklists on a given dataset. We pair our method with specialized techniques that speed up its ability to train a predictive checklist that performs well and has a small optimality gap. We benchmark the performance of our method on seven clinical classification problems, and demonstrate its practical benefits by training a short-form checklist for PTSD screening. Our results show that our method can fit simple predictive checklists that perform well and that can easily be customized to obey a rich class of custom constraints.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Medical Dead-ends and Learning to Identify High-risk States and Treatments

Machine learning has successfully framed many sequential decision making problems as either supervised prediction, or optimal decision-making policy identification via reinforcement learning. In data-constrained offline settings, both approaches may fail as they assume fully optimal behavior or rely on exploring alternatives that may not exist. We introduce an inherently different approach that identifies possible "dead-ends" of a state space. We focus on the condition of patients in the intensive care unit, where a "medical dead-end" indicates that a patient will expire, regardless of all potential future treatment sequences. We postulate "treatment security" as avoiding treatments with probability proportional to their chance of leading to dead-ends, present a formal proof, and frame discovery as an RL problem. We then train three independent deep neural models for automated state construction, dead-end discovery and confirmation. Our empirical results discover that dead-ends exist in real clinical data among septic patients, and further reveal gaps between secure treatments and those that were administered.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Semi-Markov Offline Reinforcement Learning for Healthcare

Reinforcement learning (RL) tasks are typically framed as Markov Decision Processes (MDPs), assuming that decisions are made at fixed time intervals. However, many applications of great importance, including healthcare, do not satisfy this assumption, yet they are commonly modelled as MDPs after an artificial reshaping of the data. In addition, most healthcare (and similar) problems are offline by nature, allowing for only retrospective studies. To address both challenges, we begin by discussing the Semi-MDP (SMDP) framework, which formally handles actions of variable timings. We next present a formal way to apply SMDP modifications to nearly any given value-based offline RL method. We use this theory to introduce three SMDP-based offline RL algorithms, namely, SDQN, SDDQN, and SBCQ. We then experimentally demonstrate that only these SMDP-based algorithms learn the optimal policy in variable-time environments, whereas their MDP counterparts do not. Finally, we apply our new algorithms to a real-world offline dataset pertaining to warfarin dosing for stroke prevention and demonstrate similar results.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

The Road to Explainability is Paved with Bias: Measuring the Fairness of Explanations

Machine learning models in safety-critical settings like healthcare are often blackboxes: they contain a large number of parameters which are not transparent to users. Post-hoc explainability methods where a simple, human-interpretable model imitates the behavior of these blackbox models are often proposed to help users trust model predictions. In this work, we audit the quality of such explanations for different protected subgroups using real data from four settings in finance, healthcare, college admissions, and the US justice system. Across two different blackbox model architectures and four popular explainability methods, we find that the approximation quality of explanation models, also known as the fidelity, differs significantly between subgroups. We also demonstrate that pairing explainability methods with recent advances in robust machine learning can improve explanation fairness in some settings. However, we highlight the importance of communicating details of non-zero fidelity gaps to users, since a single solution might not exist across all settings. Finally, we discuss the implications of unfair explanation models as a challenging and understudied problem facing the machine learning community.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Reading Race: AI Recognises Patient's Racial Identity In Medical Images

Background: In medical imaging, prior studies have demonstrated disparate AI performance by race, yet there is no known correlation for race on medical imaging that would be obvious to the human expert interpreting the images. Methods: Using private and public datasets we evaluate: A) performance quantification of deep learning models to detect race from medical images, including the ability of these models to generalize to external environments and across multiple imaging modalities, B) assessment of possible confounding anatomic and phenotype population features, such as disease distribution and body habitus as predictors of race, and C) investigation into the underlying mechanism by which AI models can recognize race. Findings: Standard deep learning models can be trained to predict race from medical images with high performance across multiple imaging modalities. Our findings hold under external validation conditions, as well as when models are optimized to perform clinically motivated tasks. We demonstrate this detection is not due to trivial proxies or imaging-related surrogate covariates for race, such as underlying disease distribution. Finally, we show that performance persists over all anatomical regions and frequency spectrum of the images suggesting that mitigation efforts will be challenging and demand further study. Interpretation: We emphasize that model ability to predict self-reported race is itself not the issue of importance. However, our findings that AI can trivially predict self-reported race -- even from corrupted, cropped, and noised medical images -- in a setting where clinical experts cannot, creates an enormous risk for all model deployments in medical imaging: if an AI model secretly used its knowledge of self-reported race to misclassify all Black patients, radiologists would not be able to tell using the same data the model has access to.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

A Comprehensive Evaluation of Multi-task Learning and Multi-task Pre-training on EHR Time-series Data

Multi-task learning (MTL) is a machine learning technique aiming to improve model performance by leveraging information across many tasks. It has been used extensively on various data modalities, including electronic health record (EHR) data. However, despite significant use on EHR data, there has been little systematic investigation of the utility of MTL across the diverse set of possible tasks and training schemes of interest in healthcare. In this work, we examine MTL across a battery of tasks on EHR time-series data. We find that while MTL does suffer from common negative transfer, we can realize significant gains via MTL pre-training combined with single-task fine-tuning. We demonstrate that these gains can be achieved in a task-independent manner and offer not only minor improvements under traditional learning, but also notable gains in a few-shot learning context, thereby suggesting this could be a scalable vehicle to offer improved performance in important healthcare contexts.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

CheXpert++: Approximating the CheXpert labeler for Speed,Differentiability, and Probabilistic Output

It is often infeasible or impossible to obtain ground truth labels for medical data. To circumvent this, one may build rule-based or other expert-knowledge driven labelers to ingest data and yield silver labels absent any ground-truth training data. One popular such labeler is CheXpert, a labeler that produces diagnostic labels for chest X-ray radiology reports. CheXpert is very useful, but is relatively computationally slow, especially when integrated with end-to-end neural pipelines, is non-differentiable so can't be used in any applications that require gradients to flow through the labeler, and does not yield probabilistic outputs, which limits our ability to improve the quality of the silver labeler through techniques such as active learning. In this work, we solve all three of these problems with $\texttt{CheXpert++}$, a BERT-based, high-fidelity approximation to CheXpert. $\texttt{CheXpert++}$ achieves 99.81\% parity with CheXpert, which means it can be reliably used as a drop-in replacement for CheXpert, all while being significantly faster, fully differentiable, and probabilistic in output. Error analysis of $\texttt{CheXpert++}$ also demonstrates that $\texttt{CheXpert++}$ has a tendency to actually correct errors in the CheXpert labels, with $\texttt{CheXpert++}$ labels being more often preferred by a clinician over CheXpert labels (when they disagree) on all but one disease task. To further demonstrate the utility of these advantages in this model, we conduct a proof-of-concept active learning study, demonstrating we can improve accuracy on an expert labeled random subset of report sentences by approximately 8\% over raw, unaltered CheXpert by using one-iteration of active-learning inspired re-training. These findings suggest that simple techniques in co-learning and active learning can yield high-quality labelers under minimal, and controllable human labeling demands.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Hurtful Words: Quantifying Biases in Clinical Contextual Word Embeddings

In this work, we examine the extent to which embeddings may encode marginalized populations differently, and how this may lead to a perpetuation of biases and worsened performance on clinical tasks. We pretrain deep embedding models (BERT) on medical notes from the MIMIC-III hospital dataset, and quantify potential disparities using two approaches. First, we identify dangerous latent relationships that are captured by the contextual word embeddings using a fill-in-the-blank method with text from real clinical notes and a log probability bias score quantification. Second, we evaluate performance gaps across different definitions of fairness on over 50 downstream clinical prediction tasks that include detection of acute and chronic conditions. We find that classifiers trained from BERT representations exhibit statistically significant differences in performance, often favoring the majority group with regards to gender, language, ethnicity, and insurance status. Finally, we explore shortcomings of using adversarial debiasing to obfuscate subgroup information in contextual word embeddings, and recommend best practices for such deep embedding models in clinical settings.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

MIMIC-Extract: A Data Extraction, Preprocessing, and Representation Pipeline for MIMIC-III

Robust machine learning relies on access to data that can be used with standardized frameworks in important tasks and the ability to develop models whose performance can be reasonably reproduced. In machine learning for healthcare, the community faces reproducibility challenges due to a lack of publicly accessible data and a lack of standardized data processing frameworks. We present MIMIC-Extract, an open-source pipeline for transforming raw electronic health record (EHR) data for critical care patients contained in the publicly-available MIMIC-III database into dataframes that are directly usable in common machine learning pipelines. MIMIC-Extract addresses three primary challenges in making complex health records data accessible to the broader machine learning community. First, it provides standardized data processing functions, including unit conversion, outlier detection, and aggregating semantically equivalent features, thus accounting for duplication and reducing missingness. Second, it preserves the time series nature of clinical data and can be easily integrated into clinically actionable prediction tasks in machine learning for health. Finally, it is highly extensible so that other researchers with related questions can easily use the same pipeline. We demonstrate the utility of this pipeline by showcasing several benchmark tasks and baseline results.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Predicting COVID-19 Pneumonia Severity on Chest X-ray with Deep Learning

Purpose: The need to streamline patient management for COVID-19 has become more pressing than ever. Chest X-rays provide a non-invasive (potentially bedside) tool to monitor the progression of the disease. In this study, we present a severity score prediction model for COVID-19 pneumonia for frontal chest X-ray images. Such a tool can gauge severity of COVID-19 lung infections (and pneumonia in general) that can be used for escalation or de-escalation of care as well as monitoring treatment efficacy, especially in the ICU. Methods: Images from a public COVID-19 database were scored retrospectively by three blinded experts in terms of the extent of lung involvement as well as the degree of opacity. A neural network model that was pre-trained on large (non-COVID-19) chest X-ray datasets is used to construct features for COVID-19 images which are predictive for our task. Results: This study finds that training a regression model on a subset of the outputs from an this pre-trained chest X-ray model predicts our geographic extent score (range 0-8) with 1.14 mean absolute error (MAE) and our lung opacity score (range 0-6) with 0.78 MAE. Conclusions: These results indicate that our model's ability to gauge severity of COVID-19 lung infections could be used for escalation or de-escalation of care as well as monitoring treatment efficacy, especially in the intensive care unit (ICU). A proper clinical trial is needed to evaluate efficacy. To enable this we make our code, labels, and data available online at https://github.com/mlmed/torchxrayvision/tree/master/scripts/covid-severity and https://github.com/ieee8023/covid-chestxray-dataset

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

The Cells Out of Sample (COOS) dataset and benchmarks for measuring out-of-sample generalization of image classifiers

Understanding if classifiers generalize to out-of-sample datasets is a central problem in machine learning. Microscopy images provide a standardized way to measure the generalization capacity of image classifiers, as we can image the same classes of objects under increasingly divergent, but controlled factors of variation. We created a public dataset of 132,209 images of mouse cells, COOS-7 (Cells Out Of Sample 7-Class). COOS-7 provides a classification setting where four test datasets have increasing degrees of covariate shift: some images are random subsets of the training data, while others are from experiments reproduced months later and imaged by different instruments. We benchmarked a range of classification models using different representations, including transferred neural network features, end-to-end classification with a supervised deep CNN, and features from a self-supervised CNN. While most classifiers perform well on test datasets similar to the training dataset, all classifiers failed to generalize their performance to datasets with greater covariate shifts. These baselines highlight the challenges of covariate shifts in image data, and establish metrics for improving the generalization capacity of image classifiers.

0 citations0 reviewsNo code linkedOpen access