pwc-archive/papers-with-abstracts huggingface dataset:
Sparse algorithms for EEG source localization
Authors: Teja Mannepalli, Aurobinda Routray
Date: 2022-01-31 00:00:00
Tasks: EEG, Electroencephalogram (EEG)

Source localization using EEG is important in diagnosing various physiological and psychiatric diseases related to the brain. The high temporal resolution of EEG helps medical professionals assess the internal physiology of the brain in a more informative way. The internal sources are obtained from EEG by an inversion process. The number of sources in the brain outnumbers the number of measurements. In this article, a comprehensive review of the state of the art sparse source localization methods in this field is presented. A recently developed method, certainty based reduced sparse solution (CARSS), is implemented and is examined. A vast comparative study is performed using a sixty four channel setup involving two source spaces. The first source space has 5004 sources and the other has 2004 sources. Four test cases with one, three, five, and seven simulated active sources are considered. Two noise levels are also being added to the noiseless data. The CARSS is also evaluated. The results are examined. A real EEG study is also attempted.
Probabilistically Robust Optimization of IRS-aided SWIPT Under Coordinated Spectrum Underlay
Authors: Konstantinos Ntougias, Ioannis Krikidis
Date: 2022-01-31 00:00:00
Tasks: Robust Design

This study considers the Joint Transmit/Reflect Beamforming and Power Splitting (JTRBPS) optimization problem in a spectrum underlay setting, such that the transmit sum-energy of the intelligent reflecting surface (IRS)-aided secondary transmitter (ST) is minimized subject to the quality-of-service requirements of the PS-simultaneous wireless information and power transfer (SWIPT) secondary receivers and the interference constraints of the primary receivers (PR). The interference at the PRs caused by the reception of IRS-reflected signals sent by the primary transmitter is taken into account. A coordinated channel state information (CSI) acquisition protocol is proposed. Next, assuming availability at the ST of perfect CSI for all direct and IRS-cascaded transmitter--receiver channels, two penalty-based iterative algorithms are developed: an alternating minimization algorithm that involves semi-definite relaxation in JTBPS design and successive convex approximation in RB optimization, and a block coordinate descent algorithm that employs the Riemannian conjugate gradient algorithm in RB updates. Finally, an outage-constrained robust design under imperfect CSI is devised. Numerical simulations highlight the performance gains of the proposed strategies over benchmarks, corroborate the benefits of using an IRS, and provide valuable insights.
Joint Vehicular Localization and Reflective Mapping Based on Team Channel-SLAM
Authors: Xinghe Chu, Zhaoming Lu, David Gesbert, Luhan Wang, Xiangming Wen, Muqing Wu, Meiling Li
Date: 2022-01-30 00:00:00
Tasks: Position

This paper addresses high-resolution vehicle positioning and tracking. In recent work, it was shown that a fleet of independent but neighboring vehicles can cooperate for the task of localization by capitalizing on the existence of common surrounding reflectors, using the concept of Team Channel-SLAM. This approach exploits an initial (e.g. GPS-based) vehicle position information and allows subsequent tracking of vehicles by exploiting the shared nature of virtual transmitters associated to the reflecting surfaces. In this paper, we show that the localization can be greatly enhanced by joint sensing and mapping of reflecting surfaces. To this end, we propose a combined approach coined Team Channel-SLAM Evolution (TCSE) which exploits the intertwined relation between (i) the position of virtual transmitters, (ii) the shape of reflecting surfaces, and (iii) the paths described by the radio propagation rays, in order to achieve high-resolution vehicle localization. Overall, TCSE yields a complete picture of the trajectories followed by dominant paths together with a mapping of reflecting surfaces. While joint localization and mapping is a well researched topic within robotics using inputs such as radar and vision, this paper is first to demonstrate such an approach within mobile networking framework based on radio data.
A Probabilistic Graph Coupling View of Dimension Reduction
Authors: Hugues van Assel, Thibault Espinasse, Julien Chiquet, Franck Picard
Date: 2022-01-31 00:00:00
Tasks: Dimensionality Reduction

Most popular dimension reduction (DR) methods like t-SNE and UMAP are based on minimizing a cost between input and latent pairwise similarities. Though widely used, these approaches lack clear probabilistic foundations to enable a full understanding of their properties and limitations. To that extent, we introduce a unifying statistical framework based on the coupling of hidden graphs using cross entropy. These graphs induce a Markov random field dependency structure among the observations in both input and latent spaces. We show that existing pairwise similarity DR methods can be retrieved from our framework with particular choices of priors for the graphs. Moreover this reveals that these methods suffer from a statistical deficiency that explains poor performances in conserving coarse-grain dependencies. Our model is leveraged and extended to address this issue while new links are drawn with Laplacian eigenmaps and PCA.
Optimal Support for Distressed Subsidiaries -- a Systemic Risk Perspective
Authors: Maxim Bichuch, Nils Detering
Date: 2022-01-30 00:00:00

We consider a network of bank holdings, where every holding has two subsidiaries of different types. A subsidiary can trade with another holding's subsidiary of the same type. Holdings support their subsidiaries up to a certain level when they would otherwise fail to honor their financial obligations. We investigate the spread of contagion in this banking network when the number of bank holdings is large, and find the final number of defaulted subsidiaries under different rules for the holding support. We also consider resilience of this multilayered network to small shocks. Our work sheds light onto the role that holding structures can play in the amplification of financial stress. We find that depending on the capitalization of the network, a holding structure can be beneficial as compared to smaller separated entities. In other instances, it can be harmful and actually increase contagion. We illustrate our results in a numerical case study and also determine the optimal level of holding support from a regulator perspective.
AI for Chemical Space Gap Filling and Novel Compound Generation
Authors: Monee Y. McGrady, Sean M. Colby, Jamie R Nuñez, Ryan S. Renslow, Thomas O. Metz
Date: 2022-01-28 00:00:00
Tasks: valid

When considering large sets of molecules, it is helpful to place them in the context of a "chemical space" - a multidimensional space defined by a set of descriptors that can be used to visualize and analyze compound grouping as well as identify regions that might be void of valid structures. The chemical space of all possible molecules in a given biological or environmental sample can be vast and largely unexplored, mainly due to current limitations in processing of 'big data' by brute force methods (e.g., enumeration of all possible compounds in a space). Recent advances in artificial intelligence (AI) have led to multiple new cheminformatics tools that incorporate AI techniques to characterize and learn the structure and properties of molecules in order to generate plausible compounds, thereby contributing to more accessible and explorable regions of chemical space without the need for brute force methods. We have used one such tool, a deep-learning software called DarkChem, which learns a representation of the molecular structure of compounds by compressing them into a latent space. With DarkChem's design, distance in this latent space is often associated with compound similarity, making sparse regions interesting targets for compound generation due to the possibility of generating novel compounds. In this study, we used 1 million small molecules (less than 1000 Da) to create a representative chemical space (defined by calculated molecular properties) of all small molecules. We identified regions with few or no compounds and investigated their location in DarkChem's latent space. From these spaces, we generated 694,645 valid molecules, all of which represent molecules not found in any chemical database to date. These molecules filled 50.8% of the probed empty spaces in molecular property space. Generated molecules are provided in the supporting information.
A detailed model of gene promoter dynamics reveals the entry into productive elongation to be a highly punctual process
Authors: Jaroslav Albert
Date: 2022-01-31 00:00:00

Gene transcription is a stochastic process that involves thousands of reactions. The first set of these reactions, which happen near a gene promoter, are considered to be the most important in the context of stochastic noise. The most common models of transcription are primarily concerned with the effect of activators/repressors on the overall transcription rate and approximate the basal transcription processes as a one step event. According to such effective models, the Fano factor of mRNA copy distributions is always greater than (super-Poissonian) or equal to 1 (Poissonian), and the only way to go below this limit (sub-Poissonian) is via a negative feedback. It is partly due to this limit that the first stage of transcription is held responsible for most of the stochastic noise in mRNA copy numbers. However, by considering all major reactions that build and drive the basal transcription machinery, from the first protein that binds a promoter to the entrance of the transcription complex (TC) into productive elongation, it is shown that the first two stages of transcription, namely the pre-initiation complex (PIC) formation and the promoter proximal pausing (PPP), is a highly punctual process. In other words, the time between the first and the last step of this process is narrowly distributed, which gives rise to sub-Poissonian distributions for the number of TCs that have entered productive elongation. In fact, having simulated the PIC formation and the PPP via the Gillespie algorithm using 2000 distinct parameter sets and 4 different reaction network topologies, it is shown that only 4.4% give rise to a Fano factor that is > 1 with the upper bound of 1.7, while for 31% of cases the Fano factor is below 0.5, with 0.19 as the lower bound. These results cast doubt on the notion that most of the stochastic noise observed in mRNA distributions always originates at the promoter.
Novel Machine Learning Approaches for Improving the Reproducibility and Reliability of Functional and Effective Connectivity from Functional MRI
Authors: Cooper J. Mellema, Albert Montillo
Date: 2022-01-31 00:00:00
Tasks: BIG-bench Machine Learning, Feature Importance, Functional Connectivity

Objective: New measures of human brain connectivity are needed to address gaps in the existing measures and facilitate the study of brain function, cognitive capacity, and identify early markers of human disease. Traditional approaches to measure functional connectivity between pairs of brain regions in functional MRI, such as correlation and partial correlation, fail to capture nonlinear aspects in the regional associations. We propose a new machine learning based measure of functional connectivity which efficiently captures linear and nonlinear aspects. Approach: We propose two new EC measures. The first, a machine learning based measure of effective connectivity, measures nonlinear aspects across the entire brain. The second, Structurally Projected Granger Causality adapts Granger Causal connectivity to efficiently characterize and regularize the whole brain EC connectome to respect underlying biological structural connectivity. The proposed measures are compared to traditional measures in terms of reproducibility and the ability to predict individual traits in order to demonstrate these measures internal validity. We use four repeat scans of the same individuals from the Human Connectome Project and measure the ability of the measures to predict individual subject physiologic and cognitive traits. Main results: The proposed new FC measure of ML.FC attains high reproducibility with an R squared of 0.44, while the proposed EC measure of SP.GC attains the highest predictive power with an R squared of 0.66. Significance: The proposed methods are highly suitable for achieving high reproducibility and predictiveness.
Deep Learning in fNIRS: A review
Authors: Condell Eastmond, Aseem Subedi, Suvranu De, Xavier Intes
Date: 2022-01-31 00:00:00
Tasks: Brain Computer Interface, Classification, Data Augmentation, Deep Learning

Significance: Optical neuroimaging has become a well-established clinical and research tool to monitor cortical activations in the human brain. It is notable that outcomes of functional Near-InfraRed Spectroscopy (fNIRS) studies depend heavily on the data processing pipeline and classification model employed. Recently, Deep Learning (DL) methodologies have demonstrated fast and accurate performances in data processing and classification tasks across many biomedical fields. Aim: We aim to review the emerging DL applications in fNIRS studies. Approach: We first introduce some of the commonly used DL techniques. Then the review summarizes current DL work in some of the most active areas of this field, including brain-computer interface, neuro-impairment diagnosis, and neuroscience discovery. Results: Of the 63 papers considered in this review, 32 report a comparative study of deep learning techniques to traditional machine learning techniques where 26 have been shown outperforming the latter in terms of classification accuracy. Additionally, 8 studies also utilize deep learning to reduce the amount of preprocessing typically done with fNIRS data or increase the amount of data via data augmentation. Conclusions: The application of DL techniques to fNIRS studies has shown to mitigate many of the hurdles present in fNIRS studies such as lengthy data preprocessing or small sample sizes while achieving comparable or improved classification accuracy.
Associations between depression symptom severity and daily-life gait characteristics derived from long-term acceleration signals in real-world settings
Authors: Yuezhou Zhang, Amos A Folarin, Shaoxiong Sun, NIcholas Cummins, Srinivasan Vairavan, Linglong Qian, Yatharth Ranjan, Zulqarnain Rashid, Pauline Conde, Callum Stewart, Petroula Laiou, Heet Sankesara, Faith Matcham, Katie M White, Carolin Oetzmann, Alina Ivan, Femke Lamers, Sara Siddi, Sara Simblett, Aki Rintala, David C Mohr, Inez Myin-Germeys, Til Wykes, Josep Maria Haro, Brenda WJH Penninx, Vaibhav A Narayan, Peter Annas, Matthew Hotopf, Richard JB Dobson, RADAR-CNS consortium
Date: 2022-01-29 00:00:00

Gait is an essential manifestation of depression. Laboratory gait characteristics have been found to be closely associated with depression. However, the gait characteristics of daily walking in real-world scenarios and their relationships with depression are yet to be fully explored. This study aimed to explore associations between depression symptom severity and daily-life gait characteristics derived from acceleration signals in real-world settings. In this study, we used two ambulatory datasets: a public dataset with 71 elder adults' 3-day acceleration signals collected by a wearable device, and a subset of an EU longitudinal depression study with 215 participants and their phone-collected acceleration signals (average 463 hours per participant). We detected participants' gait cycles and force from acceleration signals and extracted 20 statistics-based daily-life gait features to describe the distribution and variance of gait cadence and force over a long-term period corresponding to the self-reported depression score. The gait cadence of faster steps (75th percentile) over a long-term period has a significant negative association with the depression symptom severity of this period in both datasets. Daily-life gait features could significantly improve the goodness of fit of evaluating depression severity relative to laboratory gait patterns and demographics, which was assessed by likelihood-ratio tests in both datasets. This study indicated that the significant links between daily-life walking characteristics and depression symptom severity could be captured by both wearable devices and mobile phones. The gait cadence of faster steps in daily-life walking has the potential to be a biomarker for evaluating depression severity, which may contribute to clinical tools to remotely monitor mental health in real-world settings.
Gate-based Quantum Computing for Protein Design
Authors: Mohammad Hassan Khatami, Udson C. Mendes, Nathan Wiebe, Philip M. Kim
Date: 2022-01-29 00:00:00
Tasks: Protein Design

Protein design is a technique to engineer proteins by modifying their sequence to obtain novel functionalities. In this method, amino acids in the sequence are permutated to find the low energy states satisfying the configuration. However, exploring all possible combinations of amino acids is generally impossible to achieve on conventional computers due to the exponential growth of possibilities with the number of designable sites. Thus, sampling methods are currently used as a conventional approach to address the protein design problems. Recently, quantum computation methods have shown the potential to solve similar types of problems. In the present work, we use the general idea of Grover's algorithm, a pure quantum computation method, to design circuits at the gate-based level and address the protein design problem. In our quantum algorithms, we use custom pair-wise energy tables consisting of eight different amino acids. Also, the distance reciprocals between designable sites are included in calculating energies in the circuits. Due to the noisy state of current quantum computers, we mainly use quantum computer simulators for this study. However, a very simple version of our circuits is implemented on real quantum devices to examine their capabilities to run these algorithms. Our results show that using $\mathcal{O}(\sqrt N)$ iterations, the circuits find the correct results among all $N$ possibilities, providing the expected quadratic speed up of Grover's algorithm over classical methods.
A Computational Framework for Atrioventricular Valve Modeling using Open-Source Software
Authors: Wensi Wu, Stephen Ching, Steve A. Maas, Andras Lasso, Patricia Sabin, Jeffrey A. Weiss, Matthew A. Jolley
Date: 2022-01-31 00:00:00

Atrioventricular valve regurgitation is a significant cause of morbidity and mortality in patients with acquired and congenital cardiac valve disease. Image-derived computational modeling of atrioventricular valves has advanced substantially over the last decade and holds particular promise to inform valve repair in small and heterogeneous populations which are less likely to be optimized through empiric clinical application. While an abundance of computational biomechanics studies have investigated mitral and tricuspid valve disease in adults, few studies have investigated application to vulnerable pediatric and congenital heart populations. Further, to date, investigators have primarily relied upon a series of commercial applications that are neither designed for image-derived modeling of cardiac valves, nor freely available to facilitate transparent and reproducible valve science. To address this deficiency, we aimed to build an open-source computational framework for the image-derived biomechanical analysis of atrioventricular valves. In the present work, we integrated an open-source valve modeling platform, SlicerHeart, and an open-source biomechanics finite element modeling software, FEBio, to facilitate image-derived atrioventricular valve model creation and finite element analysis. We present a detailed verification and sensitivity analysis to demonstrate the fidelity of this modeling in application to 3D echocardiography-derived pediatric mitral and tricuspid valve models. Our analyses achieved excellent agreement with those reported in the literature. As such, this evolving computational framework offers a promising initial foundation for future development and investigation of valve mechanics, in particular collaborative efforts targeting the development of improved repairs for children with congenital heart disease.
Deep Convolutional Network for Handwritten Chinese Character Recognition
Authors: Yuhao Zhang
Date: 2015-01-01 00:00:00
Proceeding: standford.edu 2015 1

In this project we explored the performance of deep convolutional
neural network on recognizing handwritten Chinese
characters. We ran experiments on a 200-class and a
3755-class dataset using convolutional networks with different
depth and filter numbers. Experimental results show
that deeper network with larger filter numbers give better
test accuracy. We also provide a visualization of the learned
network on the handwritten Chinese characters.
On Label-Eﬀicient Computer Vision: Building Fast and Effective Few-Shot Image Classifiers
Authors: Peyman Bateni
Date: 2021-10-19 00:00:00
Proceeding: University of British Columbia Theses and Dissertations 2021 10
Tasks: Active Learning, Continual Learning, Cross-Domain Few-Shot, Few-Shot Learning, Meta-Learning, Object Recognition, Transductive Learning

Modern deep learning requires large-scale extensively labelled datasets for training. Few-shot learning aims to alleviate this issue by learning effectively from few labelled examples. In previously proposed few-shot visual classifiers, it is assumed that the feature manifold arriving at the classifier has uncorrelated feature dimensions and uniform feature variance. In this work, we focus on addressing the limitations arising from this assumption by proposing a variance-sensitive class of models that operates in a low-label regime. The first method, Simple CNAPS, employs a hierarchically regularized Mahalanobis-distance based classifier combined with a state of the art neural adaptive feature extractor to achieve strong performance on Meta-Dataset, mini-ImageNet and tiered-ImageNet benchmarks. We further extend this approach to a transductive learning setting, proposing Transductive CNAPS. This transductive method combines a soft k-means parameter refinement procedure with a two-step task encoder to achieve improved test-time classification accuracy using unlabelled data. Transductive CNAPS achieves state of the art performance across all major few-shot learning benchmarks. Finally, we explore the use of our methods (Simple and Transductive) for “out of the box” continual and active learning. Extensive experiments on large scale benchmarks illustrate robustness and versatility of this, relatively speaking, simple class of models. All trained model checkpoints and corresponding source codes are made publicly available at github. com/plai-group/simple-cnaps.