pwc-archive/papers-with-abstracts huggingface dataset:
Parameter Estimation for the SEIR Model Using Recurrent Nets
Authors: Chun Fan, Yuxian Meng, Xiaofei Sun, Fei Wu, Tianwei Zhang, Jiwei Li
Date: 2021-05-30 00:00:00
Tasks: parameter estimation

The standard way to estimate the parameters $\Theta_\text{SEIR}$ (e.g., the transmission rate $\beta$) of an SEIR model is to use grid search, where simulations are performed on each set of parameters, and the parameter set leading to the least $L_2$ distance between predicted number of infections and observed infections is selected. This brute-force strategy is not only time consuming, as simulations are slow when the population is large, but also inaccurate, since it is impossible to enumerate all parameter combinations. To address these issues, in this paper, we propose to transform the non-differentiable problem of finding optimal $\Theta_\text{SEIR}$ to a differentiable one, where we first train a recurrent net to fit a small number of simulation data. Next, based on this recurrent net that is able to generalize SEIR simulations, we are able to transform the objective to a differentiable one with respect to $\Theta_\text{SEIR}$, and straightforwardly obtain its optimal value. The proposed strategy is both time efficient as it only relies on a small number of SEIR simulations, and accurate as we are able to find the optimal $\Theta_\text{SEIR}$ based on the differentiable objective. On two COVID-19 datasets, we observe that the proposed strategy leads to significantly better parameter estimations with a smaller number of simulations.
RFCBF: enhance the performance and stability of Fast Correlation-Based Filter
Authors: Xiongshi Deng, Min Li, Lei Wang, Qikang Wan
Date: 2021-05-30 00:00:00
Tasks: feature selection

Feature selection is a preprocessing step which plays a crucial role in the domain of machine learning and data mining. Feature selection methods have been shown to be effctive in removing redundant and irrelevant features, improving the learning algorithm's prediction performance. Among the various methods of feature selection based on redundancy, the fast correlation-based filter (FCBF) is one of the most effective. In this paper, we proposed a novel extension of FCBF, called RFCBF, which combines resampling technique to improve classification accuracy. We performed comprehensive experiments to compare the RFCBF with other state-of-the-art feature selection methods using the KNN classifier on 12 publicly available data sets. The experimental results show that the RFCBF algorithm yields significantly better results than previous state-of-the-art methods in terms of classification accuracy and runtime.
Generating Ten BCI Commands Using Four Simple Motor Imageries
Authors: Nuri Korkan, Tamer Olmez, Zumray Dokur
Date: 2021-05-30 00:00:00
Tasks: Brain Computer Interface, EEG, Electroencephalogram (EEG), Motor Imagery

The brain computer interface (BCI) systems are utilized for transferring information among humans and computers by analyzing electroencephalogram (EEG) recordings.The process of mentally previewing a motor movement without generating the corporal output can be described as motor imagery (MI).In this emerging research field, the number of commands is also limited in relation to the number of MI tasks; in the current literature, mostly two or four commands (classes) are studied. As a solution to this problem, it is recommended to use mental tasks as well as MI tasks. Unfortunately, the use of this approach reduces the classification performance of MI EEG signals. The fMRI analyses show that the resources in the brain associated with the motor imagery can be activated independently. It is assumed that the brain activity induced by the MI of the combination of body parts corresponds to the superposition of the activities generated during each body parts's simple MI. In this study, in order to create more than four BCI commands, we suggest to generate combined MI EEG signals artificially by using left hand, right hand, tongue, and feet motor imageries in pairs. A maximum of ten different BCI commands can be generated by using four motor imageries in pairs.This study aims to achieve high classification performances for BCI commands produced from four motor imageries by implementing a small-sized deep neural network (DNN).The presented method is evaluated on the four-class datasets of BCI Competitions III and IV, and an average classification performance of 81.8% is achieved for ten classes. The above assumption is also validated on a different dataset which consists of simple and combined MI EEG signals acquired in real time. Trained with the artificially generated combined MI EEG signals, DivFE resulted in an average of 76.5% success rate for the combined MI EEG signals acquired in real-time.
How Attentive are Graph Attention Networks?
Authors: Shaked Brody, Uri Alon, Eran Yahav
Date: 2021-05-30 00:00:00
Proceeding: ICLR 2022 4
Tasks: Graph Attention, Graph Classification, Graph Property Prediction, Graph Regression, Link Prediction, Molecular Property Prediction, Node Property Prediction, Representation Learning

Graph Attention Networks (GATs) are one of the most popular GNN architectures and are considered as the state-of-the-art architecture for representation learning with graphs. In GAT, every node attends to its neighbors given its own representation as the query. However, in this paper we show that GAT computes a very limited kind of attention: the ranking of the attention scores is unconditioned on the query node. We formally define this restricted kind of attention as static attention and distinguish it from a strictly more expressive dynamic attention. Because GATs use a static attention mechanism, there are simple graph problems that GAT cannot express: in a controlled problem, we show that static attention hinders GAT from even fitting the training data. To remove this limitation, we introduce a simple fix by modifying the order of operations and propose GATv2: a dynamic graph attention variant that is strictly more expressive than GAT. We perform an extensive evaluation and show that GATv2 outperforms GAT across 11 OGB and other benchmarks while we match their parametric costs. Our code is available at https://github.com/tech-srl/how_attentive_are_gats . GATv2 is available as part of the PyTorch Geometric library, the Deep Graph Library, and the TensorFlow GNN library.
Relational Graph Neural Network Design via Progressive Neural Architecture Search
Authors: Ailing Zeng, Minhao Liu, Zhiwei Liu, Ruiyuan Gao, Jing Qin, Qiang Xu
Date: 2021-05-30 00:00:00
Tasks: Graph Neural Network, Neural Architecture Search, Node Classification, Representation Learning

We propose a novel solution to addressing a long-standing dilemma in the representation learning of graph neural networks (GNNs): how to effectively capture and represent useful information embedded in long-distance nodes to improve the performance of nodes with low homophily without leading to performance degradation in nodes with high homophily. This dilemma limits the generalization capability of existing GNNs. Intuitively, interactions with distant nodes introduce more noise for a node than those with close neighbors. However, in most existing works, messages being passed among nodes are mingled together, which is inefficient from a communication perspective. Our solution is based on a novel, simple, yet effective aggregation scheme, resulting in a ladder-style GNN architecture, namely LADDER-GNN. Specifically, we separate messages from different hops, assign different dimensions for them, and then concatenate them to obtain node representations. Such disentangled representations facilitate improving the information-to-noise ratio of messages passed from different hops. To explore an effective hop-dimension relationship, we develop a conditionally progressive neural architecture search strategy. Based on the searching results, we further propose an efficient approximate hop-dimension relation function to facilitate the rapid configuration of the proposed LADDER-GNN. We verify the proposed LADDER-GNN on seven diverse semi-supervised node classification datasets. Experimental results show that our solution achieves better performance than most existing GNNs. We further analyze our aggregation scheme with two commonly used GNN architectures, and the results corroborate that our scheme outperforms existing schemes in classifying low homophily nodes by a large margin.
CSCAD: Correlation Structure-based Collective Anomaly Detection in Complex System
Authors: Huiling Qin, Xianyuan Zhan, Yu Zheng
Date: 2021-05-30 00:00:00
Tasks: Anomaly Detection

Detecting anomalies in large complex systems is a critical and challenging task. The difficulties arise from several aspects. First, collecting ground truth labels or prior knowledge for anomalies is hard in real-world systems, which often lead to limited or no anomaly labels in the dataset. Second, anomalies in large systems usually occur in a collective manner due to the underlying dependency structure among devices or sensors. Lastly, real-time anomaly detection for high-dimensional data requires efficient algorithms that are capable of handling different types of data (i.e. continuous and discrete). We propose a correlation structure-based collective anomaly detection (CSCAD) model for high-dimensional anomaly detection problem in large systems, which is also generalizable to semi-supervised or supervised settings. Our framework utilize graph convolutional network combining a variational autoencoder to jointly exploit the feature space correlation and reconstruction deficiency of samples to perform anomaly detection. We propose an extended mutual information (EMI) metric to mine the internal correlation structure among different data features, which enhances the data reconstruction capability of CSCAD. The reconstruction loss and latent standard deviation vector of a sample obtained from reconstruction network can be perceived as two natural anomalous degree measures. An anomaly discriminating network can then be trained using low anomalous degree samples as positive samples, and high anomalous degree samples as negative samples. Experimental results on five public datasets demonstrate that our approach consistently outperforms all the competing baselines.
Maximizing Parallelism in Distributed Training for Huge Neural Networks
Authors: Zhengda Bian, Qifan Xu, Boxiang Wang, Yang You
Date: 2021-05-30 00:00:00

The recent Natural Language Processing techniques have been refreshing the state-of-the-art performance at an incredible speed. Training huge language models is therefore an imperative demand in both industry and academy. However, huge language models impose challenges to both hardware and software. Graphical processing units (GPUs) are iterated frequently to meet the exploding demand, and a variety of ASICs like TPUs are spawned. However, there is still a tension between the fast growth of the extremely huge models and the fact that Moore's law is approaching the end. To this end, many model parallelism techniques are proposed to distribute the model parameters to multiple devices, so as to alleviate the tension on both memory and computation. Our work is the first to introduce a 3-dimensional model parallelism for expediting huge language models. By reaching a perfect load balance, our approach presents smaller memory and communication cost than existing state-of-the-art 1-D and 2-D model parallelism. Our experiments on 64 TACC's V100 GPUs show that our 3-D parallelism outperforms the 1-D and 2-D parallelism with 2.32x and 1.57x speedup, respectively.
Overparameterization of deep ResNet: zero loss and mean-field analysis
Authors: Zhiyan Ding, Shi Chen, Qin Li, Stephen Wright
Date: 2021-05-30 00:00:00

Finding parameters in a deep neural network (NN) that fit training data is a nonconvex optimization problem, but a basic first-order optimization method (gradient descent) finds a global optimizer with perfect fit (zero-loss) in many practical situations. We examine this phenomenon for the case of Residual Neural Networks (ResNet) with smooth activation functions in a limiting regime in which both the number of layers (depth) and the number of weights in each layer (width) go to infinity. First, we use a mean-field-limit argument to prove that the gradient descent for parameter training becomes a gradient flow for a probability distribution that is characterized by a partial differential equation (PDE) in the large-NN limit. Next, we show that under certain assumptions, the solution to the PDE converges in the training time to a zero-loss solution. Together, these results suggest that the training of the ResNet gives a near-zero loss if the ResNet is large enough. We give estimates of the depth and width needed to reduce the loss below a given threshold, with high probability.
Machine learning moment closure models for the radiative transfer equation II: enforcing global hyperbolicity in gradient based closures
Authors: Juntao Huang, Yingda Cheng, Andrew J. Christlieb, Luke F. Roberts, Wen-An Yong
Date: 2021-05-30 00:00:00
Tasks: RTE

This is the second paper in a series in which we develop machine learning (ML) moment closure models for the radiative transfer equation (RTE). In our previous work \cite{huang2021gradient}, we proposed an approach to directly learn the gradient of the unclosed high order moment, which performs much better than learning the moment itself and the conventional $P_N$ closure. However, the ML moment closure model in \cite{huang2021gradient} is not able to guarantee hyperbolicity and long time stability. We propose in this paper a method to enforce the global hyperbolicity of the ML closure model. The main idea is to seek a symmetrizer (a symmetric positive definite matrix) for the closure system, and derive constraints such that the system is globally symmetrizable hyperbolic. It is shown that the new ML closure system inherits the dissipativeness of the RTE and preserves the correct diffusion limit as the Knunsden number goes to zero. Several benchmark tests including the Gaussian source problem and the two-material problem show the good accuracy, long time stability and generalizability of our globally hyperbolic ML closure model.
A Matrix Autoencoder Framework to Align the Functional and Structural Connectivity Manifolds as Guided by Behavioral Phenotypes
Authors: Niharika Shimona D'Souza, Mary Beth Nebel, Deana Crocetti, Nicholas Wymbs, Joshua Robinson, Stewart Mostofsky, Archana Venkataraman
Date: 2021-05-30 00:00:00
Tasks: Decoder

We propose a novel matrix autoencoder to map functional connectomes from resting state fMRI (rs-fMRI) to structural connectomes from Diffusion Tensor Imaging (DTI), as guided by subject-level phenotypic measures. Our specialized autoencoder infers a low dimensional manifold embedding for the rs-fMRI correlation matrices that mimics a canonical outer-product decomposition. The embedding is simultaneously used to reconstruct DTI tractography matrices via a second manifold alignment decoder and to predict inter-subject phenotypic variability via an artificial neural network. We validate our framework on a dataset of 275 healthy individuals from the Human Connectome Project database and on a second clinical dataset consisting of 57 subjects with Autism Spectrum Disorder. We demonstrate that the model reliably recovers structural connectivity patterns across individuals, while robustly extracting predictive and interpretable brain biomarkers in a cross-validated setting. Finally, our framework outperforms several baselines at predicting behavioral phenotypes in both real-world datasets.
Re-evaluating Word Mover's Distance
Authors: Ryoma Sato, Makoto Yamada, Hisashi Kashima
Date: 2021-05-30 00:00:00

The word mover's distance (WMD) is a fundamental technique for measuring the similarity of two documents. As the crux of WMD, it can take advantage of the underlying geometry of the word space by employing an optimal transport formulation. The original study on WMD reported that WMD outperforms classical baselines such as bag-of-words (BOW) and TF-IDF by significant margins in various datasets. In this paper, we point out that the evaluation in the original study could be misleading. We re-evaluate the performances of WMD and the classical baselines and find that the classical baselines are competitive with WMD if we employ an appropriate preprocessing, i.e., L1 normalization. In addition, we introduce an analogy between WMD and L1-normalized BOW and find that not only the performance of WMD but also the distance values resemble those of BOW in high dimensional spaces.
SyReNets: Symbolic Residual Neural Networks
Authors: Carlos Magno C. O. Valle, Sami Haddadin
Date: 2021-05-30 00:00:00

Despite successful seminal works on passive systems in the literature, learning free-form physical laws for controlled dynamical systems given experimental data is still an open problem. For decades, symbolic mathematical equations and system identification were the golden standards. Unfortunately, a set of assumptions about the properties of the underlying system is required, which makes the model very rigid and unable to adapt to unforeseen changes in the physical system. Neural networks, on the other hand, are known universal function approximators but are prone to over-fit, limited accuracy, and bias problems, which makes them alone unreliable candidates for such tasks. In this paper, we propose SyReNets, an approach that leverages neural networks for learning symbolic relations to accurately describe dynamic physical systems from data. It explores a sequence of symbolic layers that build, in a residual manner, mathematical relations that describes a given desired output from input variables. We apply it to learn the symbolic equation that describes the Lagrangian of a given physical system. We do this by only observing random samples of position, velocity, and acceleration as input and torque as output. Therefore, using the Lagrangian as a latent representation from which we derive torque using the Euler-Lagrange equations. The approach is evaluated using a simulated controlled double pendulum and compared with neural networks, genetic programming, and traditional system identification. The results demonstrate that, compared to neural networks and genetic programming, SyReNets converges to representations that are more accurate and precise throughout the state space. Despite having slower convergence than traditional system identification, similar to neural networks, the approach remains flexible enough to adapt to an unforeseen change in the physical system structure.
On Centralized and Distributed Mirror Descent: Convergence Analysis Using Quadratic Constraints
Authors: Youbang Sun, Mahyar Fazlyab, Shahin Shahrampour
Date: 2021-05-29 00:00:00

Mirror descent (MD) is a powerful first-order optimization technique that subsumes several optimization algorithms including gradient descent (GD). In this work, we develop a semi-definite programming (SDP) framework to analyze the convergence rate of MD in centralized and distributed settings under both strongly convex and non-strongly convex assumptions. We view MD with a dynamical system lens and leverage quadratic constraints (QCs) to provide explicit convergence rates based on Lyapunov stability. For centralized MD under strongly convex assumption, we develop a SDP that certifies exponential convergence rates. We prove that the SDP always has a feasible solution that recovers the optimal GD rate as a special case. We complement our analysis by providing the $O(1/k)$ convergence rate for convex problems. Next, we analyze the convergence of distributed MD and characterize the rate using SDP. To the best of our knowledge, the numerical rate of distributed MD has not been previously reported in the literature. We further prove an $O(1/k)$ convergence rate for distributed MD in the convex setting. Our numerical experiments on strongly convex problems indicate that our framework certifies superior convergence rates compared to the existing rates for distributed GD.
Ten Quick Tips for Deep Learning in Biology
Authors: Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander J. Titus, Michael D. Kessler, Alexandra J. Lee, Marc G. Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M. Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J. Fertig, Alexandr A. Kalinin, Beth Signal, Benjamin J. Lengerich, Timothy J. Triche Jr, Simina M. Boca
Date: 2021-05-29 00:00:00
Tasks: BIG-bench Machine Learning, Deep Learning

Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive modeling. Artificial neural networks are a particular class of machine learning algorithms and models that evolved into what is now described as deep learning. Given the computational advances made in the last decade, deep learning can now be applied to massive data sets and in innumerable contexts. Therefore, deep learning has become its own subfield of machine learning. In the context of biological research, it has been increasingly used to derive novel insights from high-dimensional biological data. To make the biological applications of deep learning more accessible to scientists who have some experience with machine learning, we solicited input from a community of researchers with varied biological and deep learning interests. These individuals collaboratively contributed to this manuscript's writing using the GitHub version control platform and the Manubot manuscript generation toolset. The goal was to articulate a practical, accessible, and concise set of guidelines and suggestions to follow when using deep learning. In the course of our discussions, several themes became clear: the importance of understanding and applying machine learning fundamentals as a baseline for utilizing deep learning, the necessity for extensive model comparisons with careful evaluation, and the need for critical thought in interpreting results generated by deep learning, among others.
Fit without fear: remarkable mathematical phenomena of deep learning through the prism of interpolation
Authors: Mikhail Belkin
Date: 2021-05-29 00:00:00
Tasks: BIG-bench Machine Learning

In the past decade the mathematical theory of machine learning has lagged far behind the triumphs of deep neural networks on practical challenges. However, the gap between theory and practice is gradually starting to close. In this paper I will attempt to assemble some pieces of the remarkable and still incomplete mathematical mosaic emerging from the efforts to understand the foundations of deep learning. The two key themes will be interpolation, and its sibling, over-parameterization. Interpolation corresponds to fitting data, even noisy data, exactly. Over-parameterization enables interpolation and provides flexibility to select a right interpolating model. As we will see, just as a physical prism separates colors mixed within a ray of light, the figurative prism of interpolation helps to disentangle generalization and optimization properties within the complex picture of modern Machine Learning. This article is written with belief and hope that clearer understanding of these issues brings us a step closer toward a general theory of deep learning and machine learning.