arXiv subjects

James Zou

Publications and source records attributed to James Zou.

At least 325 records · Page 18Linked to original sources

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.

cs.CL↗

arXiv2018

Interpretation of Neural Networks is Fragile

In order for machine learning to be deployed and trusted in many applications, it is crucial to be able to reliably explain why the machine learning algorithm makes certain predictions. For example, if an algorithm classifies a given pathology image to be a malignant tumor, then the doctor may need to know which parts of the image led the algorithm to this classification. How to interpret black-box predictors is thus an important and active area of research. A fundamental question is: how much can we trust the interpretation itself? In this paper, we show that interpretation of deep learning predictions is extremely fragile in the following sense: two perceptively indistinguishable inputs with the same predicted label can be assigned very different interpretations. We systematically characterize the fragility of several widely-used feature-importance interpretation methods (saliency maps, relevance propagation, and DeepLIFT) on ImageNet and CIFAR-10. Our experiments show that even small random perturbation can change the feature importance and new systematic perturbations can lead to dramatically different interpretations without changing the label. We extend these results to show that interpretations based on exemplars (e.g. influence functions) are similarly fragile. Our analysis of the geometry of the Hessian matrix gives insight on why fragility could be a fundamental challenge to the current interpretation approaches.

stat.ML↗

arXiv2018

Minimizing Close-k Aggregate Loss Improves Classification

In classification, the de facto method for aggregating individual losses is the average loss. When the actual metric of interest is 0-1 loss, it is common to minimize the average surrogate loss for some well-behaved (e.g. convex) surrogate. Recently, several other aggregate losses such as the maximal loss and average top-$k$ loss were proposed as alternative objectives to address shortcomings of the average loss. However, we identify common classification settings, e.g. the data is imbalanced, has too many easy or ambiguous examples, etc., when average, maximal and average top-$k$ all suffer from suboptimal decision boundaries, even on an infinitely large training set. To address this problem, we propose a new classification objective called the close-$k$ aggregate loss, where we adaptively minimize the loss for points close to the decision boundary. We provide theoretical guarantees for the 0-1 accuracy when we optimize close-$k$ aggregate loss. We also conduct systematic experiments across the PMLB and OpenML benchmark datasets. Close-$k$ achieves significant gains in 0-1 test accuracy, improvements of $\geq 2$% and $p<0.05$, in over 25% of the datasets compared to average, maximal and average top-$k$. In contrast, the previous aggregate losses outperformed close-$k$ in less than 2% of the datasets.

cs.LG↗

arXiv2018

Contingent Payment Mechanisms for Resource Utilization

We introduce the problem of assigning resources to improve their utilization. The motivation comes from settings where agents have uncertainty about their own values for using a resource, and where it is in the interest of a group that resources be used and not wasted. Done in the right way, improved utilization maximizes social welfare--- balancing the utility of a high value but unreliable agent with the group's preference that resources be used. We introduce the family of contingent payment mechanisms (CP), which may charge an agent contingent on use (a penalty). A CP mechanism is parameterized by a maximum penalty, and has a dominant-strategy equilibrium. Under a set of axiomatic properties, we establish welfare-optimality for the special case CP(W), with CP instantiated for a maximum penalty equal to societal value W for utilization. CP(W) is not dominated for expected welfare by any other mechanism, and second, amongst mechanisms that always allocate the resource and have a simple indirect structure, CP(W) strictly dominates every other mechanism. The special case with no upper bound on penalty, the contingent second-price mechanism, maximizes utilization. We extend the mechanisms to assign multiple, heterogeneous resources, and present a simulation study of the welfare properties of these mechanisms.

cs.GT↗

arXiv2018

Contrastive Multivariate Singular Spectrum Analysis

We introduce Contrastive Multivariate Singular Spectrum Analysis, a novel unsupervised method for dimensionality reduction and signal decomposition of time series data. By utilizing an appropriate background dataset, the method transforms a target time series dataset in a way that evinces the sub-signals that are enhanced in the target dataset, as opposed to only those that account for the greatest variance. This shifts the goal from finding signals that explain the most variance to signals that matter the most to the analyst. We demonstrate our method on an illustrative synthetic example, as well as show the utility of our method in the downstream clustering of electrocardiogram signals from the public MHEALTH dataset.

stat.ML↗

arXiv2018

Autowarp: Learning a Warping Distance from Unlabeled Time Series Using Sequence Autoencoders

Measuring similarities between unlabeled time series trajectories is an important problem in domains as diverse as medicine, astronomy, finance, and computer vision. It is often unclear what is the appropriate metric to use because of the complex nature of noise in the trajectories (e.g. different sampling rates or outliers). Domain experts typically hand-craft or manually select a specific metric, such as dynamic time warping (DTW), to apply on their data. In this paper, we propose Autowarp, an end-to-end algorithm that optimizes and learns a good metric given unlabeled trajectories. We define a flexible and differentiable family of warping metrics, which encompasses common metrics such as DTW, Euclidean, and edit distance. Autowarp then leverages the representation power of sequence autoencoders to optimize for a member of this warping distance family. The output is a metric which is easy to interpret and can be robustly learned from relatively few trajectories. In systematic experiments across different domains, we show that Autowarp often outperforms hand-crafted trajectory similarity metrics.

cs.LG↗

arXiv2018

DeepTag: inferring all-cause diagnoses from clinical notes in under-resourced medical domain

Large scale veterinary clinical records can become a powerful resource for patient care and research. However, clinicians lack the time and resource to annotate patient records with standard medical diagnostic codes and most veterinary visits are captured in free text notes. The lack of standard coding makes it challenging to use the clinical data to improve patient care. It is also a major impediment to cross-species translational research, which relies on the ability to accurately identify patient cohorts with specific diagnostic criteria in humans and animals. In order to reduce the coding burden for veterinary clinical practice and aid translational research, we have developed a deep learning algorithm, DeepTag, which automatically infers diagnostic codes from veterinary free text notes. DeepTag is trained on a newly curated dataset of 112,558 veterinary notes manually annotated by experts. DeepTag extends multi-task LSTM with an improved hierarchical objective that captures the semantic structures between diseases. To foster human-machine collaboration, DeepTag also learns to abstain in examples when it is uncertain and defers them to human experts, resulting in improved performance. DeepTag accurately infers disease codes from free text even in challenging cross-hospital settings where the text comes from different clinical settings than the ones used for training. It enables automated disease annotation across a broad range of clinical diagnoses with minimal pre-processing. The technical framework in this work can be applied in other medical domains that currently lack medical coding resources.

cs.CL↗

arXiv2018

Multiaccuracy: Black-Box Post-Processing for Fairness in Classification

Prediction systems are successfully deployed in applications ranging from disease diagnosis, to predicting credit worthiness, to image recognition. Even when the overall accuracy is high, these systems may exhibit systematic biases that harm specific subpopulations; such biases may arise inadvertently due to underrepresentation in the data used to train a machine-learning model, or as the result of intentional malicious discrimination. We develop a rigorous framework of *multiaccuracy* auditing and post-processing to ensure accurate predictions across *identifiable subgroups*. Our algorithm, MULTIACCURACY-BOOST, works in any setting where we have black-box access to a predictor and a relatively small set of labeled data for auditing; importantly, this black-box framework allows for improved fairness and accountability of predictions, even when the predictor is minimally transparent. We prove that MULTIACCURACY-BOOST converges efficiently and show that if the initial model is accurate on an identifiable subgroup, then the post-processed model will be also. We experimentally demonstrate the effectiveness of the approach to improve the accuracy among minority subgroups in diverse applications (image classification, finance, population health). Interestingly, MULTIACCURACY-BOOST can improve subpopulation accuracy (e.g. for "black women") even when the sensitive features (e.g. "race", "gender") are not given to the algorithm explicitly.

cs.LG↗

arXiv2018

CoVeR: Learning Covariate-Specific Vector Representations with Tensor Decompositions

Word embedding is a useful approach to capture co-occurrence structures in large text corpora. However, in addition to the text data itself, we often have additional covariates associated with individual corpus documents---e.g. the demographic of the author, time and venue of publication---and we would like the embedding to naturally capture this information. We propose CoVeR, a new tensor decomposition model for vector embeddings with covariates. CoVeR jointly learns a \emph{base} embedding for all the words as well as a weighted diagonal matrix to model how each covariate affects the base embedding. To obtain author or venue-specific embedding, for example, we can then simply multiply the base embedding by the associated transformation matrix. The main advantages of our approach are data efficiency and interpretability of the covariate transformation. Our experiments demonstrate that our joint model learns substantially better covariate-specific embeddings compared to the standard approach of learning a separate embedding for each covariate using only the relevant subset of data, as well as other related methods. Furthermore, CoVeR encourages the embeddings to be "topic-aligned" in that the dimensions have specific independent meanings. This allows our covariate-specific embeddings to be compared by topic, enabling downstream differential analysis. We empirically evaluate the benefits of our algorithm on datasets, and demonstrate how it can be used to address many natural questions about covariate effects. Accompanying code to this paper can be found at http://github.com/kjtian/CoVeR.

cs.CL↗

arXiv2018

Feedback GAN (FBGAN) for DNA: a Novel Feedback-Loop Architecture for Optimizing Protein Functions

Generative Adversarial Networks (GANs) represent an attractive and novel approach to generate realistic data, such as genes, proteins, or drugs, in synthetic biology. Here, we apply GANs to generate synthetic DNA sequences encoding for proteins of variable length. We propose a novel feedback-loop architecture, called Feedback GAN (FBGAN), to optimize the synthetic gene sequences for desired properties using an external function analyzer. The proposed architecture also has the advantage that the analyzer need not be differentiable. We apply the feedback-loop mechanism to two examples: 1) generating synthetic genes coding for antimicrobial peptides, and 2) optimizing synthetic genes for the secondary structure of their resulting peptides. A suite of metrics demonstrate that the GAN generated proteins have desirable biophysical properties. The FBGAN architecture can also be used to optimize GAN-generated datapoints for useful properties in domains beyond genomics.

q-bio.GN↗

arXiv2018

Stochastic EM for Shuffled Linear Regression

We consider the problem of inference in a linear regression model in which the relative ordering of the input features and output labels is not known. Such datasets naturally arise from experiments in which the samples are shuffled or permuted during the protocol. In this work, we propose a framework that treats the unknown permutation as a latent variable. We maximize the likelihood of observations using a stochastic expectation-maximization (EM) approach. We compare this to the dominant approach in the literature, which corresponds to hard EM in our framework. We show on synthetic data that the stochastic EM algorithm we develop has several advantages, including lower parameter error, less sensitivity to the choice of initialization, and significantly better performance on datasets that are only partially shuffled. We conclude by performing two experiments on real datasets that have been partially shuffled, in which we show that the stochastic EM algorithm can recover the weights with modest error.

stat.ML↗

arXiv2017

Why Adaptively Collected Data Have Negative Bias and How to Correct for It

From scientific experiments to online A/B testing, the previously observed data often affects how future experiments are performed, which in turn affects which data will be collected. Such adaptivity introduces complex correlations between the data and the collection procedure. In this paper, we prove that when the data collection procedure satisfies natural conditions, then sample means of the data have systematic \emph{negative} biases. As an example, consider an adaptive clinical trial where additional data points are more likely to be tested for treatments that show initial promise. Our surprising result implies that the average observed treatment effects would underestimate the true effects of each treatment. We quantitatively analyze the magnitude and behavior of this negative bias in a variety of settings. We also propose a novel debiasing algorithm based on selective inference techniques. In experiments, our method can effectively reduce bias and estimation error.

stat.ML↗

arXiv2017

Contrastive Principal Component Analysis

We present a new technique called contrastive principal component analysis (cPCA) that is designed to discover low-dimensional structure that is unique to a dataset, or enriched in one dataset relative to other data. The technique is a generalization of standard PCA, for the setting where multiple datasets are available -- e.g. a treatment and a control group, or a mixed versus a homogeneous population -- and the goal is to explore patterns that are specific to one of the datasets. We conduct a wide variety of experiments in which cPCA identifies important dataset-specific patterns that are missed by PCA, demonstrating that it is useful for many applications: subgroup discovery, visualizing trends, feature selection, denoising, and data-dependent standardization. We provide geometrical interpretations of cPCA and show that it satisfies desirable theoretical guarantees. We also extend cPCA to nonlinear settings in the form of kernel cPCA. We have released our code as a python package and documentation is on Github.

stat.ML↗

arXiv2017

Word Embeddings Quantify 100 Years of Gender and Ethnic Stereotypes

Word embeddings use vectors to represent words such that the geometry between vectors captures semantic relationship between the words. In this paper, we develop a framework to demonstrate how the temporal dynamics of the embedding can be leveraged to quantify changes in stereotypes and attitudes toward women and ethnic minorities in the 20th and 21st centuries in the United States. We integrate word embeddings trained on 100 years of text data with the U.S. Census to show that changes in the embedding track closely with demographic and occupation shifts over time. The embedding captures global social shifts -- e.g., the women's movement in the 1960s and Asian immigration into the U.S -- and also illuminates how specific adjectives and occupations became more closely associated with certain populations over time. Our framework for temporal analysis of word embedding opens up a powerful new intersection between machine learning and quantitative social science.

cs.CL↗

arXiv2017

NeuralFDR: Learning Discovery Thresholds from Hypothesis Features

As datasets grow richer, an important challenge is to leverage the full features in the data to maximize the number of useful discoveries while controlling for false positives. We address this problem in the context of multiple hypotheses testing, where for each hypothesis, we observe a p-value along with a set of features specific to that hypothesis. For example, in genetic association studies, each hypothesis tests the correlation between a variant and the trait. We have a rich set of features for each variant (e.g. its location, conservation, epigenetics etc.) which could inform how likely the variant is to have a true association. However popular testing approaches, such as Benjamini-Hochberg's procedure (BH) and independent hypothesis weighting (IHW), either ignore these features or assume that the features are categorical or uni-variate. We propose a new algorithm, NeuralFDR, which automatically learns a discovery threshold as a function of all the hypothesis features. We parametrize the discovery threshold as a neural network, which enables flexible handling of multi-dimensional discrete and continuous features as well as efficient end-to-end optimization. We prove that NeuralFDR has strong false discovery rate (FDR) guarantees, and show that it makes substantially more discoveries in synthetic and real datasets. Moreover, we demonstrate that the learned discovery threshold is directly interpretable.

stat.ME↗

arXiv2017

The Effects of Memory Replay in Reinforcement Learning

Experience replay is a key technique behind many recent advances in deep reinforcement learning. Allowing the agent to learn from earlier memories can speed up learning and break undesirable temporal correlations. Despite its wide-spread application, very little is understood about the properties of experience replay. How does the amount of memory kept affect learning dynamics? Does it help to prioritize certain experiences? In this paper, we address these questions by formulating a dynamical systems ODE model of Q-learning with experience replay. We derive analytic solutions of the ODE for a simple setting. We show that even in this very simple setting, the amount of memory kept can substantially affect the agent's performance. Too much or too little memory both slow down learning. Moreover, we characterize regimes where prioritized replay harms the agent's learning. We show that our analytic solutions have excellent agreement with experiments. Finally, we propose a simple algorithm for adaptively changing the memory buffer size which achieves consistently good empirical performance.

cs.AI↗