arXiv subjects

Pengtao Xie

Publications and source records attributed to Pengtao Xie.

At least 109 records · Page 6Linked to original sources

arXiv2018

Missing Value Imputation Based on Deep Generative Models

Missing values widely exist in many real-world datasets, which hinders the performing of advanced data analytics. Properly filling these missing values is crucial but challenging, especially when the missing rate is high. Many approaches have been proposed for missing value imputation (MVI), but they are mostly heuristics-based, lacking a principled foundation and do not perform satisfactorily in practice. In this paper, we propose a probabilistic framework based on deep generative models for MVI. Under this framework, imputing the missing entries amounts to seeking a fixed-point solution between two conditional distributions defined on the missing entries and latent variables respectively. These distributions are parameterized by deep neural networks (DNNs) which possess high approximation power and can capture the nonlinear relationships between missing entries and the observed values. The learning of weight parameters of DNNs is performed by maximizing an approximation of the log-likelihood of observed values. We conducted extensive evaluation on 13 datasets and compared with 11 baselines methods, where our methods largely outperforms the baselines.

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arXiv2018

On the Automatic Generation of Medical Imaging Reports

Medical imaging is widely used in clinical practice for diagnosis and treatment. Report-writing can be error-prone for unexperienced physicians, and time- consuming and tedious for experienced physicians. To address these issues, we study the automatic generation of medical imaging reports. This task presents several challenges. First, a complete report contains multiple heterogeneous forms of information, including findings and tags. Second, abnormal regions in medical images are difficult to identify. Third, the re- ports are typically long, containing multiple sentences. To cope with these challenges, we (1) build a multi-task learning framework which jointly performs the pre- diction of tags and the generation of para- graphs, (2) propose a co-attention mechanism to localize regions containing abnormalities and generate narrations for them, (3) develop a hierarchical LSTM model to generate long paragraphs. We demonstrate the effectiveness of the proposed methods on two publicly available datasets.

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arXiv2018

Orthogonality-Promoting Distance Metric Learning: Convex Relaxation and Theoretical Analysis

Distance metric learning (DML), which learns a distance metric from labeled "similar" and "dissimilar" data pairs, is widely utilized. Recently, several works investigate orthogonality-promoting regularization (OPR), which encourages the projection vectors in DML to be close to being orthogonal, to achieve three effects: (1) high balancedness -- achieving comparable performance on both frequent and infrequent classes; (2) high compactness -- using a small number of projection vectors to achieve a "good" metric; (3) good generalizability -- alleviating overfitting to training data. While showing promising results, these approaches suffer three problems. First, they involve solving non-convex optimization problems where achieving the global optimal is NP-hard. Second, it lacks a theoretical understanding why OPR can lead to balancedness. Third, the current generalization error analysis of OPR is not directly on the regularizer. In this paper, we address these three issues by (1) seeking convex relaxations of the original nonconvex problems so that the global optimal is guaranteed to be achievable; (2) providing a formal analysis on OPR's capability of promoting balancedness; (3) providing a theoretical analysis that directly reveals the relationship between OPR and generalization performance. Experiments on various datasets demonstrate that our convex methods are more effective in promoting balancedness, compactness, and generalization, and are computationally more efficient, compared with the nonconvex methods.

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arXiv2017

Convolutional Neural Networks for Medical Diagnosis from Admission Notes

$\textbf{Objective}$ Develop an automatic diagnostic system which only uses textual admission information from Electronic Health Records (EHRs) and assist clinicians with a timely and statistically proved decision tool. The hope is that the tool can be used to reduce mis-diagnosis. $\textbf{Materials and Methods}$ We use the real-world clinical notes from MIMIC-III, a freely available dataset consisting of clinical data of more than forty thousand patients who stayed in intensive care units of the Beth Israel Deaconess Medical Center between 2001 and 2012. We proposed a Convolutional Neural Network model to learn semantic features from unstructured textual input and automatically predict primary discharge diagnosis. $\textbf{Results}$ The proposed model achieved an overall 96.11% accuracy and 80.48% weighted F1 score values on 10 most frequent disease classes, significantly outperforming four strong baseline models by at least 12.7% in weighted F1 score. $\textbf{Discussion}$ Experimental results imply that the CNN model is suitable for supporting diagnosis decision making in the presence of complex, noisy and unstructured clinical data while at the same time using fewer layers and parameters that other traditional Deep Network models. $\textbf{Conclusion}$ Our model demonstrated capability of representing complex medical meaningful features from unstructured clinical notes and prediction power for commonly misdiagnosed frequent diseases. It can use easily adopted in clinical setting to provide timely and statistically proved decision support. $\textbf{Keywords}$ Convolutional neural network, text classification, discharge diagnosis prediction, admission information from EHRs.

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arXiv2017

Predicting Discharge Medications at Admission Time Based on Deep Learning

Predicting discharge medications right after a patient being admitted is an important clinical decision, which provides physicians with guidance on what type of medication regimen to plan for and what possible changes on initial medication may occur during an inpatient stay. It also facilitates medication reconciliation process with easy detection of medication discrepancy at discharge time to improve patient safety. However, since the information available upon admission is limited and patients' condition may evolve during an inpatient stay, these predictions could be a difficult decision for physicians to make. In this work, we investigate how to leverage deep learning technologies to assist physicians in predicting discharge medications based on information documented in the admission note. We build a convolutional neural network which takes an admission note as input and predicts the medications placed on the patient at discharge time. Our method is able to distill semantic patterns from unstructured and noisy texts, and is capable of capturing the pharmacological correlations among medications. We evaluate our method on 25K patient visits and compare with 4 strong baselines. Our methods demonstrate a 20% increase in macro-averaged F1 score than the best baseline.

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arXiv2017

Towards Automated ICD Coding Using Deep Learning

International Classification of Diseases(ICD) is an authoritative health care classification system of different diseases and conditions for clinical and management purposes. Considering the complicated and dedicated process to assign correct codes to each patient admission based on overall diagnosis, we propose a hierarchical deep learning model with attention mechanism which can automatically assign ICD diagnostic codes given written diagnosis. We utilize character-aware neural language models to generate hidden representations of written diagnosis descriptions and ICD codes, and design an attention mechanism to address the mismatch between the numbers of descriptions and corresponding codes. Our experimental results show the strong potential of automated ICD coding from diagnosis descriptions. Our best model achieves 0.53 and 0.90 of F1 score and area under curve of receiver operating characteristic respectively. The result outperforms those achieved using character-unaware encoding method or without attention mechanism. It indicates that our proposed deep learning model can code automatically in a reasonable way and provide a framework for computer-auxiliary ICD coding.

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arXiv2017

Stacked Kernel Network

Kernel methods are powerful tools to capture nonlinear patterns behind data. They implicitly learn high (even infinite) dimensional nonlinear features in the Reproducing Kernel Hilbert Space (RKHS) while making the computation tractable by leveraging the kernel trick. Classic kernel methods learn a single layer of nonlinear features, whose representational power may be limited. Motivated by recent success of deep neural networks (DNNs) that learn multi-layer hierarchical representations, we propose a Stacked Kernel Network (SKN) that learns a hierarchy of RKHS-based nonlinear features. SKN interleaves several layers of nonlinear transformations (from a linear space to a RKHS) and linear transformations (from a RKHS to a linear space). Similar to DNNs, a SKN is composed of multiple layers of hidden units, but each parameterized by a RKHS function rather than a finite-dimensional vector. We propose three ways to represent the RKHS functions in SKN: (1)nonparametric representation, (2)parametric representation and (3)random Fourier feature representation. Furthermore, we expand SKN into CNN architecture called Stacked Kernel Convolutional Network (SKCN). SKCN learning a hierarchy of RKHS-based nonlinear features by convolutional operation with each filter also parameterized by a RKHS function rather than a finite-dimensional matrix in CNN, which is suitable for image inputs. Experiments on various datasets demonstrate the effectiveness of SKN and SKCN, which outperform the competitive methods.

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arXiv2017

Learning Less-Overlapping Representations

In representation learning (RL), how to make the learned representations easy to interpret and less overfitted to training data are two important but challenging issues. To address these problems, we study a new type of regulariza- tion approach that encourages the supports of weight vectors in RL models to have small overlap, by simultaneously promoting near-orthogonality among vectors and sparsity of each vector. We apply the proposed regularizer to two models: neural networks (NNs) and sparse coding (SC), and develop an efficient ADMM-based algorithm for regu- larized SC. Experiments on various datasets demonstrate that weight vectors learned under our regularizer are more interpretable and have better generalization performance.

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arXiv2017

Diversity-Promoting Bayesian Learning of Latent Variable Models

To address three important issues involved in latent variable models (LVMs), including capturing infrequent patterns, achieving small-sized but expressive models and alleviating overfitting, several studies have been devoted to "diversifying" LVMs, which aim at encouraging the components in LVMs to be diverse. Most existing studies fall into a frequentist-style regularization framework, where the components are learned via point estimation. In this paper, we investigate how to "diversify" LVMs in the paradigm of Bayesian learning. We propose two approaches that have complementary advantages. One is to define a diversity-promoting mutual angular prior which assigns larger density to components with larger mutual angles and use this prior to affect the posterior via Bayes' rule. We develop two efficient approximate posterior inference algorithms based on variational inference and MCMC sampling. The other approach is to impose diversity-promoting regularization directly over the post-data distribution of components. We also extend our approach to "diversify" Bayesian nonparametric models where the number of components is infinite. A sampling algorithm based on slice sampling and Hamiltonian Monte Carlo is developed. We apply these methods to "diversify" Bayesian mixture of experts model and infinite latent feature model. Experiments on various datasets demonstrate the effectiveness and efficiency of our methods.

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arXiv2017

Medical Diagnosis From Laboratory Tests by Combining Generative and Discriminative Learning

A primary goal of computational phenotype research is to conduct medical diagnosis. In hospital, physicians rely on massive clinical data to make diagnosis decisions, among which laboratory tests are one of the most important resources. However, the longitudinal and incomplete nature of laboratory test data casts a significant challenge on its interpretation and usage, which may result in harmful decisions by both human physicians and automatic diagnosis systems. In this work, we take advantage of deep generative models to deal with the complex laboratory tests. Specifically, we propose an end-to-end architecture that involves a deep generative variational recurrent neural networks (VRNN) to learn robust and generalizable features, and a discriminative neural network (NN) model to learn diagnosis decision making, and the two models are trained jointly. Our experiments are conducted on a dataset involving 46,252 patients, and the 50 most frequent tests are used to predict the 50 most common diagnoses. The results show that our model, VRNN+NN, significantly (p<0.001) outperforms other baseline models. Moreover, we demonstrate that the representations learned by the joint training are more informative than those learned by pure generative models. Finally, we find that our model offers a surprisingly good imputation for missing values.

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arXiv2017

Poseidon: An Efficient Communication Architecture for Distributed Deep Learning on GPU Clusters

Deep learning models can take weeks to train on a single GPU-equipped machine, necessitating scaling out DL training to a GPU-cluster. However, current distributed DL implementations can scale poorly due to substantial parameter synchronization over the network, because the high throughput of GPUs allows more data batches to be processed per unit time than CPUs, leading to more frequent network synchronization. We present Poseidon, an efficient communication architecture for distributed DL on GPUs. Poseidon exploits the layered model structures in DL programs to overlap communication and computation, reducing bursty network communication. Moreover, Poseidon uses a hybrid communication scheme that optimizes the number of bytes required to synchronize each layer, according to layer properties and the number of machines. We show that Poseidon is applicable to different DL frameworks by plugging Poseidon into Caffe and TensorFlow. We show that Poseidon enables Caffe and TensorFlow to achieve 15.5x speed-up on 16 single-GPU machines, even with limited bandwidth (10GbE) and the challenging VGG19-22K network for image classification. Moreover, Poseidon-enabled TensorFlow achieves 31.5x speed-up with 32 single-GPU machines on Inception-V3, a 50% improvement over the open-source TensorFlow (20x speed-up).

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arXiv2015

Strategies and Principles of Distributed Machine Learning on Big Data

The rise of Big Data has led to new demands for Machine Learning (ML) systems to learn complex models with millions to billions of parameters, that promise adequate capacity to digest massive datasets and offer powerful predictive analytics thereupon. In order to run ML algorithms at such scales, on a distributed cluster with 10s to 1000s of machines, it is often the case that significant engineering efforts are required --- and one might fairly ask if such engineering truly falls within the domain of ML research or not. Taking the view that Big ML systems can benefit greatly from ML-rooted statistical and algorithmic insights --- and that ML researchers should therefore not shy away from such systems design --- we discuss a series of principles and strategies distilled from our recent efforts on industrial-scale ML solutions. These principles and strategies span a continuum from application, to engineering, and to theoretical research and development of Big ML systems and architectures, with the goal of understanding how to make them efficient, generally-applicable, and supported with convergence and scaling guarantees. They concern four key questions which traditionally receive little attention in ML research: How to distribute an ML program over a cluster? How to bridge ML computation with inter-machine communication? How to perform such communication? What should be communicated between machines? By exposing underlying statistical and algorithmic characteristics unique to ML programs but not typically seen in traditional computer programs, and by dissecting successful cases to reveal how we have harnessed these principles to design and develop both high-performance distributed ML software as well as general-purpose ML frameworks, we present opportunities for ML researchers and practitioners to further shape and grow the area that lies between ML and systems.

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arXiv2015

Latent Variable Modeling with Diversity-Inducing Mutual Angular Regularization

Latent Variable Models (LVMs) are a large family of machine learning models providing a principled and effective way to extract underlying patterns, structure and knowledge from observed data. Due to the dramatic growth of volume and complexity of data, several new challenges have emerged and cannot be effectively addressed by existing LVMs: (1) How to capture long-tail patterns that carry crucial information when the popularity of patterns is distributed in a power-law fashion? (2) How to reduce model complexity and computational cost without compromising the modeling power of LVMs? (3) How to improve the interpretability and reduce the redundancy of discovered patterns? To addresses the three challenges discussed above, we develop a novel regularization technique for LVMs, which controls the geometry of the latent space during learning to enable the learned latent components of LVMs to be diverse in the sense that they are favored to be mutually different from each other, to accomplish long-tail coverage, low redundancy, and better interpretability. We propose a mutual angular regularizer (MAR) to encourage the components in LVMs to have larger mutual angles. The MAR is non-convex and non-smooth, entailing great challenges for optimization. To cope with this issue, we derive a smooth lower bound of the MAR and optimize the lower bound instead. We show that the monotonicity of the lower bound is closely aligned with the MAR to qualify the lower bound as a desirable surrogate of the MAR. Using neural network (NN) as an instance, we analyze how the MAR affects the generalization performance of NN. On two popular latent variable models --- restricted Boltzmann machine and distance metric learning, we demonstrate that MAR can effectively capture long-tail patterns, reduce model complexity without sacrificing expressivity and improve interpretability.

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arXiv2015

Poseidon: A System Architecture for Efficient GPU-based Deep Learning on Multiple Machines

Deep learning (DL) has achieved notable successes in many machine learning tasks. A number of frameworks have been developed to expedite the process of designing and training deep neural networks (DNNs), such as Caffe, Torch and Theano. Currently they can harness multiple GPUs on a single machine, but are unable to use GPUs that are distributed across multiple machines; as even average-sized DNNs can take days to train on a single GPU with 100s of GBs to TBs of data, distributed GPUs present a prime opportunity for scaling up DL. However, the limited bandwidth available on commodity Ethernet networks presents a bottleneck to distributed GPU training, and prevents its trivial realization. To investigate how to adapt existing frameworks to efficiently support distributed GPUs, we propose Poseidon, a scalable system architecture for distributed inter-machine communication in existing DL frameworks. We integrate Poseidon with Caffe and evaluate its performance at training DNNs for object recognition. Poseidon features three key contributions that accelerate DNN training on clusters: (1) a three-level hybrid architecture that allows Poseidon to support both CPU-only and GPU-equipped clusters, (2) a distributed wait-free backpropagation (DWBP) algorithm to improve GPU utilization and to balance communication, and (3) a structure-aware communication protocol (SACP) to minimize communication overheads. We empirically show that Poseidon converges to same objectives as a single machine, and achieves state-of-art training speedup across multiple models and well-established datasets using a commodity GPU cluster of 8 nodes (e.g. 4.5x speedup on AlexNet, 4x on GoogLeNet, 4x on CIFAR-10). On the much larger ImageNet22K dataset, Poseidon with 8 nodes achieves better speedup and competitive accuracy to recent CPU-based distributed systems such as Adam and Le et al., which use 10s to 1000s of nodes.

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arXiv2015

Distributed Training of Deep Neural Networks with Theoretical Analysis: Under SSP Setting

We propose a distributed approach to train deep neural networks (DNNs), which has guaranteed convergence theoretically and great scalability empirically: close to 6 times faster on instance of ImageNet data set when run with 6 machines. The proposed scheme is close to optimally scalable in terms of number of machines, and guaranteed to converge to the same optima as the undistributed setting. The convergence and scalability of the distributed setting is shown empirically across different datasets (TIMIT and ImageNet) and machine learning tasks (image classification and phoneme extraction). The convergence analysis provides novel insights into this complex learning scheme, including: 1) layerwise convergence, and 2) convergence of the weights in probability.

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arXiv2015

Distributed Machine Learning via Sufficient Factor Broadcasting

Matrix-parametrized models, including multiclass logistic regression and sparse coding, are used in machine learning (ML) applications ranging from computer vision to computational biology. When these models are applied to large-scale ML problems starting at millions of samples and tens of thousands of classes, their parameter matrix can grow at an unexpected rate, resulting in high parameter synchronization costs that greatly slow down distributed learning. To address this issue, we propose a Sufficient Factor Broadcasting (SFB) computation model for efficient distributed learning of a large family of matrix-parameterized models, which share the following property: the parameter update computed on each data sample is a rank-1 matrix, i.e., the outer product of two "sufficient factors" (SFs). By broadcasting the SFs among worker machines and reconstructing the update matrices locally at each worker, SFB improves communication efficiency --- communication costs are linear in the parameter matrix's dimensions, rather than quadratic --- without affecting computational correctness. We present a theoretical convergence analysis of SFB, and empirically corroborate its efficiency on four different matrix-parametrized ML models.

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arXiv2015

On the Generalization Error Bounds of Neural Networks under Diversity-Inducing Mutual Angular Regularization

Recently diversity-inducing regularization methods for latent variable models (LVMs), which encourage the components in LVMs to be diverse, have been studied to address several issues involved in latent variable modeling: (1) how to capture long-tail patterns underlying data; (2) how to reduce model complexity without sacrificing expressivity; (3) how to improve the interpretability of learned patterns. While the effectiveness of diversity-inducing regularizers such as the mutual angular regularizer has been demonstrated empirically, a rigorous theoretical analysis of them is still missing. In this paper, we aim to bridge this gap and analyze how the mutual angular regularizer (MAR) affects the generalization performance of supervised LVMs. We use neural network (NN) as a model instance to carry out the study and the analysis shows that increasing the diversity of hidden units in NN would reduce estimation error and increase approximation error. In addition to theoretical analysis, we also present empirical study which demonstrates that the MAR can greatly improve the performance of NN and the empirical observations are in accordance with the theoretical analysis.

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arXiv2015

Distributed Machine Learning via Sufficient Factor Broadcasting

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