Transfer Learning Improving Predictive Mortality Models for Patients in End-Stage Renal Disease

Deep learning is becoming a fundamental piece in the paradigm shift from evidence-based to data-based medicine. However, its learning capacity is rarely exploited when working with small data sets. Through transfer learning (TL), information from a source domain is transferred to a target one to enhance a learning task in such domain. The proposed TL mechanisms are based on sample and feature space augmentation. Thus, deep autoencoders extract complex representations for the data in the TL approach. Their latent representations, the so-called codes, are handled to transfer information among domains. The transfer of samples is carried out by computing a latent space mapping matrix that links codes from both domains for later reconstruction. The feature space augmentation is based on the computation of the average of the most similar codes from one domain. Such an average augments the features in a target domain. The proposed framework is evaluated in the prediction of mortality in patients in end-stage renal disease, transferring information related to the mortality of patients with acute kidney injury from the massive database MIMIC-III. Compared to other TL mechanisms, the proposed approach improves 6-11% in previous mortality predictive models. The integration of TL approaches into learning tasks in pathologies with data volume issues could encourage the use of data-based medicine in a clinical setting

The Geometry of Self-supervised Learning Models and its Impact on Transfer Learning

Self-supervised learning (SSL) has emerged as a desirable paradigm in computer vision due to the inability of supervised models to learn representations that can generalize in domains with limited labels. The recent popularity of SSL has led to the development of several models that make use of diverse training strategies, architectures, and data augmentation policies with no existing unified framework to study or assess their effectiveness in transfer learning. We propose a data-driven geometric strategy to analyze different SSL models using local neighborhoods in the feature space induced by each. Unlike existing approaches that consider mathematical approximations of the parameters, individual components, or optimization landscape, our work aims to explore the geometric properties of the representation manifolds learned by SSL models. Our proposed manifold graph metrics (MGMs) provide insights into the geometric similarities and differences between available SSL models, their invariances with respect to specific augmentations, and their performances on transfer learning tasks. Our key findings are two fold: (i) contrary to popular belief, the geometry of SSL models is not tied to its training paradigm (contrastive, non-contrastive, and cluster-based); (ii) we can predict the transfer learning capability for a specific model based on the geometric properties of its semantic and augmentation manifolds.Comment: 22 page

불충분한 고장 데이터에 대한 딥러닝 기반 회전 기계 진단기술 학습방법 연구

학위논문(박사)--서울대학교 대학원 :공과대학 기계항공공학부,2020. 2. 윤병동.Deep Learning is a promising approach for fault diagnosis in mechanical applications. Deep learning techniques are capable of processing lots of data in once, and modelling them into desired diagnostic model. In industrial fields, however, we can acquire tons of data but barely useful including fault or failure data because failure in industrial fields is usually unacceptable. To cope with this insufficient fault data problem to train diagnostic model for rotating machinery, this thesis proposes three research thrusts: 1) filter-envelope blocks in convolution neural networks (CNNs) to incorporate the preprocessing steps for vibration signal; frequency filtering and envelope extraction for more optimal solution and reduced efforts in building diagnostic model, 2) cepstrum editing based data augmentation (CEDA) for diagnostic dataset consist of vibration signals from rotating machinery, and 3) selective parameter freezing (SPF) for efficient parameter transfer in transfer learning. The first research thrust proposes noble types of functional blocks for neural networks in order to learn robust feature to the vibration data. Conventional neural networks including convolution neural network (CNN), is tend to learn biased features when the training data is acquired from small cases of conditions. This can leads to unfavorable performance to the different conditions or other similar equipment. Therefore this research propose two neural network blocks which can be incorporated to the conventional neural networks and minimize the preprocessing steps, filter block and envelope block. Each block is designed to learn frequency filter and envelope extraction function respectively, in order to induce the neural network to learn more robust and generalized features from limited vibration samples. The second thrust presents a new data augmentation technique specialized for diagnostic data of vibration signals. Many data augmentation techniques exist for image data with no consideration for properties of vibration data. Conventional techniques for data augmentation, such as flipping, rotating, or shearing are not proper for 1-d vibration data can harm the natural property of vibration signal. To augment vibration data without losing the properties of its physics, the proposed method generate new samples by editing the cepstrum which can be done by adjusting the cepstrum component of interest. By doing reverse transform to the edited cepstrum, the new samples is obtained and this results augmented dataset which leads to higher accuracy for the diagnostic model. The third research thrust suggests a new parameter repurposing method for parameter transfer, which is used for transfer learning. The proposed SPF selectively freezes transferred parameters from source network and re-train only unnecessary parameters for target domain to reduce overfitting and preserve useful source features when the target data is limited to train diagnostic model.딥러닝은 기계 응용 분야의 결함 진단을 위한 유망한 접근 방식이다. 딥러닝 기술은 많은 양의 데이터를 학습하여 진단 모델의 개발을 용이하게 한다. 그러나 산업 분야에서는 많은 양의 데이터를 얻을 수 없거나 얻을 수 있더라도 고장 데이터는 일반적으로 획득하기 매우 어렵기 때문에 딥러닝 방법의 사용은 쉽지 않다. 회전 기계의 진단을 위하여 딥러닝을 학습시킬 때 발생하는 고장 데이터 부족 문제에 대처하기 위해 이 논문은 3 가지 연구를 제안한다. 1) 향상된 진동 특징 학습을 위한 필터-엔벨롭 네트워크 구조 2) 진동데이터 생성을 위한 Cepstrum 기반 데이터 증량법3) 전이 학습에서 효율적인 파라미터 전이를 위한 선택적 파라미터 동결법. 첫 번째 연구는 진동 데이터에 대한 강건한 특징을 배우기 위해 신경망에 대한 새로운 형태의 네트워크 블록들을 제안한다. 합성곱 신경망을 포함하는 종래의 신경망은 학습 데이터가 작은 경우에 데이터로부터 편향된 특징을 배우는 경향이 있으며, 이는 다른 조건에서 작동하는 경우나 다른 시스템에 대해 적용되었을 때 낮은 진단 성능을 보인다. 따라서 본 연구는 기존의 신경망에 함께 사용될 수 있는 필터 블록 및 엔벨롭 블록을 제안한다. 각 블록은 주파수 필터와 엔벨롭 추출 기능을 네트워크 내에서 스스로 학습하여 신경망이 제한된 학습 진동데이터로부터 보다 강건하고 일반화 된 특징을 학습하도록 한다. 두 번째 연구는 진동 신호의 진단 데이터에 특화된 새로운 데이터 증량법을 제안한다. 뒤집기, 회전 또는 전단과 같은 데이터 확대를 위한 이미지 데이터를 위한 기존의 기술이 1 차원 진동 데이터에 적합하지 않으며, 진동 신호의 물리적 특성에 맞지 않는 신호를 생성할 수 있다. 물리적 특성을 잃지 않고 진동 데이터를 증량하기 위해 제안된 방법은 cepstrum의 주요성분을 추출하고 조정하여 역 cepstrum을 수행하는 방식으로 새로운 샘플을 생성한다. 제안된 방법을 통해 데이터를 생성하여 증량돤 데이터세트는 진단 모델 학습에 대해 성능향상을 가져온다. 세 번째 연구는 전이 학습에 사용되는 파라미터 전이를 위한 새로운 파라미터 재학습법을 제안한다. 제안된 선택적 파라미터 동결법은 소스 네트워크에서 전이된 파라미터를 선택적으로 동결하고 대상 도메인에 대해 불필요한 파라미터만 재학습하여 대상 데이터가 진단 모델에 재학습될 때의 과적합을 줄이고 소스 네트워크의 성능을 보존한다. 제안된 세 방법은 독립적으로 또는 동시에 진단모델에 사용되어 부족한 고장데이터로 인한 진단성능의 감소를 경감하거나 더 높은 성능을 이끌어낼 수 있다.Chapter 1 Introduction 13 1.1 Motivation 13 1.2 Research Scope and Overview 15 1.3 Structure of the Thesis 19 Chapter 2 Literature Review 20 2.1 Deep Neural Networks 20 2.2 Transfer Learning and Parameter Transfer 23 Chapter 3 Description of Testbed Data 26 3.1 Bearing Data I: Case Western Reserve University Data 26 3.2 Bearing Data II: Accelerated Life Test Test-bed 27 Chapter 4 Filter-Envelope Blocks in Neural Network for Robust Feature Learning 32 4.1 Preliminary Study of Problems In Use of CNN for Vibration Signals 34 4.1.1 Class Confusion Problem of CNN Model to Different Conditions 34 4.1.2 Benefits of Frequency Filtering and Envelope Extraction for Fault Diagnosis in Vibration Signals 37 4.2 Proposed Network Block 1: Filter Block 41 4.2.1 Spectral Feature Learning in Neural Network 42 4.2.2 FIR Band-pass Filter in Neural Network 45 4.2.3 Result and Discussion 48 4.3 Proposed Neural Block 2: Envelope Block 48 4.3.1 Max-Average Pooling Block for Envelope Extraction 51 4.3.2 Adaptive Average Pooling for Learnable Envelope Extractor 52 4.3.3 Result and Discussion 54 4.4 Filter-Envelope Network for Fault Diagnosis 56 4.4.1 Combinations of Filter-Envelope Blocks for the use of Rolling Element Bearing Fault Diagnosis 56 4.4.2 Summary and Discussion 58 Chapter 5 Cepstrum Editing Based Data Augmentation for Vibration Signals 59 5.1 Brief Review of Data Augmentation for Deep Learning 59 5.1.1 Image Augmentation to Enlarge Training Dataset 59 5.1.2 Data Augmentation for Vibration Signal 61 5.2 Cepstrum Editing based Data Augmentation 62 5.2.1 Cepstrum Editing as a Signal Preprocessing 62 5.2.2 Cepstrum Editing based Data Augmentation 64 5.3 Results and Discussion 65 5.3.1 Performance validation to rolling element bearing diagnosis 65 Chapter 6 Selective Parameter Freezing for Parameter Transfer with Small Dataset 71 6.1 Overall Procedure of Selective Parameter Freezing 72 6.2 Determination Sensitivity of Source Network Parameters 75 6.3 Case Study 1: Transfer to Different Fault Size 76 6.3.1 Performance by hyperparameter α 77 6.3.2 Effect of the number of training samples and network size 79 6.4 Case Study 2: Transfer from Artificial to Natural Fault 81 6.4.1 Diagnostic performance for proposed method 82 6.4.2 Visualization of frozen parameters by hyperparameter α 83 6.4.3 Visual inspection of feature space 85 6.5 Conclusion 87 Chapter 7 91 7.1 Contributions and Significance 91Docto

Integrating Semantic Knowledge to Tackle Zero-shot Text Classification

Insufficient or even unavailable training data of emerging classes is a big challenge of many classification tasks, including text classification. Recognising text documents of classes that have never been seen in the learning stage, so-called zero-shot text classification, is therefore difficult and only limited previous works tackled this problem. In this paper, we propose a two-phase framework together with data augmentation and feature augmentation to solve this problem. Four kinds of semantic knowledge (word embeddings, class descriptions, class hierarchy, and a general knowledge graph) are incorporated into the proposed framework to deal with instances of unseen classes effectively. Experimental results show that each and the combination of the two phases achieve the best overall accuracy compared with baselines and recent approaches in classifying real-world texts under the zero-shot scenario.Comment: Accepted NAACL-HLT 201

Unsupervised Domain Adaptation for Face Recognition in Unlabeled Videos

Despite rapid advances in face recognition, there remains a clear gap between the performance of still image-based face recognition and video-based face recognition, due to the vast difference in visual quality between the domains and the difficulty of curating diverse large-scale video datasets. This paper addresses both of those challenges, through an image to video feature-level domain adaptation approach, to learn discriminative video frame representations. The framework utilizes large-scale unlabeled video data to reduce the gap between different domains while transferring discriminative knowledge from large-scale labeled still images. Given a face recognition network that is pretrained in the image domain, the adaptation is achieved by (i) distilling knowledge from the network to a video adaptation network through feature matching, (ii) performing feature restoration through synthetic data augmentation and (iii) learning a domain-invariant feature through a domain adversarial discriminator. We further improve performance through a discriminator-guided feature fusion that boosts high-quality frames while eliminating those degraded by video domain-specific factors. Experiments on the YouTube Faces and IJB-A datasets demonstrate that each module contributes to our feature-level domain adaptation framework and substantially improves video face recognition performance to achieve state-of-the-art accuracy. We demonstrate qualitatively that the network learns to suppress diverse artifacts in videos such as pose, illumination or occlusion without being explicitly trained for them.Comment: accepted for publication at International Conference on Computer Vision (ICCV) 201

Ranking Medical Terms to Support Expansion of Lay Language Resources for Patient Comprehension of Electronic Health Record Notes: Adapted Distant Supervision Approach

BACKGROUND: Medical terms are a major obstacle for patients to comprehend their electronic health record (EHR) notes. Clinical natural language processing (NLP) systems that link EHR terms to lay terms or definitions allow patients to easily access helpful information when reading through their EHR notes, and have shown to improve patient EHR comprehension. However, high-quality lay language resources for EHR terms are very limited in the public domain. Because expanding and curating such a resource is a costly process, it is beneficial and even necessary to identify terms important for patient EHR comprehension first. OBJECTIVE: We aimed to develop an NLP system, called adapted distant supervision (ADS), to rank candidate terms mined from EHR corpora. We will give EHR terms ranked as high by ADS a higher priority for lay language annotation-that is, creating lay definitions for these terms. METHODS: Adapted distant supervision uses distant supervision from consumer health vocabulary and transfer learning to adapt itself to solve the problem of ranking EHR terms in the target domain. We investigated 2 state-of-the-art transfer learning algorithms (ie, feature space augmentation and supervised distant supervision) and designed 5 types of learning features, including distributed word representations learned from large EHR data for ADS. For evaluating ADS, we asked domain experts to annotate 6038 candidate terms as important or nonimportant for EHR comprehension. We then randomly divided these data into the target-domain training data (1000 examples) and the evaluation data (5038 examples). We compared ADS with 2 strong baselines, including standard supervised learning, on the evaluation data. RESULTS: The ADS system using feature space augmentation achieved the best average precision, 0.850, on the evaluation set when using 1000 target-domain training examples. The ADS system using supervised distant supervision achieved the best average precision, 0.819, on the evaluation set when using only 100 target-domain training examples. The 2 ADS systems both performed significantly better than the baseline systems (P \u3c .001 for all measures and all conditions). Using a rich set of learning features contributed to ADS\u27s performance substantially. CONCLUSIONS: ADS can effectively rank terms mined from EHRs. Transfer learning improved ADS\u27s performance even with a small number of target-domain training examples. EHR terms prioritized by ADS were used to expand a lay language resource that supports patient EHR comprehension. The top 10,000 EHR terms ranked by ADS are available upon request