arXiv subjects

James Zou

Publications and source records attributed to James Zou.

At least 271 records · Page 15Linked to original sources

arXiv2022

Improving genetic risk prediction across diverse population by disentangling ancestry representations

Risk prediction models using genetic data have seen increasing traction in genomics. However, most of the polygenic risk models were developed using data from participants with similar (mostly European) ancestry. This can lead to biases in the risk predictors resulting in poor generalization when applied to minority populations and admixed individuals such as African Americans. To address this bias, largely due to the prediction models being confounded by the underlying population structure, we propose a novel deep-learning framework that leverages data from diverse population and disentangles ancestry from the phenotype-relevant information in its representation. The ancestry disentangled representation can be used to build risk predictors that perform better across minority populations. We applied the proposed method to the analysis of Alzheimer's disease genetics. Comparing with standard linear and nonlinear risk prediction methods, the proposed method substantially improves risk prediction in minority populations, particularly for admixed individuals.

cs.LG↗

arXiv2022

MLDemon: Deployment Monitoring for Machine Learning Systems

Post-deployment monitoring of ML systems is critical for ensuring reliability, especially as new user inputs can differ from the training distribution. Here we propose a novel approach, MLDemon, for ML DEployment MONitoring. MLDemon integrates both unlabeled data and a small amount of on-demand labels to produce a real-time estimate of the ML model's current performance on a given data stream. Subject to budget constraints, MLDemon decides when to acquire additional, potentially costly, expert supervised labels to verify the model. On temporal datasets with diverse distribution drifts and models, MLDemon outperforms existing approaches. Moreover, we provide theoretical analysis to show that MLDemon is minimax rate optimal for a broad class of distribution drifts.

cs.LG↗

arXiv2022

MetaShift: A Dataset of Datasets for Evaluating Contextual Distribution Shifts and Training Conflicts

Understanding the performance of machine learning models across diverse data distributions is critically important for reliable applications. Motivated by this, there is a growing focus on curating benchmark datasets that capture distribution shifts. While valuable, the existing benchmarks are limited in that many of them only contain a small number of shifts and they lack systematic annotation about what is different across different shifts. We present MetaShift--a collection of 12,868 sets of natural images across 410 classes--to address this challenge. We leverage the natural heterogeneity of Visual Genome and its annotations to construct MetaShift. The key construction idea is to cluster images using its metadata, which provides context for each image (e.g. "cats with cars" or "cats in bathroom") that represent distinct data distributions. MetaShift has two important benefits: first, it contains orders of magnitude more natural data shifts than previously available. Second, it provides explicit explanations of what is unique about each of its data sets and a distance score that measures the amount of distribution shift between any two of its data sets. We demonstrate the utility of MetaShift in benchmarking several recent proposals for training models to be robust to data shifts. We find that the simple empirical risk minimization performs the best when shifts are moderate and no method had a systematic advantage for large shifts. We also show how MetaShift can help to visualize conflicts between data subsets during model training.

cs.LG↗

arXiv2022

Beta Shapley: a Unified and Noise-reduced Data Valuation Framework for Machine Learning

Data Shapley has recently been proposed as a principled framework to quantify the contribution of individual datum in machine learning. It can effectively identify helpful or harmful data points for a learning algorithm. In this paper, we propose Beta Shapley, which is a substantial generalization of Data Shapley. Beta Shapley arises naturally by relaxing the efficiency axiom of the Shapley value, which is not critical for machine learning settings. Beta Shapley unifies several popular data valuation methods and includes data Shapley as a special case. Moreover, we prove that Beta Shapley has several desirable statistical properties and propose efficient algorithms to estimate it. We demonstrate that Beta Shapley outperforms state-of-the-art data valuation methods on several downstream ML tasks such as: 1) detecting mislabeled training data; 2) learning with subsamples; and 3) identifying points whose addition or removal have the largest positive or negative impact on the model.

cs.LG↗

arXiv2022

Submix: Practical Private Prediction for Large-Scale Language Models

Recent data-extraction attacks have exposed that language models can memorize some training samples verbatim. This is a vulnerability that can compromise the privacy of the model's training data. In this work, we introduce SubMix: a practical protocol for private next-token prediction designed to prevent privacy violations by language models that were fine-tuned on a private corpus after pre-training on a public corpus. We show that SubMix limits the leakage of information that is unique to any individual user in the private corpus via a relaxation of group differentially private prediction. Importantly, SubMix admits a tight, data-dependent privacy accounting mechanism, which allows it to thwart existing data-extraction attacks while maintaining the utility of the language model. SubMix is the first protocol that maintains privacy even when publicly releasing tens of thousands of next-token predictions made by large transformer-based models such as GPT-2.

cs.LG↗

arXiv2021

How to Learn when Data Gradually Reacts to Your Model

A recent line of work has focused on training machine learning (ML) models in the performative setting, i.e. when the data distribution reacts to the deployed model. The goal in this setting is to learn a model which both induces a favorable data distribution and performs well on the induced distribution, thereby minimizing the test loss. Previous work on finding an optimal model assumes that the data distribution immediately adapts to the deployed model. In practice, however, this may not be the case, as the population may take time to adapt to the model. In many applications, the data distribution depends on both the currently deployed ML model and on the "state" that the population was in before the model was deployed. In this work, we propose a new algorithm, Stateful Performative Gradient Descent (Stateful PerfGD), for minimizing the performative loss even in the presence of these effects. We provide theoretical guarantees for the convergence of Stateful PerfGD. Our experiments confirm that Stateful PerfGD substantially outperforms previous state-of-the-art methods.

cs.LG↗

arXiv2021

Beyond Importance Scores: Interpreting Tabular ML by Visualizing Feature Semantics

Interpretability is becoming an active research topic as machine learning (ML) models are more widely used to make critical decisions. Tabular data is one of the most commonly used modes of data in diverse applications such as healthcare and finance. Much of the existing interpretability methods used for tabular data only report feature-importance scores -- either locally (per example) or globally (per model) -- but they do not provide interpretation or visualization of how the features interact. We address this limitation by introducing Feature Vectors, a new global interpretability method designed for tabular datasets. In addition to providing feature-importance, Feature Vectors discovers the inherent semantic relationship among features via an intuitive feature visualization technique. Our systematic experiments demonstrate the empirical utility of this new method by applying it to several real-world datasets. We further provide an easy-to-use Python package for Feature Vectors.

stat.ML↗

arXiv2021

Disparities in Dermatology AI: Assessments Using Diverse Clinical Images

More than 3 billion people lack access to care for skin disease. AI diagnostic tools may aid in early skin cancer detection; however most models have not been assessed on images of diverse skin tones or uncommon diseases. To address this, we curated the Diverse Dermatology Images (DDI) dataset - the first publicly available, pathologically confirmed images featuring diverse skin tones. We show that state-of-the-art dermatology AI models perform substantially worse on DDI, with ROC-AUC dropping 29-40 percent compared to the models' original results. We find that dark skin tones and uncommon diseases, which are well represented in the DDI dataset, lead to performance drop-offs. Additionally, we show that state-of-the-art robust training methods cannot correct for these biases without diverse training data. Our findings identify important weaknesses and biases in dermatology AI that need to be addressed to ensure reliable application to diverse patients and across all disease.

eess.IV↗

arXiv2021

Explaining medical AI performance disparities across sites with confounder Shapley value analysis

Medical AI algorithms can often experience degraded performance when evaluated on previously unseen sites. Addressing cross-site performance disparities is key to ensuring that AI is equitable and effective when deployed on diverse patient populations. Multi-site evaluations are key to diagnosing such disparities as they can test algorithms across a broader range of potential biases such as patient demographics, equipment types, and technical parameters. However, such tests do not explain why the model performs worse. Our framework provides a method for quantifying the marginal and cumulative effect of each type of bias on the overall performance difference when a model is evaluated on external data. We demonstrate its usefulness in a case study of a deep learning model trained to detect the presence of pneumothorax, where our framework can help explain up to 60% of the discrepancy in performance across different sites with known biases like disease comorbidities and imaging parameters.

cs.LG↗

arXiv2021

CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq

Single-cell RNA sequencing (scRNA-seq) has the potential to provide powerful, high-resolution signatures to inform disease prognosis and precision medicine. This paper takes an important first step towards this goal by developing an interpretable machine learning algorithm, CloudPred, to predict individuals' disease phenotypes from their scRNA-seq data. Predicting phenotype from scRNA-seq is challenging for standard machine learning methods -- the number of cells measured can vary by orders of magnitude across individuals and the cell populations are also highly heterogeneous. Typical analysis creates pseudo-bulk samples which are biased toward prior annotations and also lose the single cell resolution. CloudPred addresses these challenges via a novel end-to-end differentiable learning algorithm which is coupled with a biologically informed mixture of cell types model. CloudPred automatically infers the cell subpopulation that are salient for the phenotype without prior annotations. We developed a systematic simulation platform to evaluate the performance of CloudPred and several alternative methods we propose, and find that CloudPred outperforms the alternative methods across several settings. We further validated CloudPred on a real scRNA-seq dataset of 142 lupus patients and controls. CloudPred achieves AUROC of 0.98 while identifying a specific subpopulation of CD4 T cells whose presence is highly indicative of lupus. CloudPred is a powerful new framework to predict clinical phenotypes from scRNA-seq data and to identify relevant cells.

q-bio.QM↗

arXiv2021

Clustering Plotted Data by Image Segmentation

Clustering algorithms are one of the main analytical methods to detect patterns in unlabeled data. Existing clustering methods typically treat samples in a dataset as points in a metric space and compute distances to group together similar points. In this paper, we present a wholly different way of clustering points in 2-dimensional space, inspired by how humans cluster data: by training neural networks to perform instance segmentation on plotted data. Our approach, Visual Clustering, has several advantages over traditional clustering algorithms: it is much faster than most existing clustering algorithms (making it suitable for very large datasets), it agrees strongly with human intuition for clusters, and it is by default hyperparameter free (although additional steps with hyperparameters can be introduced for more control of the algorithm). We describe the method and compare it to ten other clustering methods on synthetic data to illustrate its advantages and disadvantages. We then demonstrate how our approach can be extended to higher dimensional data and illustrate its performance on real-world data. The implementation of Visual Clustering is publicly available and can be applied to any dataset in a few lines of code.

cs.LG↗

arXiv2021

Learning transport cost from subset correspondence

Learning to align multiple datasets is an important problem with many applications, and it is especially useful when we need to integrate multiple experiments or correct for confounding. Optimal transport (OT) is a principled approach to align datasets, but a key challenge in applying OT is that we need to specify a transport cost function that accurately captures how the two datasets are related. Reliable cost functions are typically not available and practitioners often resort to using hand-crafted or Euclidean cost even if it may not be appropriate. In this work, we investigate how to learn the cost function using a small amount of side information which is often available. The side information we consider captures subset correspondence -- i.e. certain subsets of points in the two data sets are known to be related. For example, we may have some images labeled as cars in both datasets; or we may have a common annotated cell type in single-cell data from two batches. We develop an end-to-end optimizer (OT-SI) that differentiates through the Sinkhorn algorithm and effectively learns the suitable cost function from side information. On systematic experiments in images, marriage-matching and single-cell RNA-seq, our method substantially outperform state-of-the-art benchmarks.

cs.LG↗

arXiv2021

Did the Model Change? Efficiently Assessing Machine Learning API Shifts

Machine learning (ML) prediction APIs are increasingly widely used. An ML API can change over time due to model updates or retraining. This presents a key challenge in the usage of the API because it is often not clear to the user if and how the ML model has changed. Model shifts can affect downstream application performance and also create oversight issues (e.g. if consistency is desired). In this paper, we initiate a systematic investigation of ML API shifts. We first quantify the performance shifts from 2020 to 2021 of popular ML APIs from Google, Microsoft, Amazon, and others on a variety of datasets. We identified significant model shifts in 12 out of 36 cases we investigated. Interestingly, we found several datasets where the API's predictions became significantly worse over time. This motivated us to formulate the API shift assessment problem at a more fine-grained level as estimating how the API model's confusion matrix changes over time when the data distribution is constant. Monitoring confusion matrix shifts using standard random sampling can require a large number of samples, which is expensive as each API call costs a fee. We propose a principled adaptive sampling algorithm, MASA, to efficiently estimate confusion matrix shifts. MASA can accurately estimate the confusion matrix shifts in commercial ML APIs using up to 90% fewer samples compared to random sampling. This work establishes ML API shifts as an important problem to study and provides a cost-effective approach to monitor such shifts.

stat.ML↗

arXiv2021

Adversarial Training Helps Transfer Learning via Better Representations

Transfer learning aims to leverage models pre-trained on source data to efficiently adapt to target setting, where only limited data are available for model fine-tuning. Recent works empirically demonstrate that adversarial training in the source data can improve the ability of models to transfer to new domains. However, why this happens is not known. In this paper, we provide a theoretical model to rigorously analyze how adversarial training helps transfer learning. We show that adversarial training in the source data generates provably better representations, so fine-tuning on top of this representation leads to a more accurate predictor of the target data. We further demonstrate both theoretically and empirically that semi-supervised learning in the source data can also improve transfer learning by similarly improving the representation. Moreover, performing adversarial training on top of semi-supervised learning can further improve transferability, suggesting that the two approaches have complementary benefits on representations. We support our theories with experiments on popular data sets and deep learning architectures.

cs.LG↗

arXiv2021

Group-Structured Adversarial Training

Robust training methods against perturbations to the input data have received great attention in the machine learning literature. A standard approach in this direction is adversarial training which learns a model using adversarially-perturbed training samples. However, adversarial training performs suboptimally against perturbations structured across samples such as universal and group-sparse shifts that are commonly present in biological data such as gene expression levels of different tissues. In this work, we seek to close this optimality gap and introduce Group-Structured Adversarial Training (GSAT) which learns a model robust to perturbations structured across samples. We formulate GSAT as a non-convex concave minimax optimization problem which minimizes a group-structured optimal transport cost. Specifically, we focus on the applications of GSAT for group-sparse and rank-constrained perturbations modeled using group and nuclear norm penalties. In order to solve GSAT's non-smooth optimization problem in those cases, we propose a new minimax optimization algorithm called GDADMM by combining Gradient Descent Ascent (GDA) and Alternating Direction Method of Multipliers (ADMM). We present several applications of the GSAT framework to gain robustness against structured perturbations for image recognition and computational biology datasets.

cs.LG↗

arXiv2021

Improving Generalization in Meta-learning via Task Augmentation

Meta-learning has proven to be a powerful paradigm for transferring the knowledge from previous tasks to facilitate the learning of a novel task. Current dominant algorithms train a well-generalized model initialization which is adapted to each task via the support set. The crux lies in optimizing the generalization capability of the initialization, which is measured by the performance of the adapted model on the query set of each task. Unfortunately, this generalization measure, evidenced by empirical results, pushes the initialization to overfit the meta-training tasks, which significantly impairs the generalization and adaptation to novel tasks. To address this issue, we actively augment a meta-training task with "more data" when evaluating the generalization. Concretely, we propose two task augmentation methods, including MetaMix and Channel Shuffle. MetaMix linearly combines features and labels of samples from both the support and query sets. For each class of samples, Channel Shuffle randomly replaces a subset of their channels with the corresponding ones from a different class. Theoretical studies show how task augmentation improves the generalization of meta-learning. Moreover, both MetaMix and Channel Shuffle outperform state-of-the-art results by a large margin across many datasets and are compatible with existing meta-learning algorithms.

cs.LG↗

arXiv2021

Identifying Invariant Factors Across Multiple Environments with KL Regression

Many datasets are collected from multiple environments (e.g. different labs, perturbations, etc.), and it is often advantageous to learn models and relations that are invariant across environments. Invariance can improve robustness to unknown confounders and improve generalization to new domains. We develop a novel framework -- KL regression -- to reliably estimate regression coefficients in a challenging multi-environment setting, where latent confounders affect the data from each environment. KL regression is based on a new objective of simultaneously minimizing the KL- divergence between a parametric model and the observed data from each environment. We prove that KL regression recovers the true invariant factors under a flexible confounding setup. Moreover, it is computationally efficient as we derive an analytic solution for its global optimum. In systematic experiments, we validate the improved performance of KL regression compared to commonly used approaches.

stat.ME↗

arXiv2021

Neural Group Testing to Accelerate Deep Learning

Recent advances in deep learning have made the use of large, deep neural networks with tens of millions of parameters. The sheer size of these networks imposes a challenging computational burden during inference. Existing work focuses primarily on accelerating each forward pass of a neural network. Inspired by the group testing strategy for efficient disease testing, we propose neural group testing, which accelerates by testing a group of samples in one forward pass. Groups of samples that test negative are ruled out. If a group tests positive, samples in that group are then retested adaptively. A key challenge of neural group testing is to modify a deep neural network so that it could test multiple samples in one forward pass. We propose three designs to achieve this without introducing any new parameters and evaluate their performances. We applied neural group testing in an image moderation task to detect rare but inappropriate images. We found that neural group testing can group up to 16 images in one forward pass and reduce the overall computation cost by over 73% while improving detection performance.

cs.LG↗