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.
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.
$\textbf{Objective}$ 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.
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.
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.
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.
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.
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.
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.
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).