OpenRaiser/Intern-Atlas huggingface dataset:
EEG to fMRI Synthesis: Is Deep Learning a candidate?
Venue: arXiv cs.LG 2020
Year: 2020

Advances on signal, image and video generation underly major breakthroughs on generative medical imaging tasks, including Brain Image Synthesis. Still, the extent to which functional Magnetic Ressonance Imaging (fMRI) can be mapped from the brain electrophysiology remains largely unexplored. This work provides the first comprehensive view on how to use state-of-the-art principles from Neural Processing to synthesize fMRI data from electroencephalographic (EEG) data. Given the distinct spatiotemporal nature of haemodynamic and electrophysiological signals, this problem is formulated as the task of learning a mapping function between multivariate time series with highly dissimilar structures. A comparison of state-of-the-art synthesis approaches, including Autoencoders, Generative Adversarial Networks and Pairwise Learning, is undertaken. Results highlight the feasibility of EEG to fMRI brain image mappings, pinpointing the role of current advances in Machine Learning and showing the relevance of upcoming contributions to further improve performance. EEG to fMRI synthesis offers a way to enhance and augment brain image data, and guarantee access to more affordable, portable and long-lasting protocols of brain activity monitoring. The code used in this manuscript is available in Github and the datasets are open source.
Score-level Multi Cue Fusion for Sign Language Recognition
Venue: arXiv cs.CV 2020
Year: 2020

Sign Languages are expressed through hand and upper body gestures as well as facial expressions. Therefore, Sign Language Recognition (SLR) needs to focus on all such cues. Previous work uses hand-crafted mechanisms or network aggregation to extract the different cue features, to increase SLR performance. This is slow and involves complicated architectures. We propose a more straightforward approach that focuses on training separate cue models specializing on the dominant hand, hands, face, and upper body regions. We compare the performance of 3D Convolutional Neural Network (CNN) models specializing in these regions, combine them through score-level fusion, and use the weighted alternative. Our experimental results have shown the effectiveness of mixed convolutional models. Their fusion yields up to 19% accuracy improvement over the baseline using the full upper body. Furthermore, we include a discussion for fusion settings, which can help future work on Sign Language Translation (SLT).
Unbalanced Sobolev Descent
Venue: arXiv cs.LG 2020
Year: 2020

We introduce Unbalanced Sobolev Descent (USD), a particle descent algorithm for transporting a high dimensional source distribution to a target distribution that does not necessarily have the same mass. We define the Sobolev-Fisher discrepancy between distributions and show that it relates to advection-reaction transport equations and the Wasserstein-Fisher-Rao metric between distributions. USD transports particles along gradient flows of the witness function of the Sobolev-Fisher discrepancy (advection step) and reweighs the mass of particles with respect to this witness function (reaction step). The reaction step can be thought of as a birth-death process of the particles with rate of growth proportional to the witness function. When the Sobolev-Fisher witness function is estimated in a Reproducing Kernel Hilbert Space (RKHS), under mild assumptions we show that USD converges asymptotically (in the limit of infinite particles) to the target distribution in the Maximum Mean Discrepancy (MMD) sense. We then give two methods to estimate the Sobolev-Fisher witness with neural networks, resulting in two Neural USD algorithms. The first one implements the reaction step with mirror descent on the weights, while the second implements it through a birth-death process of particles. We show on synthetic examples that USD transports distributions with or without conservation of mass faster than previous particle descent algorithms, and finally demonstrate its use for molecular biology analyses where our method is naturally suited to match developmental stages of populations of differentiating cells based on their single-cell RNA sequencing profile. Code is available at https://github.com/ibm/usd .
Clustering under Perturbation Stability in Near-Linear Time
Venue: arXiv cs.DS 2020
Year: 2020

We consider the problem of center-based clustering in low-dimensional Euclidean spaces under the perturbation stability assumption. An instance is $α$-stable if the underlying optimal clustering continues to remain optimal even when all pairwise distances are arbitrarily perturbed by a factor of at most $α$. Our main contribution is in presenting efficient exact algorithms for $α$-stable clustering instances whose running times depend near-linearly on the size of the data set when $α\ge 2 + \sqrt{3}$. For $k$-center and $k$-means problems, our algorithms also achieve polynomial dependence on the number of clusters, $k$, when $α\geq 2 + \sqrt{3} + ε$ for any constant $ε> 0$ in any fixed dimension. For $k$-median, our algorithms have polynomial dependence on $k$ for $α> 5$ in any fixed dimension; and for $α\geq 2 + \sqrt{3}$ in two dimensions. Our algorithms are simple, and only require applying techniques such as local search or dynamic programming to a suitably modified metric space, combined with careful choice of data structures.
Development of Word Embeddings for Uzbek Language
Venue: arXiv cs.CL 2020
Year: 2020

In this paper, we share the process of developing word embeddings for the Cyrillic variant of the Uzbek language. The result of our work is the first publicly available set of word vectors trained on the word2vec, GloVe, and fastText algorithms using a high-quality web crawl corpus developed in-house. The developed word embeddings can be used in many natural language processing downstream tasks.
Towards Adaptive Semantic Segmentation by Progressive Feature Refinement
Venue: arXiv cs.CV 2020
Year: 2020

As one of the fundamental tasks in computer vision, semantic segmentation plays an important role in real world applications. Although numerous deep learning models have made notable progress on several mainstream datasets with the rapid development of convolutional networks, they still encounter various challenges in practical scenarios. Unsupervised adaptive semantic segmentation aims to obtain a robust classifier trained with source domain data, which is able to maintain stable performance when deployed to a target domain with different data distribution. In this paper, we propose an innovative progressive feature refinement framework, along with domain adversarial learning to boost the transferability of segmentation networks. Specifically, we firstly align the multi-stage intermediate feature maps of source and target domain images, and then a domain classifier is adopted to discriminate the segmentation output. As a result, the segmentation models trained with source domain images can be transferred to a target domain without significant performance degradation. Experimental results verify the efficiency of our proposed method compared with state-of-the-art methods.
A Virtual Reality Game as a Tool to Assess Physiological Correlations of Stress
Venue: arXiv cs.HC 2020
Year: 2020

The objective of this study is to develop and use a virtual reality game as a tool to assess the effects of realistic stress on the behavioral and physiological responses of participants. The game is based on a popular Steam game called Keep Talking Nobody Explodes, where the player collaborates with another person to defuse a bomb. Varying levels of difficulties in solving a puzzle and time pressures will result in different stress levels that can be measured in terms of errors, response time lengths, and other physiological measurements. The game was developed using 3D programming tools including Blender and virtual reality development kit (VRTK). To measure response times accurately, we added LSL (Lab Stream Layer) Markers to collect and synchronize physiological signals, behavioral data, and the timing of game events. We recorded Electrocardiogram (ECG) data during gameplay to assess heart rate and heart-rate variability (HRV) that have been shown as reliable indicators of stress. Our empirical results showed that heart rate increased significantly while HRV reduced significantly when the participants under high stress, which are consistent with the prior mainstream stress research. We further experimented with other tools to enhance communication between two players under adverse conditions and found that an automatic speech recognition software effectively enhanced the communication between the players by displaying keywords into the player's headset that lead to the facilitation of finding the solution of the puzzles or modules. This VR game framework is publicly available in Github and allows researchers to measure and synchronize other physiological signals such as electroencephalogram, electromyogram, and pupillometry.
A task-based approach to parallel parametric linear programming solving, and application to polyhedral computations
Venue: arXiv cs.CG 2020
Year: 2020

Parametric linear programming is a central operation for polyhedral computations, as well as in certain control applications.Here we propose a task-based scheme for parallelizing it, with quasi-linear speedup over large problems.This type of parallel applications is challenging, because several tasks mightbe computing the same region. In this paper, we are presenting thealgorithm itself with a parallel redundancy elimination algorithm, andconducting a thorough performance analysis.
Spectral Embedding of Graph Networks
Venue: arXiv cs.LG 2020
Year: 2020

We introduce an unsupervised graph embedding that trades off local node similarity and connectivity, and global structure. The embedding is based on a generalized graph Laplacian, whose eigenvectors compactly capture both network structure and neighborhood proximity in a single representation. The key idea is to transform the given graph into one whose weights measure the centrality of an edge by the fraction of the number of shortest paths that pass through that edge, and employ its spectral proprieties in the representation. Testing the resulting graph network representation shows significant improvement over the sate of the art in data analysis tasks including social networks and material science. We also test our method on node classification from the human-SARS CoV-2 protein-protein interactome.
Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices
Venue: arXiv cs.DC 2020
Year: 2020

Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene location. Performance and scalability of protein similarity searches have proven to be a bottleneck in many bioinformatics pipelines due to increases in cheap and abundant sequencing data. This work presents a new distributed-memory software, PASTIS. PASTIS relies on sparse matrix computations for efficient identification of possibly similar proteins. We use distributed sparse matrices for scalability and show that the sparse matrix infrastructure is a great fit for protein similarity searches when coupled with a fully-distributed dictionary of sequences that allows remote sequence requests to be fulfilled. Our algorithm incorporates the unique bias in amino acid sequence substitution in searches without altering the basic sparse matrix model, and in turn, achieves ideal scaling up to millions of protein sequences.
System measurement of Intel AEP Optane DIMM
Venue: arXiv cs.AR 2020
Year: 2020

In recent years, memory wall has been a great performance bottleneck of computer system. To overcome it, Non-Volatile Main Memory (NVMM) technology has been discussed widely to provide a much larger main memory capacity. Last year, Intel released AEP Optane DIMM, which provides hundreds of GB capacity as a promising replacement of traditional DRAM memory. But as most key parameters of AEP is not open to users, there is a need to get to know them because they will guide a direction of further NVMM research. In this paper, we focus on measuring performance and architecture features of AEP DIMM. Together, we explore the design of DRAM cache which is an important part of DRAM-AEP hybrid memory system. As a result, we estimate the write latency of AEP DIMM which has not been measured accurately. And, we discover the current design parameters of DRAM cache, such as tag organization, cache associativity and set index mapping. All of these features are first published on academic paper which are greatly helpful to future NVMM optimizations.
Turbulent Details Simulation for SPH Fluids via Vorticity Refinement
Venue: arXiv cs.GR 2020
Year: 2020

A major issue in Smoothed Particle Hydrodynamics (SPH) approaches is the numerical dissipation during the projection process, especially under coarse discretizations. High-frequency details, such as turbulence and vortices, are smoothed out, leading to unrealistic results. To address this issue, we introduce a Vorticity Refinement (VR) solver for SPH fluids with negligible computational overhead. In this method, the numerical dissipation of the vorticity field is recovered by the difference between the theoretical and the actual vorticity, so as to enhance turbulence details. Instead of solving the Biot-Savart integrals, a stream function, which is easier and more efficient to solve, is used to relate the vorticity field to the velocity field. We obtain turbulence effects of different intensity levels by changing an adjustable parameter. Since the vorticity field is enhanced according to the curl field, our method can not only amplify existing vortices, but also capture additional turbulence. Our VR solver is straightforward to implement and can be easily integrated into existing SPH methods.
Accelerating Sparse Matrix-Matrix Multiplication with GPU Tensor Cores
Venue: arXiv cs.MS 2020
Year: 2020

Sparse general matrix-matrix multiplication (spGEMM) is an essential component in many scientific and data analytics applications. However, the sparsity pattern of the input matrices and the interaction of their patterns make spGEMM challenging. Modern GPUs include Tensor Core Units (TCUs), which specialize in dense matrix multiplication. Our aim is to re-purpose TCUs for sparse matrices. The key idea of our spGEMM algorithm, tSparse, is to multiply sparse rectangular blocks using the mixed precision mode of TCUs. tSparse partitions the input matrices into tiles and operates only on tiles which contain one or more elements. It creates a task list of the tiles, and performs matrix multiplication of these tiles using TCUs. To the best of our knowledge, this is the first time that TCUs are used in the context of spGEMM. We show that spGEMM, with our tiling approach, benefits from TCUs. Our approach significantly improves the performance of spGEMM in comparison to cuSPARSE, CUSP, RMerge2, Nsparse, AC-SpGEMM and spECK.
Legal Judgment Prediction (LJP) Amid the Advent of Autonomous AI Legal Reasoning
Venue: arXiv cs.CY 2020
Year: 2020

Legal Judgment Prediction (LJP) is a longstanding and open topic in the theory and practice-of-law. Predicting the nature and outcomes of judicial matters is abundantly warranted, keenly sought, and vigorously pursued by those within the legal industry and also by society as a whole. The tenuous act of generating judicially laden predictions has been limited in utility and exactitude, requiring further advancement. Various methods and techniques to predict legal cases and judicial actions have emerged over time, especially arising via the advent of computer-based modeling. There has been a wide range of approaches attempted, including simple calculative methods to highly sophisticated and complex statistical models. Artificial Intelligence (AI) based approaches have also been increasingly utilized. In this paper, a review of the literature encompassing Legal Judgment Prediction is undertaken, along with innovatively proposing that the advent of AI Legal Reasoning (AILR) will have a pronounced impact on how LJP is performed and its predictive accuracy. Legal Judgment Prediction is particularly examined using the Levels of Autonomy (LoA) of AI Legal Reasoning, plus, other considerations are explored including LJP probabilistic tendencies, biases handling, actor predictors, transparency, judicial reliance, legal case outcomes, and other crucial elements entailing the overarching legal judicial milieu.
Driver Anomaly Detection: A Dataset and Contrastive Learning Approach
Venue: arXiv cs.CV 2020
Year: 2020

Distracted drivers are more likely to fail to anticipate hazards, which result in car accidents. Therefore, detecting anomalies in drivers' actions (i.e., any action deviating from normal driving) contains the utmost importance to reduce driver-related accidents. However, there are unbounded many anomalous actions that a driver can do while driving, which leads to an 'open set recognition' problem. Accordingly, instead of recognizing a set of anomalous actions that are commonly defined by previous dataset providers, in this work, we propose a contrastive learning approach to learn a metric to differentiate normal driving from anomalous driving. For this task, we introduce a new video-based benchmark, the Driver Anomaly Detection (DAD) dataset, which contains normal driving videos together with a set of anomalous actions in its training set. In the test set of the DAD dataset, there are unseen anomalous actions that still need to be winnowed out from normal driving. Our method reaches 0.9673 AUC on the test set, demonstrating the effectiveness of the contrastive learning approach on the anomaly detection task. Our dataset, codes and pre-trained models are publicly available.
An Online Learning Algorithm for a Neuro-Fuzzy Classifier with Mixed-Attribute Data
Venue: arXiv cs.LG 2020
Year: 2020

General fuzzy min-max neural network (GFMMNN) is one of the efficient neuro-fuzzy systems for data classification. However, one of the downsides of its original learning algorithms is the inability to handle and learn from the mixed-attribute data. While categorical features encoding methods can be used with the GFMMNN learning algorithms, they exhibit a lot of shortcomings. Other approaches proposed in the literature are not suitable for on-line learning as they require entire training data available in the learning phase. With the rapid change in the volume and velocity of streaming data in many application areas, it is increasingly required that the constructed models can learn and adapt to the continuous data changes in real-time without the need for their full retraining or access to the historical data. This paper proposes an extended online learning algorithm for the GFMMNN. The proposed method can handle the datasets with both continuous and categorical features. The extensive experiments confirmed superior and stable classification performance of the proposed approach in comparison to other relevant learning algorithms for the GFMM model.
A Framework to Handle Multi-modal Multi-objective Optimization in Decomposition-based Evolutionary Algorithms
Venue: arXiv cs.NE 2020
Year: 2020

Multi-modal multi-objective optimization is to locate (almost) equivalent Pareto optimal solutions as many as possible. While decomposition-based evolutionary algorithms have good performance for multi-objective optimization, they are likely to perform poorly for multi-modal multi-objective optimization due to the lack of mechanisms to maintain the solution space diversity. To address this issue, this paper proposes a framework to improve the performance of decomposition-based evolutionary algorithms for multi-modal multi-objective optimization. Our framework is based on three operations: assignment, deletion, and addition operations. One or more individuals can be assigned to the same subproblem to handle multiple equivalent solutions. In each iteration, a child is assigned to a subproblem based on its objective vector, i.e., its location in the objective space. The child is compared with its neighbors in the solution space assigned to the same subproblem. The performance of improved versions of six decomposition-based evolutionary algorithms by our framework is evaluated on various test problems regarding the number of objectives, decision variables, and equivalent Pareto optimal solution sets. Results show that the improved versions perform clearly better than their original algorithms.
Deterministic PRAM Approximate Shortest Paths in Polylogarithmic Time and Slightly Super-Linear Work
Venue: arXiv cs.DC 2020
Year: 2020

We study a $(1+ε)$-approximate single-source shortest paths (henceforth, $(1+ε)$-SSSP) in $n$-vertex undirected, weighted graphs in the parallel (PRAM) model of computation. A randomized algorithm with polylogarithmic time and slightly super-linear work $\tilde{O}(|E|\cdot n^ρ)$, for an arbitrarily small $ρ>0$, was given by Cohen [Coh94] more than $25$ years ago. Exciting progress on this problem was achieved in recent years [ElkinN17,ElkinN19,Li19,AndoniSZ19], culminating in randomized polylogarithmic time and $\tilde{O}(|E|)$ work. However, the question of whether there exists a deterministic counterpart of Cohen's algorithm remained wide open. In the current paper we devise the first deterministic polylogarithmic-time algorithm for this fundamental problem, with work $\tilde{O}(|E|\cdot n^ρ)$, for an arbitrarily small $ρ>0$. This result is based on the first efficient deterministic parallel algorithm for building hopsets, which we devise in this paper.
Retrieving and mining professional experience of software practice from grey literature: an exploratory review
Venue: arXiv cs.SE 2020
Year: 2020

Background: Retrieving and mining practitioners' self--reports of their professional experience of software practice could provide valuable evidence for research. We are, however, unaware of any existing reviews of research conducted in this area. Objective: To review and classify previous research, and to identify insights into the challenges research confronts when retrieving and mining practitioners' self-reports of their experience of software practice. Method: We conduct an exploratory review to identify and classify 42 articles. We analyse a selection of those articles for insights on challenges to mining professional experience. Results: We identify only one directly relevant article. Even then this article concerns the software professional's emotional experiences rather than the professional's reporting of behaviour and events occurring during software practice. We discuss challenges concerning: the prevalence of professional experience; definitions, models and theories; the sparseness of data; units of discourse analysis; annotator agreement; evaluation of the performance of algorithms; and the lack of replications. Conclusion: No directly relevant prior research appears to have been conducted in this area. We discuss the value of reporting negative results in secondary studies. There are a range of research opportunities but also considerable challenges. We formulate a set of guiding questions for further research in this area.