arXiv subjects

James Zou

Publications and source records attributed to James Zou.

At least 307 records · Page 17Linked to original sources

arXiv2020

FrugalML: How to Use ML Prediction APIs More Accurately and Cheaply

Prediction APIs offered for a fee are a fast-growing industry and an important part of machine learning as a service. While many such services are available, the heterogeneity in their price and performance makes it challenging for users to decide which API or combination of APIs to use for their own data and budget. We take a first step towards addressing this challenge by proposing FrugalML, a principled framework that jointly learns the strength and weakness of each API on different data, and performs an efficient optimization to automatically identify the best sequential strategy to adaptively use the available APIs within a budget constraint. Our theoretical analysis shows that natural sparsity in the formulation can be leveraged to make FrugalML efficient. We conduct systematic experiments using ML APIs from Google, Microsoft, Amazon, IBM, Baidu and other providers for tasks including facial emotion recognition, sentiment analysis and speech recognition. Across various tasks, FrugalML can achieve up to 90% cost reduction while matching the accuracy of the best single API, or up to 5% better accuracy while matching the best API's cost.

cs.LG↗

arXiv2020

Improving Training on Noisy Stuctured Labels

Fine-grained annotations---e.g. dense image labels, image segmentation and text tagging---are useful in many ML applications but they are labor-intensive to generate. Moreover there are often systematic, structured errors in these fine-grained annotations. For example, a car might be entirely unannotated in the image, or the boundary between a car and street might only be coarsely annotated. Standard ML training on data with such structured errors produces models with biases and poor performance. In this work, we propose a novel framework of Error-Correcting Networks (ECN) to address the challenge of learning in the presence structured error in fine-grained annotations. Given a large noisy dataset with commonly occurring structured errors, and a much smaller dataset with more accurate annotations, ECN is able to substantially improve the prediction of fine-grained annotations compared to standard approaches for training on noisy data. It does so by learning to leverage the structures in the annotations and in the noisy labels. Systematic experiments on image segmentation and text tagging demonstrate the strong performance of ECN in improving training on noisy structured labels.

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arXiv2020

A Distributional Framework for Data Valuation

Shapley value is a classic notion from game theory, historically used to quantify the contributions of individuals within groups, and more recently applied to assign values to data points when training machine learning models. Despite its foundational role, a key limitation of the data Shapley framework is that it only provides valuations for points within a fixed data set. It does not account for statistical aspects of the data and does not give a way to reason about points outside the data set. To address these limitations, we propose a novel framework -- distributional Shapley -- where the value of a point is defined in the context of an underlying data distribution. We prove that distributional Shapley has several desirable statistical properties; for example, the values are stable under perturbations to the data points themselves and to the underlying data distribution. We leverage these properties to develop a new algorithm for estimating values from data, which comes with formal guarantees and runs two orders of magnitude faster than state-of-the-art algorithms for computing the (non-distributional) data Shapley values. We apply distributional Shapley to diverse data sets and demonstrate its utility in a data market setting.

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arXiv2019

Making AI Forget You: Data Deletion in Machine Learning

Intense recent discussions have focused on how to provide individuals with control over when their data can and cannot be used --- the EU's Right To Be Forgotten regulation is an example of this effort. In this paper we initiate a framework studying what to do when it is no longer permissible to deploy models derivative from specific user data. In particular, we formulate the problem of efficiently deleting individual data points from trained machine learning models. For many standard ML models, the only way to completely remove an individual's data is to retrain the whole model from scratch on the remaining data, which is often not computationally practical. We investigate algorithmic principles that enable efficient data deletion in ML. For the specific setting of k-means clustering, we propose two provably efficient deletion algorithms which achieve an average of over 100X improvement in deletion efficiency across 6 datasets, while producing clusters of comparable statistical quality to a canonical k-means++ baseline.

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arXiv2019

How much does your data exploration overfit? Controlling bias via information usage

Modern data is messy and high-dimensional, and it is often not clear a priori what are the right questions to ask. Instead, the analyst typically needs to use the data to search for interesting analyses to perform and hypotheses to test. This is an adaptive process, where the choice of analysis to be performed next depends on the results of the previous analyses on the same data. Ultimately, which results are reported can be heavily influenced by the data. It is widely recognized that this process, even if well-intentioned, can lead to biases and false discoveries, contributing to the crisis of reproducibility in science. But while %the adaptive nature of exploration any data-exploration renders standard statistical theory invalid, experience suggests that different types of exploratory analysis can lead to disparate levels of bias, and the degree of bias also depends on the particulars of the data set. In this paper, we propose a general information usage framework to quantify and provably bound the bias and other error metrics of an arbitrary exploratory analysis. We prove that our mutual information based bound is tight in natural settings, and then use it to give rigorous insights into when commonly used procedures do or do not lead to substantially biased estimation. Through the lens of information usage, we analyze the bias of specific exploration procedures such as filtering, rank selection and clustering. Our general framework also naturally motivates randomization techniques that provably reduces exploration bias while preserving the utility of the data analysis. We discuss the connections between our approach and related ideas from differential privacy and blinded data analysis, and supplement our results with illustrative simulations.

stat.ML↗

arXiv2019

Towards Automatic Concept-based Explanations

Interpretability has become an important topic of research as more machine learning (ML) models are deployed and widely used to make important decisions. Most of the current explanation methods provide explanations through feature importance scores, which identify features that are important for each individual input. However, how to systematically summarize and interpret such per sample feature importance scores itself is challenging. In this work, we propose principles and desiderata for \emph{concept} based explanation, which goes beyond per-sample features to identify higher-level human-understandable concepts that apply across the entire dataset. We develop a new algorithm, ACE, to automatically extract visual concepts. Our systematic experiments demonstrate that \alg discovers concepts that are human-meaningful, coherent and important for the neural network's predictions.

stat.ML↗

arXiv2019

LitGen: Genetic Literature Recommendation Guided by Human Explanations

As genetic sequencing costs decrease, the lack of clinical interpretation of variants has become the bottleneck in using genetics data. A major rate limiting step in clinical interpretation is the manual curation of evidence in the genetic literature by highly trained biocurators. What makes curation particularly time-consuming is that the curator needs to identify papers that study variant pathogenicity using different types of approaches and evidences---e.g. biochemical assays or case control analysis. In collaboration with the Clinical Genomic Resource (ClinGen)---the flagship NIH program for clinical curation---we propose the first machine learning system, LitGen, that can retrieve papers for a particular variant and filter them by specific evidence types used by curators to assess for pathogenicity. LitGen uses semi-supervised deep learning to predict the type of evidence provided by each paper. It is trained on papers annotated by ClinGen curators and systematically evaluated on new test data collected by ClinGen. LitGen further leverages rich human explanations and unlabeled data to gain 7.9%-12.6% relative performance improvement over models learned only on the annotated papers. It is a useful framework to improve clinical variant curation.

cs.CL↗

arXiv2019

Data Shapley: Equitable Valuation of Data for Machine Learning

As data becomes the fuel driving technological and economic growth, a fundamental challenge is how to quantify the value of data in algorithmic predictions and decisions. For example, in healthcare and consumer markets, it has been suggested that individuals should be compensated for the data that they generate, but it is not clear what is an equitable valuation for individual data. In this work, we develop a principled framework to address data valuation in the context of supervised machine learning. Given a learning algorithm trained on $n$ data points to produce a predictor, we propose data Shapley as a metric to quantify the value of each training datum to the predictor performance. Data Shapley value uniquely satisfies several natural properties of equitable data valuation. We develop Monte Carlo and gradient-based methods to efficiently estimate data Shapley values in practical settings where complex learning algorithms, including neural networks, are trained on large datasets. In addition to being equitable, extensive experiments across biomedical, image and synthetic data demonstrate that data Shapley has several other benefits: 1) it is more powerful than the popular leave-one-out or leverage score in providing insight on what data is more valuable for a given learning task; 2) low Shapley value data effectively capture outliers and corruptions; 3) high Shapley value data inform what type of new data to acquire to improve the predictor.

stat.ML↗

arXiv2019

Gradio: Hassle-Free Sharing and Testing of ML Models in the Wild

Accessibility is a major challenge of machine learning (ML). Typical ML models are built by specialists and require specialized hardware/software as well as ML experience to validate. This makes it challenging for non-technical collaborators and endpoint users (e.g. physicians) to easily provide feedback on model development and to gain trust in ML. The accessibility challenge also makes collaboration more difficult and limits the ML researcher's exposure to realistic data and scenarios that occur in the wild. To improve accessibility and facilitate collaboration, we developed an open-source Python package, Gradio, which allows researchers to rapidly generate a visual interface for their ML models. Gradio makes accessing any ML model as easy as sharing a URL. Our development of Gradio is informed by interviews with a number of machine learning researchers who participate in interdisciplinary collaborations. Their feedback identified that Gradio should support a variety of interfaces and frameworks, allow for easy sharing of the interface, allow for input manipulation and interactive inference by the domain expert, as well as allow embedding the interface in iPython notebooks. We developed these features and carried out a case study to understand Gradio's usefulness and usability in the setting of a machine learning collaboration between a researcher and a cardiologist.

cs.LG↗

arXiv2019

Knockoffs for the mass: new feature importance statistics with false discovery guarantees

An important problem in machine learning and statistics is to identify features that causally affect the outcome. This is often impossible to do from purely observational data, and a natural relaxation is to identify features that are correlated with the outcome even conditioned on all other observed features. For example, we want to identify that smoking really is correlated with cancer conditioned on demographics. The knockoff procedure is a recent breakthrough in statistics that, in theory, can identify truly correlated features while guaranteeing that the false discovery is limited. The idea is to create synthetic data -- knockoffs -- that captures correlations amongst the features. However there are substantial computational and practical challenges to generating and using knockoffs. This paper makes several key advances that enable knockoff application to be more efficient and powerful. We develop an efficient algorithm to generate valid knockoffs from Bayesian Networks. Then we systematically evaluate knockoff test statistics and develop new statistics with improved power. The paper combines new mathematical guarantees with systematic experiments on real and synthetic data.

stat.ML↗

arXiv2019

Improving the Stability of the Knockoff Procedure: Multiple Simultaneous Knockoffs and Entropy Maximization

The Model-X knockoff procedure has recently emerged as a powerful approach for feature selection with statistical guarantees. The advantage of knockoff is that if we have a good model of the features X, then we can identify salient features without knowing anything about how the outcome Y depends on X. An important drawback of knockoffs is its instability: running the procedure twice can result in very different selected features, potentially leading to different conclusions. Addressing this instability is critical for obtaining reproducible and robust results. Here we present a generalization of the knockoff procedure that we call simultaneous multi-knockoffs. We show that multi-knockoff guarantees false discovery rate (FDR) control, and is substantially more stable and powerful compared to the standard (single) knockoff. Moreover we propose a new algorithm based on entropy maximization for generating Gaussian multi-knockoffs. We validate the improved stability and power of multi-knockoffs in systematic experiments. We also illustrate how multi-knockoffs can improve the accuracy of detecting genetic mutations that are causally linked to phenotypes.

stat.ML↗

arXiv2019

Discovering Conditionally Salient Features with Statistical Guarantees

The goal of feature selection is to identify important features that are relevant to explain an outcome variable. Most of the work in this domain has focused on identifying globally relevant features, which are features that are related to the outcome using evidence across the entire dataset. We study a more fine-grained statistical problem: conditional feature selection, where a feature may be relevant depending on the values of the other features. For example in genetic association studies, variant $A$ could be associated with the phenotype in the entire dataset, but conditioned on variant $B$ being present it might be independent of the phenotype. In this sense, variant $A$ is globally relevant, but conditioned on $B$ it is no longer locally relevant in that region of the feature space. We present a generalization of the knockoff procedure that performs conditional feature selection while controlling a generalization of the false discovery rate (FDR) to the conditional setting. By exploiting the feature/response model-free framework of the knockoffs, the quality of the statistical FDR guarantee is not degraded even when we perform conditional feature selections. We implement this method and present an algorithm that automatically partitions the feature space such that it enhances the differences between selected sets in different regions, and validate the statistical theoretical results with experiments.

stat.ML↗

arXiv2019

A Knowledge Graph-based Approach for Exploring the U.S. Opioid Epidemic

The United States is in the midst of an opioid epidemic with recent estimates indicating that more than 130 people die every day due to drug overdose. The over-prescription and addiction to opioid painkillers, heroin, and synthetic opioids, has led to a public health crisis and created a huge social and economic burden. Statistical learning methods that use data from multiple clinical centers across the US to detect opioid over-prescribing trends and predict possible opioid misuse are required. However, the semantic heterogeneity in the representation of clinical data across different centers makes the development and evaluation of such methods difficult and non-trivial. We create the Opioid Drug Knowledge Graph (ODKG) -- a network of opioid-related drugs, active ingredients, formulations, combinations, and brand names. We use the ODKG to normalize drug strings in a clinical data warehouse consisting of patient data from over 400 healthcare facilities in 42 different states. We showcase the use of ODKG to generate summary statistics of opioid prescription trends across US regions. These methods and resources can aid the development of advanced and scalable models to monitor the opioid epidemic and to detect illicit opioid misuse behavior. Our work is relevant to policymakers and pain researchers who wish to systematically assess factors that contribute to opioid over-prescribing and iatrogenic opioid addiction in the US.

cs.CY↗

arXiv2019

Adaptive Monte Carlo Multiple Testing via Multi-Armed Bandits

Monte Carlo (MC) permutation test is considered the gold standard for statistical hypothesis testing, especially when standard parametric assumptions are not clear or likely to fail. However, in modern data science settings where a large number of hypothesis tests need to be performed simultaneously, it is rarely used due to its prohibitive computational cost. In genome-wide association studies, for example, the number of hypothesis tests $m$ is around $10^6$ while the number of MC samples $n$ for each test could be greater than $10^8$, totaling more than $nm$=$10^{14}$ samples. In this paper, we propose Adaptive MC multiple Testing (AMT) to estimate MC p-values and control false discovery rate in multiple testing. The algorithm outputs the same result as the standard full MC approach with high probability while requiring only $\tilde{O}(\sqrt{n}m)$ samples. This sample complexity is shown to be optimal. On a Parkinson GWAS dataset, the algorithm reduces the running time from 2 months for full MC to an hour. The AMT algorithm is derived based on the theory of multi-armed bandits.

stat.ME↗

arXiv2019

Analyzing Polarization in Social Media: Method and Application to Tweets on 21 Mass Shootings

We provide an NLP framework to uncover four linguistic dimensions of political polarization in social media: topic choice, framing, affect and illocutionary force. We quantify these aspects with existing lexical methods, and propose clustering of tweet embeddings as a means to identify salient topics for analysis across events; human evaluations show that our approach generates more cohesive topics than traditional LDA-based models. We apply our methods to study 4.4M tweets on 21 mass shootings. We provide evidence that the discussion of these events is highly polarized politically and that this polarization is primarily driven by partisan differences in framing rather than topic choice. We identify framing devices, such as grounding and the contrasting use of the terms "terrorist" and "crazy", that contribute to polarization. Results pertaining to topic choice, affect and illocutionary force suggest that Republicans focus more on the shooter and event-specific facts (news) while Democrats focus more on the victims and call for policy changes. Our work contributes to a deeper understanding of the way group divisions manifest in language and to computational methods for studying them.

cs.CL↗

arXiv2019

Contrastive Variational Autoencoder Enhances Salient Features

Variational autoencoders are powerful algorithms for identifying dominant latent structure in a single dataset. In many applications, however, we are interested in modeling latent structure and variation that are enriched in a target dataset compared to some background---e.g. enriched in patients compared to the general population. Contrastive learning is a principled framework to capture such enriched variation between the target and background, but state-of-the-art contrastive methods are limited to linear models. In this paper, we introduce the contrastive variational autoencoder (cVAE), which combines the benefits of contrastive learning with the power of deep generative models. The cVAE is designed to identify and enhance salient latent features. The cVAE is trained on two related but unpaired datasets, one of which has minimal contribution from the salient latent features. The cVAE explicitly models latent features that are shared between the datasets, as well as those that are enriched in one dataset relative to the other, which allows the algorithm to isolate and enhance the salient latent features. The algorithm is straightforward to implement, has a similar run-time to the standard VAE, and is robust to noise and dataset purity. We conduct experiments across diverse types of data, including gene expression and facial images, showing that the cVAE effectively uncovers latent structure that is salient in a particular analysis.

cs.LG↗

arXiv2019

Concrete Autoencoders for Differentiable Feature Selection and Reconstruction

We introduce the concrete autoencoder, an end-to-end differentiable method for global feature selection, which efficiently identifies a subset of the most informative features and simultaneously learns a neural network to reconstruct the input data from the selected features. Our method is unsupervised, and is based on using a concrete selector layer as the encoder and using a standard neural network as the decoder. During the training phase, the temperature of the concrete selector layer is gradually decreased, which encourages a user-specified number of discrete features to be learned. During test time, the selected features can be used with the decoder network to reconstruct the remaining input features. We evaluate concrete autoencoders on a variety of datasets, where they significantly outperform state-of-the-art methods for feature selection and data reconstruction. In particular, on a large-scale gene expression dataset, the concrete autoencoder selects a small subset of genes whose expression levels can be use to impute the expression levels of the remaining genes. In doing so, it improves on the current widely-used expert-curated L1000 landmark genes, potentially reducing measurement costs by 20%. The concrete autoencoder can be implemented by adding just a few lines of code to a standard autoencoder.

cs.LG↗

arXiv2018

Large-scale Generative Modeling to Improve Automated Veterinary Disease Coding

Supervised learning is limited both by the quantity and quality of the labeled data. In the field of medical record tagging, writing styles between hospitals vary drastically. The knowledge learned from one hospital might not transfer well to another. This problem is amplified in veterinary medicine domain because veterinary clinics rarely apply medical codes to their records. We proposed and trained the first large-scale generative modeling algorithm in automated disease coding. We demonstrate that generative modeling can learn discriminative features when additionally trained with supervised fine-tuning. We systematically ablate and evaluate the effect of generative modeling on the final system's performance. We compare the performance of our model with several baselines in a challenging cross-hospital setting with substantial domain shift. We outperform competitive baselines by a large margin. In addition, we provide interpretation for what is learned by our model.

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