To whom correspondence should be addressed. Abstract As proteins with similar structures often have similar funct ions, analysis of protein structures can help predict protein functions and is thus imp ortant. We consider the problem of protein structure classification, which computati onally classifies the structures of proteins into predefined groups. We develop a weighted network that depicts the protein structures, and more importantly, we propose the firs t graphlet-based measure that applies to weighted networks. Further, we develop a de ep neural network (DNN) composed of both convolutional and recurrent layers to use this measure for classification. Put together, our approach shows dramatic improvements in performance over existing graphlet-based approaches on 36 real datasets. E ven comparing with the state-of-the-art approach, it almost halves the classification error. In addition to protein structure networks, our weighted-graphlet measure and DNN cla ssifier can potentially be applied to classification of other weighted networks in computational biology as well as in other domains. Proteins are the building molecules of life, and their diver se functions define the mechanisms of sophisticated organisms [1].

We study how well Local Causal Discovery (LCD), a simple and efficient constraint-based method for causal discovery, is able to predict causal effects in large-scale gene expression data. We construct practical estimators specific to the high-dimensional regime. Inspired by ICP, we use an optional preselection method and two different statistical tests. Empirically, the resulting LCD estimator is seen to closely approach the accuracy of ICP, the state-of-the-art method, while it is algorithmically simpler and computationally more efficient.

We study the following three fundamental problems about ridge regression: (1) what is the structure of the estimator? (2) how to correctly use cross-validation to choose the regularization parameter? and (3) how to accelerate computation without losing too much accuracy? We consider the three problems in a unified large-data linear model. We give a precise representation of ridge regression as a covariance matrix-dependent linear combination of the true parameter and the noise. We study the bias of $K$-fold cross-validation for choosing the regularization parameter, and propose a simple bias-correction. We analyze the accuracy of primal and dual sketching for ridge regression, showing they are surprisingly accurate. Our results are illustrated by simulations and by analyzing empirical data.

Automatic representation learning of key entities in electronic health record (EHR) data is a critical step for healthcare informatics that turns heterogeneous medical records into structured and actionable information. Here we propose ME2Vec, an algorithmic framework for learning low-dimensional vectors of the most common entities in EHR: medical services, doctors, and patients. ME2Vec leverages diverse graph embedding techniques to cater for the unique characteristic of each medical entity. Using real-world clinical data, we demonstrate the efficacy of ME2Vec over competitive baselines on disease diagnosis prediction.

We consider clustering based on significance tests for Gaussian Mixture Models (GMMs). Our starting point is the SigClust method developed by Liu et al. (2008), which introduces a test based on the k-means objective (with k = 2) to decide whether the data should be split into two clusters. When applied recursively, this test yields a method for hierarchical clustering that is equipped with a significance guarantee. We study the limiting distribution and power of this approach in some examples and show that there are large regions of the parameter space where the power is low. We then introduce a new test based on the idea of relative fit. Unlike prior work, we test for whether a mixture of Gaussians provides a better fit relative to a single Gaussian, without assuming that either model is correct. The proposed test has a simple critical value and provides provable error control. One version of our test provides exact, finite sample control of the type I error. We show how our tests can be used for hierarchical clustering as well as in a sequential manner for model selection. We conclude with an extensive simulation study and a cluster analysis of a gene expression dataset.

Graph kernels are kernel methods measuring graph similarity and serve as a standard tool for graph classification. However, the use of kernel methods for node classification, which is a related problem to graph representation learning, is still ill-posed and the state-of-the-art methods are heavily based on heuristics. Here, we present a novel theoretical kernel-based framework for node classification that can bridge the gap between these two representation learning problems on graphs. Our approach is motivated by graph kernel methodology but extended to learn the node representations capturing the structural information in a graph. We theoretically show that our formulation is as powerful as any positive semidefinite kernels. To efficiently learn the kernel, we propose a novel mechanism for node feature aggregation and a data-driven similarity metric employed during the training phase. More importantly, our framework is flexible and complementary to other graph-based deep learning models, e.g., Graph Convolutional Networks (GCNs). We empirically evaluate our approach on a number of standard node classification benchmarks, and demonstrate that our model sets the new state of the art.

ICU readmission is associated with longer hospitalization, mortality and adverse outcomes. An early recognition of ICU re-admission can help prevent patients from worse situation and lower treatment cost. As the abundance of Electronics Health Records (EHR), it is popular to design clinical decision tools with machine learning technique manipulating on healthcare large scale data. We designed data-driven predictive models to estimate the risk of ICU readmission. The discharge summary of each hospital admission was carefully represented by natural language processing techniques. Unified Medical Language System (UMLS) was further used to standardize inconsistency of discharge summaries. 5 machine learning classifiers were adopted to construct predictive models. The best configuration yielded a competitive AUC of 0.748. Our work suggests that natural language processing of discharge summaries is capable to send clinicians warning of unplanned 30-day readmission upon discharge.

However, as the development of computer technology, the application of machine learning introduced new ideas for seizure forecasting. Applying machine learning model onto the predication of epileptic seizure co uld help us obtain a better result and there have been plenty of scientists who have been doing such works so that there are sufficient medical data provided for researchers to do training of machine learning models. In our research, we applied traditional machine learning algorithms, such as Linear SVM, Logistic Regression, KNN (K Nearest Neighbors), and Neural Networks, like CNN (Convolutional Neural Networks), RNN (Recurrent Neural Networks), and LSTM (Long Short - Term Memory), for prediction. The emphasi s of our research is to compare the AUC (Area Under the Curve) and accuracy of various models. The research result indicates that machine learning has made epileptic seizure prediction an achievable reality.

Generative Adversarial Networks (GAN) training process, in most cases, apply uniform and Gaussian sampling methods in latent space, which probably spends most of the computation on examples that can be properly handled and easy to generate. Theoretically, importance sampling speeds up stochastic gradient algorithms for supervised learning by prioritizing training examples. In this paper, we explore the possibility for adapting importance sampling into adversarial learning. We use importance sampling to replace uniform and Gaussian sampling methods in latent space and combine normalizing flow with importance sampling to approximate latent space posterior distribution by density estimation. Empirically, results on MNIST and Fashion-MNIST demonstrate that our method significantly accelerates the convergence of generative process while retaining visual fidelity in generated samples.

This paper develops mfEGRA, a multifidelity active learning method using data-driven adaptively refined surrogates for failure boundary location in reliability analysis. This work addresses the issue of prohibitive cost of reliability analysis using Monte Carlo sampling for expensive-to-evaluate high-fidelity models by using cheaper-to-evaluate approximations of the high-fidelity model. The method builds on the Efficient Global Reliability Analysis (EGRA) method, which is a surrogate-based method that uses adaptive sampling for refining Gaussian process surrogates for failure boundary location using a single fidelity model. Our method introduces a two-stage adaptive sampling criterion that uses a multifidelity Gaussian process surrogate to leverage multiple information sources with different fidelities. The method combines expected feasibility criterion from EGRA with one-step lookahead information gain to refine the surrogate around the failure boundary. The computational savings from mfEGRA depends on the discrepancy between the different models, and the relative cost of evaluating the different models as compared to the high-fidelity model. We show that accurate estimation of reliability using mfEGRA leads to computational savings of around 50% for an analytical multimodal test problem and 24% for an acoustic horn problem, when compared to single fidelity EGRA.