pwc-archive/papers-with-abstracts huggingface dataset:
Correlation-based feature selection to identify functional dynamics in proteins
Authors: Georg Diez, Daniel Nagel, Gerhard Stock
Date: 2022-04-06 00:00:00
Tasks: Clustering, Community Detection, Dimensionality Reduction, feature selection

To interpret molecular dynamics simulations of biomolecular systems, systematic dimensionality reduction methods are commonly employed. Among others, this includes principal component analysis (PCA) and time-lagged independent component analysis (TICA), which aim to maximize the variance and the timescale of the first components, respectively. A crucial first step of such an analysis is the identification of suitable and relevant input coordinates (the so-called features), such as backbone dihedral angles and interresidue distances. As typically only a small subset of those coordinates is involved in a specific biomolecular process, it is important to discard the remaining uncorrelated motions or weakly correlated noise coordinates. This is because they may exhibit large amplitudes or long timescales and therefore will be erroneously be considered important by PCA and TICA, respectively. To discriminate collective motions underlying functional dynamics from uncorrelated motions, the correlation matrix of the input coordinates is block-diagonalized by a clustering method. This strategy avoids possible bias due to presumed functional observables and conformational states or variation principles that maximize variance or timescales. Considering several linear and nonlinear correlation measures and various clustering algorithms, it is shown that the combination of linear correlation and the Leiden community detection algorithm yields excellent results for all considered model systems. These include the functional motion of T4 lysozyme to demonstrate the successful identification of collective motion, as well as the folding of villin headpiece to highlight the physical interpretation of the correlated motions in terms of a functional mechanism.
Revealing directed effective connectivity of cortical neuronal networks from measurements
Authors: Chumin Sun, K. C. Lin, C. Y. Yeung, Emily S. C. Ching, Yu-Ting Huang, Pik-Yin Lai, C. K. Chan
Date: 2022-04-06 00:00:00
Tasks: Functional Connectivity

In the study of biological networks, one of the major challenges is to understand the relationships between network structure and dynamics. In this paper, we model in vitro cortical neuronal cultures as stochastic dynamical systems and apply a method that reconstructs directed networks from dynamics [Ching and Tam, Phys. Rev. E 95, 010301(R), 2017] to reveal directed effective connectivity, namely the directed links and synaptic weights, of the neuronal cultures from voltage measurements recorded by a multielectrode array. The effective connectivity so obtained reproduces several features of cortical regions in rats and monkeys and has similar network properties as the synaptic network of the nematode C. elegans, the only organism whose entire nervous system has been mapped out as of today. The distribution of the incoming degree is bimodal and the distributions of the average incoming and outgoing synaptic strength are non-Gaussian with long tails. The effective connectivity captures different information from the commonly studied functional connectivity, estimated using statistical correlation between spiking activities. The average synaptic strengths of excitatory incoming and outgoing links are found to increase with the spiking activity in the estimated effective connectivity but not in the functional connectivity estimated using the same sets of voltage measurements. These results thus demonstrate that the reconstructed effective connectivity can capture the general properties of synaptic connections and better reveal relationships between network structure and dynamics.
Early life height and weight production functions with endogenous energy and protein inputs
Authors: Esteban Puentes, Fan Wang, Jere R. Behrman, Flávio Cunha, John Hoddinott, John A. Maluccio, Linda S. Adair, Judith B. Borja, Reynaldo Martorell, Aryeh D. Stein
Date: 2022-04-06 00:00:00

We examine effects of protein and energy intakes on height and weight growth for children between 6 and 24 months old in Guatemala and the Philippines. Using instrumental variables to control for endogeneity and estimating multiple specifications, we find that protein intake plays an important and positive role in height and weight growth in the 6-24 month period. Energy from other macronutrients, however, does not have a robust relation with these two anthropometric measures. Our estimates indicate that in contexts with substantial child undernutrition, increases in protein-rich food intake in the first 24 months can have important growth effects, which previous studies indicate are related significantly to a range of outcomes over the life cycle.
Representation Selective Self-distillation and wav2vec 2.0 Feature Exploration for Spoof-aware Speaker Verification
Authors: Jin Woo Lee, Eungbeom Kim, Junghyun Koo, Kyogu Lee
Date: 2022-04-06 00:00:00
Tasks: Attribute, Speaker Verification, text-to-speech, Text to Speech, Voice Conversion

Text-to-speech and voice conversion studies are constantly improving to the extent where they can produce synthetic speech almost indistinguishable from bona fide human speech. In this regard, the importance of countermeasures (CM) against synthetic voice attacks of the automatic speaker verification (ASV) systems emerges. Nonetheless, most end-to-end spoofing detection networks are black-box systems, and the answer to what is an effective representation for finding artifacts remains veiled. In this paper, we examine which feature space can effectively represent synthetic artifacts using wav2vec 2.0, and study which architecture can effectively utilize the space. Our study allows us to analyze which attribute of speech signals is advantageous for the CM systems. The proposed CM system achieved 0.31% equal error rate (EER) on ASVspoof 2019 LA evaluation set for the spoof detection task. We further propose a simple yet effective spoofing aware speaker verification (SASV) method, which takes advantage of the disentangled representations from our countermeasure system. Evaluation performed with the SASV Challenge 2022 database show 1.08% of SASV EER. Quantitative analysis shows that using the explored feature space of wav2vec 2.0 advantages both spoofing CM and SASV.
SFCW GPR tree roots detection enhancement by time frequency analysis in tropical areas
Authors: Wenhao Luo, Yee Hui Lee, Abdulkadir C. Yucel, Genevieve Ow, Mohamed Lokman Mohd Yusof
Date: 2022-04-06 00:00:00
Tasks: GPR

Accurate monitoring of tree roots using ground penetrating radar (GPR) is very useful in assessing the trees health. In high moisture tropical areas such as Singapore, tree fall due to root rot can cause loss of lives and properties. The tropical complex soil characteristics due to the high moisture content tends to affect penetration depth of the signal. This limits the depth range of the GPR. Typically, a wide band signal is used to increase the penetration depth and to improve the resolution of the GPR. However, this broad band frequency tends to be noisy and selective frequency filtering is required for noise reduction. Therefore, in this paper, we adapt the stepped frequency continuous wave (SFCW) GPR and propose the use of a Joint time frequency analysis (JTFA) method called short time Fourier transform (STFT), to reduce noise and enhance tree root detection. The proposed methodology is illustrated and tested with controlled experiments and real tree roots testing. The results show promising prospects of the method for tree roots detection in tropical areas.
A Novel 3D Non-Stationary Channel Model for 6G Indoor Visible Light Communication Systems
Authors: Xiuming Zhu, Cheng-Xiang Wang, Jie Huang, Ming Chen, Harald Haas
Date: 2022-04-06 00:00:00
Tasks: Diversity

The visible light communication (VLC) technology has attracted much attention in the research of the sixth generation (6G) communication systems. In this paper, a novel three dimensional (3D) space-time-frequency non-stationary geometry-based stochastic model (GBSM) is proposed for indoor VLC channels. The proposed VLC GBSM can capture unique indoor VLC channel characteristics such as the space-time-frequency non-stationarity caused by large light-emitting diode (LED) arrays in indoor scenarios, long travelling paths, and large bandwidths of visible light waves, respectively. In addition, the proposed model can support special radiation patterns of LEDs, 3D translational and rotational motions of the optical receiver (Rx), and can be applied to angle diversity receivers (ADRs). Key channel properties are simulated and analyzed, including the space-time-frequency correlation function (STFCF), received power, root mean square (RMS) delay spread, and path loss (PL). Simulation results verify the space-time-frequency non-stationarity in indoor VLC channels. Finally, the accuracy and practicality of the proposed model are validated by comparing the simulation result of channel 3dB bandwidth with the existing measurement data. The proposed channel model will play a supporting role in the design of future 6G VLC systems.
Parametric Channel Model Estimation for Large Intelligent Surface-Based Transceiver-assisted Communication System
Authors: Debamita Ghosh, Manjesh Kr. Hanawal, Nikola Zlatanov
Date: 2022-04-05 00:00:00

The number of connected mobile devices and the amount of data traffic through these devices are expected to grow many-fold in future communication networks. To support the scale of this huge data traffic, more and more base stations and wireless terminals are required to be deployed in existing networks. Nevertheless, practically deploying a large number of base stations having massive antenna arrays will substantially increase the hardware cost and power consumption of the network. A promising approach for enhancing the coverage and rate of wireless communication systems is the large intelligent surface-based transceiver (LISBT), which uses a spatially continuous surface for signal transmission and receiving. A typical LIS consists of a planar array having a large number of reflecting metamaterial elements (e.g., low-cost printed dipoles), each of which could act as a phase shift. It is also considered to be a cost effective and energy efficient solution. Accurate channel state information (CSI) in LISBT-assisted wireless communication systems is critical for achieving these goals. In this paper, we propose a channel estimation scheme based on the physical parameters of the system. that requires only five pilot signals to perfectly estimate the channel parameters assuming there is no noise at the receiver. In the presence of noise, we propose an iterative estimation algorithm that decreases the channel estimation error due to noise. The proposed scheme's training overhead and computational cost do not grow with the number of antennas, unlike previous work on enormous multiple-input multiple-output (MIMO). The channel estimate scheme based on the physical properties of the Large intelligent surface-based transceiver (LISBT)-assisted wireless communication systems is the subject of our future study.
Topological Data Analysis of Human Brain Networks Through Order Statistics
Authors: Soumya Das, D. Vijay Anand, Moo K. Chung
Date: 2022-04-06 00:00:00
Tasks: Topological Data Analysis

Understanding the common topological characteristics of the human brain network across a population is central to understanding brain functions. The abstraction of human connectome as a graph has been pivotal in gaining insights on the topological properties of the brain network. The development of group-level statistical inference procedures in brain graphs while accounting for the heterogeneity and randomness still remains a difficult task. In this study, we develop a robust statistical framework based on persistent homology using the order statistics for analyzing brain networks. The use of order statistics greatly simplifies the computation of the persistent barcodes. We validate the proposed methods using comprehensive simulation studies and subsequently apply to the resting-state functional magnetic resonance images. We found a statistically significant topological difference between the male and female brain networks.
Relevance of Wrong-Way Risk in Funding Valuation Adjustments
Authors: T. van der Zwaard, L. A. Grzelak, C. W. Oosterlee
Date: 2022-04-06 00:00:00
Tasks: Management

In March 2020, the world was thrown into financial distress. This manifested itself in increased uncertainty in the financial markets. Many interest rates collapsed, and funding spreads surged significantly, which increased due to the market turmoil. In light of these events, it is essential to understand and model Wrong-Way Risk (WWR) in a Funding Valuation Adjustment (FVA) context. WWR may currently be absent from FVA calculations in banks' Valuation Adjustment (xVA) engines. However, in this letter, we demonstrate that WWR effects are non-negligible in FVA modelling from a risk-management perspective. We look at the impact of various modelling choices, such as including the default times of the relevant parties, as well as stochastic and deterministic funding spreads. A case study is presented for interest rate derivatives.
Stochastic volatility modeling of high-frequency CSI 300 index and dynamic jump prediction driven by machine learning
Authors: Xianfei Hui, Baiqing Sun, Indranil SenGupta, Yan Zhou, Hui Jiang
Date: 2022-04-06 00:00:00
Tasks: Time Series, Time Series Analysis

This paper models stochastic process of price time series of CSI 300 index in Chinese financial market, analyzes volatility characteristics of intraday high-frequency price data. In the new generalized Barndorff-Nielsen and Shephard model, the lag caused by asynchrony of market information is considered, and the problem of lack of long-term dependence is solved. To speed up the valuation process, several machine learning and deep learning algorithms are used to estimate parameter and evaluate forecast results. Tracking historical jumps of different magnitudes offers promising avenues for simulating dynamic price processes and predicting future jumps. Numerical results show that the deterministic component of stochastic volatility processes would always be captured over short and longer-term windows. Research finding could be suitable for influence investors and regulators interested in predicting market dynamics based on realized volatility.
Bridging the Gap: Decoding the Intrinsic Nature of Time in Market Data
Authors: James B. Glattfelder, Anton Golub
Date: 2022-04-06 00:00:00
Tasks: Time Series, Time Series Analysis

Intrinsic time is an example of an event-based conception of time, used to analyze financial time series. Here, for the first time, we reveal the connection between intrinsic time and physical time. In detail, we present an analytic relationship which links the two different time paradigms. Central to this discovery are the emergence of scaling laws. Indeed, a novel empirical scaling law is presented, relating to the variability of what is know as overshoots in the intrinsic time framework. To evaluate the validity of the theoretically derived expressions, three time series are analyzed; in detail, Brownian motion and two tick-by-tick empirical currency market data sets (one crypto and one fiat). Finally, the time series analyzed in physical time can be decomposed into their liquidity and volatility components, both only visible in intrinsic time, further highlighting the utility of this temporal kinship.
Classification of NEQR Processed Classical Images using Quantum Neural Networks (QNN)
Authors: Santanu Ganguly
Date: 2022-03-29 00:00:00
Tasks: image-classification, Image Classification

A quantum neural network (QNN) is interpreted today as any quantum circuit with trainable continuous parameters. This work builds on previous works by the authors and addresses QNN for image classification with Novel Enhanced Quantum Representation of (NEQR) processed classical data where Principal component analysis (PCA) and Projected Quantum Kernel features (PQK) were investigated previously by the authors as a path to quantum advantage for the same classical dataset. For each of these cases the Fashion-MNIST dataset was downscaled using PCA to convert into quantum data where the classical NN easily outperformed the QNN. However, we demonstrated quantum advantage by using PQK where quantum models achieved more than ~90% accuracy surpassing their classical counterpart on the same training dataset as in the first case. In this current work, we use the same dataset fed into a QNN and compare that with performance of a classical NN model. We built an NEQR model circuit to pre-process the same data and feed the images into the QNN. Our results showed marginal improvements (only about ~5.0%) where the QNN performance with NEQR exceeded the performance of QNN without NEQR. We conclude that given the computational cost and the massive circuit depth associated with running NEQR, the advantage offered by this specific Quantum Image Processing (QIMP) algorithm is questionable at least for classical image dataset. No actual quantum computing hardware platform exists today that can support the circuit depth needed to run NEQR even for the reduced image sizes of our toy classical dataset.
The single-cell transcriptomic landscape of early human diabetic nephropathy
Authors: Parker C Wilson 1, Haojia Wu 2, Yuhei Kirita 2, Kohei Uchimura 2, Nicolas Ledru 2, Helmut G Rennke 3, Paul A Welling 4, Sushrut S Waikar 5, Benjamin D Humphreys 6 7
Date: 2019-09-24 00:00:00
Proceeding: Proc Natl Acad Sci U S A 2019 9

Diabetic nephropathy is characterized by damage to both the glomerulus and tubulointerstitium, but relatively little is known about accompanying cell-specific changes in gene expression. We performed unbiased single-nucleus RNA sequencing (snRNA-seq) on cryopreserved human diabetic kidney samples to generate 23,980 single-nucleus transcriptomes from 3 control and 3 early diabetic nephropathy samples. All major cell types of the kidney were represented in the final dataset. Side-by-side comparison demonstrated cell-type-specific changes in gene expression that are important for ion transport, angiogenesis, and immune cell activation. In particular, we show that the diabetic thick ascending limb, late distal convoluted tubule, and principal cells all adopt a gene expression signature consistent with increased potassium secretion, including alterations in Na+/K+-ATPase, WNK1, mineralocorticoid receptor, and NEDD4L expression, as well as decreased paracellular calcium and magnesium reabsorption. We also identify strong angiogenic signatures in glomerular cell types, proximal convoluted tubule, distal convoluted tubule, and principal cells. Taken together, these results suggest that increased potassium secretion and angiogenic signaling represent early kidney responses in human diabetic nephropathy.
CVL-DataBase: An Off-Line Database for Writer Retrieval, Writer Identification and Word Spotting
Authors: Florian Kleber, Stefan Fiel, Markus Diem, Robert Sablatnig
Date: 2013-08-25 00:00:00
Proceeding: International Conference on Document Analysis and Recognition 2013 8
Tasks: Retrieval, Writer Retrieval

In this paper a public database for writer retrieval, writer identification and word spotting is presented. The CVL-Database consists of 7 different handwritten texts (1 German and 6 English Texts) and 311 different writers. For each text an RGB color image (300 dpi) comprising the handwritten text and the printed text sample are available as well as a cropped version (only handwritten). A unique ID identifies the writer, whereas the bounding boxes for each single word are stored in an XML file. An evaluation of the best algorithms of the ICDAR and ICHFR writer identification contest has been performed on the CVL-database.
Weight-conserving characterization of complex functional brain networks
Authors: Mikail Rubinov, Olaf Sporns
Date: 2011-03-26 00:00:00

Complex functional brain networks are large networks of brain regions and functional brain connections. Statistical characterizations of these networks aim to quantify global and local properties of brain activity with a small number of network measures. Important functional network measures include measures of modularity (measures of the goodness with which a network is optimally partitioned into functional subgroups) and measures of centrality (measures of the functional influence of individual brain regions). Characterizations of functional networks are increasing in popularity, but are associated with several important methodological problems. These problems include the inability to characterize densely connected and weighted functional networks, the neglect of degenerate topologically distinct high-modularity partitions of these networks, and the absence of a network null model for testing hypotheses of association between observed nontrivial network properties and simple weighted connectivity properties. In this study we describe a set of methods to overcome these problems. Specifically, we generalize measures of modularity and centrality to fully connected and weighted complex networks, describe the detection of degenerate high-modularity partitions of these networks, and introduce a weighted-connectivity null model of these networks. We illustrate our methods by demonstrating degenerate high-modularity partitions and strong correlations between two complementary measures of centrality in resting-state functional magnetic resonance imaging (MRI) networks from the 1000 Functional Connectomes Project, an open-access repository of resting-state functional MRI datasets. Our methods may allow more sound and reliable characterizations and comparisons of functional brain networks across conditions and subjects.
End-to-End Zero-Shot HOI Detection via Vision and Language Knowledge Distillation
Authors: Mingrui Wu, Jiaxin Gu, Yunhang Shen, Mingbao Lin, Chao Chen, Xiaoshuai Sun
Date: 2022-04-01 00:00:00
Tasks: Human-Object Interaction Detection, Knowledge Distillation, Object, object-detection, Object Detection, Zero-Shot Human-Object Interaction Detection

Most existing Human-Object Interaction~(HOI) Detection methods rely heavily on full annotations with predefined HOI categories, which is limited in diversity and costly to scale further. We aim at advancing zero-shot HOI detection to detect both seen and unseen HOIs simultaneously. The fundamental challenges are to discover potential human-object pairs and identify novel HOI categories. To overcome the above challenges, we propose a novel end-to-end zero-shot HOI Detection (EoID) framework via vision-language knowledge distillation. We first design an Interactive Score module combined with a Two-stage Bipartite Matching algorithm to achieve interaction distinguishment for human-object pairs in an action-agnostic manner. Then we transfer the distribution of action probability from the pretrained vision-language teacher as well as the seen ground truth to the HOI model to attain zero-shot HOI classification. Extensive experiments on HICO-Det dataset demonstrate that our model discovers potential interactive pairs and enables the recognition of unseen HOIs. Finally, our method outperforms the previous SOTA by 8.92% on unseen mAP and 10.18% on overall mAP under UA setting, by 6.02% on unseen mAP and 9.1% on overall mAP under UC setting. Moreover, our method is generalizable to large-scale object detection data to further scale up the action sets. The source code will be available at: https://github.com/mrwu-mac/EoID.