pwc-archive/papers-with-abstracts huggingface dataset:
Real-Time Phase Contrast MRI to quantify Cerebral arterial flow change during variations breathing
Authors: Pan Liu, Sidy Fall, Serge Metanbou, Olivier Balédent
Date: 2022-07-26 00:00:00

Cerebral arterial blood flow (CABF) can be investigated in few seconds without any synchronization by Real-Time phase contrast. Significant changes in CABF were found between expiration and inspiration during normal breathing of healthy volunteers. Synopsis (100/100) Real-time phase contrast MRI has been applied to investigate cerebral arterial blood flow (CABF) during normal breathing of healthy volunteers. We developed a novel time-domain analysis method to quantify the effect of normal breathing on several parameters of CABF. We found the existence of a delay between the recorded respiratory signal from the belt sensor and the breathing frequency component present in the reconstructed arterial blood flows. During the expiratory, the mean flow rate of CABF increased by 4.4$\pm$1.7%, stroke volume of CABF increased by 9.8$\pm$3.1% and the duration of the cardiac period of CABF increased by 8.1$\pm$3%.
Flow 2.0 -a flexible, scalable, cross-platform post-processing software for realtime phase contrast sequences
Authors: Pan Liu, Sidy Fall, Olivier Balédent
Date: 2022-07-26 00:00:00
Tasks: Image Segmentation, Semantic Segmentation

Flow 2.0 is an end-to-end easy-of-use software that allows us to quickly, robustly and accurately perform a batch process real-time phase contrast data and multivariate analysis of the effect of respiration on cerebral fluids circulation. Synopsis (99/100) Real-time phase contrast sequences (RT-PC) have potential value as a scientific and clinical tool in quantifying the effects of respiration on cerebral circulation. To simplify its complicated post-processing process, we developed Flow 2.0 software, which provides a complete post-processing workflow including converting DICOM data, image segmentation, image processing, data extraction, background field correction, antialiasing filter, signal processing and analysis and a novel time-domain method for quantifying the effect of respiration on the cerebral circulation. This end-to-end software allows us to quickly, robustly and accurately perform batch process RT-PC and multivariate analysis of the effects of respiration on cerebral circulation.
When can we reconstruct the ancestral state? Beyond Brownian motion
Authors: Nhat L. Vu, Thanh P. Nguyen, Binh T. Nguyen, Vu Dinh, Lam Si Tung Ho
Date: 2022-07-26 00:00:00

Reconstructing the ancestral state of a group of species helps answer many important questions in evolutionary biology. Therefore, it is crucial to understand when we can estimate the ancestral state accurately. Previous works provide a necessary and sufficient condition, called the big bang condition, for the existence of an accurate reconstruction method under discrete trait evolution models and the Brownian motion model. In this paper, we extend this result to a wide range of continuous trait evolution models. In particular, we consider a general setting where continuous traits evolve along the tree according to stochastic processes that satisfy some regularity conditions. We verify these conditions for popular continuous trait evolution models including Ornstein-Uhlenbeck, reflected Brownian Motion, and Cox-Ingersoll-Ross.
Bugs as Features (Part I): Concepts and Foundations for the Compositional Data Analysis of the Microbiome-Gut-Brain Axis
Authors: Thomaz F. S. Bastiaanssen, Thomas P. Quinn, Amy Loughman
Date: 2022-07-25 00:00:00
Tasks: Diversity

There has been a growing acknowledgement of the involvement of the gut microbiome - the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiome-gut-brain axis. While our techniques to measure the presence and abundance of these microbes have been steadily improving, the analysis of microbiome data is non-trivial. Here, we present a perspective on the concepts and foundations of data analysis and interpretation of microbiome experiments with a focus on the microbiome-gut-brain axis domain. We give an overview of foundational considerations prior to commencing analysis alongside the core microbiome analysis approaches of alpha diversity, beta diversity, differential feature abundance and functional inference. We emphasize the compositional data analysis (CoDA) paradigm. Further, this perspective features an extensive and heavily annotated microbiome analysis in R in the supplementary materials, as a resource for new and experienced bioinformaticians alike.
Time-dependent maximum entropy model for populations of retinal ganglion cells
Authors: Geoffroy Delamare, Ulisse Ferrari
Date: 2022-07-26 00:00:00

The inverse Ising model is used in computational neuroscience to infer probability distributions of the synchronous activity of large neuronal populations. This method allows for finding the Boltzmann distribution with single neuron biases and pairwise interactions that maximizes the entropy and reproduces the empirical statistics of the recorded neuronal activity. Here we apply this strategy to large populations of retinal output neurons (ganglion cells) of different types, stimulated by multiple visual stimuli with their own statistics. The activity of retinal output neurons is driven by both the inputs from upstream neurons and the recurrent connections. We first apply the standard inverse Ising model approach, and show that it accounts well for the system's collective behavior when the input visual stimulus has short-ranged spatial correlations, but fails for long-ranged ones. This happens because stimuli with long-ranged spatial correlations synchronize the activity of neurons over long distances. This effect cannot be accounted for by pairwise interactions, and so by the pairwise Ising model. To solve this issue, we apply a previously proposed framework that includes a temporal dependence in the single neurons biases to model how neurons are driven in time by the stimulus. Thanks to this addition, the stimulus effects are taken into account by the biases, and the pairwise interactions allow for characterizing the network effect in the population activity and for reproducing the structure of the recurrent functional connections in the retinal architecture. We found that the retinal architecture splits into weakly interacting subpopulations composed of strongly interacting neurons. Overall, this temporal framework fixes the problems of the standard, static, inverse Ising model and accounts for the system's collective behavior, for stimuli with either short or long-range correlations.
Inspecting the interaction between HIV and the immune system through genetic turnover
Authors: Andrea Mazzolini, Thierry Mora, Aleksandra M Walczak
Date: 2022-07-26 00:00:00

Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely unknown and could help in disease treatment and vaccine development. Here we study a longitudinal dataset of ten HIV-infected people, where both the B-cell receptors and the virus are deeply sequenced. We focus on simple measures of turnover, which quantify how much the composition of the viral strains and the immune repertoire change between time points. At the single-patient level, the viral-host turnover rates do not show any statistically significant correlation, however they correlate if the information is aggregated across patients. In particular, we identify an anti-correlation: large changes in the viral pool composition come with small changes in the B-cell receptor repertoire. This result seems to contradict the naive expectation that when the virus mutates quickly, the immune repertoire needs to change to keep up. However, we show that the observed anti-correlation naturally emerges and can be understood in terms of simple population-genetics models.
Variational multiscale reinforcement learning for discovering reduced order closure models of nonlinear spatiotemporal transport systems
Authors: Omer San, Suraj Pawar, Adil Rasheed
Date: 2022-07-07 00:00:00
Tasks: Reinforcement Learning (RL)

A central challenge in the computational modeling and simulation of a multitude of science applications is to achieve robust and accurate closures for their coarse-grained representations due to underlying highly nonlinear multiscale interactions. These closure models are common in many nonlinear spatiotemporal systems to account for losses due to reduced order representations, including many transport phenomena in fluids. Previous data-driven closure modeling efforts have mostly focused on supervised learning approaches using high fidelity simulation data. On the other hand, reinforcement learning (RL) is a powerful yet relatively uncharted method in spatiotemporally extended systems. In this study, we put forth a modular dynamic closure modeling and discovery framework to stabilize the Galerkin projection based reduced order models that may arise in many nonlinear spatiotemporal dynamical systems with quadratic nonlinearity. However, a key element in creating a robust RL agent is to introduce a feasible reward function, which can be constituted of any difference metrics between the RL model and high fidelity simulation data. First, we introduce a multi-modal RL (MMRL) to discover mode-dependant closure policies that utilize the high fidelity data in rewarding our RL agent. We then formulate a variational multiscale RL (VMRL) approach to discover closure models without requiring access to the high fidelity data in designing the reward function. Specifically, our chief innovation is to leverage variational multiscale formalism to quantify the difference between modal interactions in Galerkin systems. Our results in simulating the viscous Burgers equation indicate that the proposed VMRL method leads to robust and accurate closure parameterizations, and it may potentially be used to discover scale-aware closure models for complex dynamical systems.
Demystifying Graph Convolution with a Simple Concatenation
Authors: Zhiqian Chen, Zonghan Zhang
Date: 2022-07-18 00:00:00
Tasks: Graph Learning, Node Classification

Graph convolution (GConv) is a widely used technique that has been demonstrated to be extremely effective for graph learning applications, most notably node categorization. On the other hand, many GConv-based models do not quantify the effect of graph topology and node features on performance, and are even surpassed by some models that do not consider graph structure or node properties. We quantify the information overlap between graph topology, node features, and labels in order to determine graph convolution's representation power in the node classification task. In this work, we first determine the linear separability of graph convoluted features using analysis of variance. Mutual information is used to acquire a better understanding of the possible non-linear relationship between graph topology, node features, and labels. Our theoretical analysis demonstrates that a simple and efficient graph operation that concatenates only graph topology and node properties consistently outperforms conventional graph convolution, especially in the heterophily case. Extensive empirical research utilizing a synthetic dataset and real-world benchmarks demonstrates that graph concatenation is a simple but more flexible alternative to graph convolution.
Pseudo-Pair based Self-Similarity Learning for Unsupervised Person Re-identification
Authors: Lin Wu, Deyin Liu, Wenying Zhang, Dapeng Chen, ZongYuan Ge, Farid Boussaid, Mohammed Bennamoun, Jialie Shen
Date: 2022-07-09 00:00:00
Tasks: Person Re-Identification, Unsupervised Person Re-Identification

Person re-identification (re-ID) is of great importance to video surveillance systems by estimating the similarity between a pair of cross-camera person shorts. Current methods for estimating such similarity require a large number of labeled samples for supervised training. In this paper, we present a pseudo-pair based self-similarity learning approach for unsupervised person re-ID without human annotations. Unlike conventional unsupervised re-ID methods that use pseudo labels based on global clustering, we construct patch surrogate classes as initial supervision, and propose to assign pseudo labels to images through the pairwise gradient-guided similarity separation. This can cluster images in pseudo pairs, and the pseudos can be updated during training. Based on pseudo pairs, we propose to improve the generalization of similarity function via a novel self-similarity learning:it learns local discriminative features from individual images via intra-similarity, and discovers the patch correspondence across images via inter-similarity. The intra-similarity learning is based on channel attention to detect diverse local features from an image. The inter-similarity learning employs a deformable convolution with a non-local block to align patches for cross-image similarity. Experimental results on several re-ID benchmark datasets demonstrate the superiority of the proposed method over the state-of-the-arts.
Learning Resolution-Adaptive Representations for Cross-Resolution Person Re-Identification
Authors: Lin Wu, Lingqiao Liu, Yang Wang, Zheng Zhang, Farid Boussaid, Mohammed Bennamoun
Date: 2022-07-09 00:00:00
Tasks: Person Re-Identification, Super-Resolution

The cross-resolution person re-identification (CRReID) problem aims to match low-resolution (LR) query identity images against high resolution (HR) gallery images. It is a challenging and practical problem since the query images often suffer from resolution degradation due to the different capturing conditions from real-world cameras. To address this problem, state-of-the-art (SOTA) solutions either learn the resolution-invariant representation or adopt super-resolution (SR) module to recover the missing information from the LR query. This paper explores an alternative SR-free paradigm to directly compare HR and LR images via a dynamic metric, which is adaptive to the resolution of a query image. We realize this idea by learning resolution-adaptive representations for cross-resolution comparison. Specifically, we propose two resolution-adaptive mechanisms. The first one disentangles the resolution-specific information into different sub-vectors in the penultimate layer of the deep neural networks, and thus creates a varying-length representation. To better extract resolution-dependent information, we further propose to learn resolution-adaptive masks for intermediate residual feature blocks. A novel progressive learning strategy is proposed to train those masks properly. These two mechanisms are combined to boost the performance of CRReID. Experimental results show that the proposed method is superior to existing approaches and achieves SOTA performance on multiple CRReID benchmarks.
CTVR-EHO TDA-IPH Topological Optimized Convolutional Visual Recurrent Network for Brain Tumor Segmentation and Classification
Authors: Dhananjay Joshi, Bhupesh Kumar Singh, Kapil Kumar Nagwanshi, Nitin S. Choubey
Date: 2022-06-06 00:00:00
Tasks: Brain Tumor Classification, Brain Tumor Segmentation, Classification, Topological Data Analysis, Transfer Learning, Tumor Segmentation

In today's world of health care, brain tumor detection has become common. However, the manual brain tumor classification approach is time-consuming. So Deep Convolutional Neural Network (DCNN) is used by many researchers in the medical field for making accurate diagnoses and aiding in the patient's treatment. The traditional techniques have problems such as overfitting and the inability to extract necessary features. To overcome these problems, we developed the Topological Data Analysis based Improved Persistent Homology (TDA-IPH) and Convolutional Transfer learning and Visual Recurrent learning with Elephant Herding Optimization hyper-parameter tuning (CTVR-EHO) models for brain tumor segmentation and classification. Initially, the Topological Data Analysis based Improved Persistent Homology is designed to segment the brain tumor image. Then, from the segmented image, features are extracted using TL via the AlexNet model and Bidirectional Visual Long Short-Term Memory (Bi-VLSTM). Next, elephant Herding Optimization (EHO) is used to tune the hyperparameters of both networks to get an optimal result. Finally, extracted features are concatenated and classified using the softmax activation layer. The simulation result of this proposed CTVR-EHO and TDA-IPH method is analyzed based on precision, accuracy, recall, loss, and F score metrics. When compared to other existing brain tumor segmentation and classification models, the proposed CTVR-EHO and TDA-IPH approaches show high accuracy (99.8%), high recall (99.23%), high precision (99.67%), and high F score (99.59%).
Exact, Complete, and Universal Continuous-Time Worldline Monte Carlo Approach to the Statistics of Discrete Quantum Systems
Authors: N. V. Prokof'ev, B. V. Svistunov, I. S. Tupitsyn
Date: 1997-03-24 00:00:00

We show how the worldline quantum Monte Carlo procedure, which usually relies on an artificial time discretization, can be formulated directly in continuous time, rendering the scheme exact. For an arbitrary system with discrete Hilbert space, none of the configuration update procedures contain small parameters. We find that the most effective update strategy involves the motion of worldline discontinuities (both in space and time), i.e., the evaluation of the Green's function. Being based on local updates only, our method nevertheless allows one to work with the grand canonical ensemble and non-zero winding numbers, and to calculate any dynamic correlation function as easily as expectation values of, e.g., total energy. The principles found for the update in continuous time generalize to any continuous variables in the space of discrete virtual transitions, and in principle also make it possible to simulate continuous systems exactly.
Few-shot Learning with Class-Covariance Metric for Hyperspectral Image Classification
Authors: Bobo Xi, Jiaojiao Li, Yunsong Li, Rui Song, Danfeng Hong, Jocelyn Chanussot.
Date: 2022-07-26 00:00:00
Proceeding: journal 2022 7
Tasks: Few-Shot Learning, Hyperspectral Image Classification, image-classification, Image Classification

Recently, embedding and metric-based few-shot learning (FSL) has been introduced into hyperspectral image classification (HSIC) and achieved impressive progress. To further enhance the performance with few labeled samples, we in this paper propose a novel FSL framework for HSIC with a class-covariance metric (CMFSL). Overall, the CMFSL learns global class representations for each training episode by interactively using training samples from the base and novel classes, and a synthesis strategy is employed on the novel classes to avoid overfitting. During the meta-training and meta-testing, the class labels are determined directly using the Mahalanobis distance measurement rather than an extra classifier. Benefiting from the task-adapted class-covariance estimations, the CMFSL can construct more flexible decision boundaries than the commonly used Euclidean metric. Additionally, a lightweight cross-scale convolutional network (LXConvNet) consisting of 3-D and 2-D convolutions is designed to thoroughly exploit the spectral-spatial information in the high-frequency and low-frequency scales with low computational complexity. Furthermore, we devise a spectral-prior-based refinement module (SPRM) in the initial stage of feature extraction, which can not only force the network to emphasize the most informative bands while suppressing the useless ones, but also alleviate the effects of the domain shift between the base and novel categories to learn a collaborative embedding mapping. Extensive experiment results on four benchmark data sets demonstrate that the proposed CMFSL can outperform the state-of-the-art methods with few-shot annotated samples.
Firebolt: Weak Supervision Under Weaker Assumptions
Authors: Zhaobin Kuang, Chidubem Arachie, Bangyong Liang, Pradyumna Narayana, Giulia Desalvo, MICHAEL QUINN, Bert Huang, Geoffrey Downs, Yang Yang
Date: 2022-03-28 00:00:00
Proceeding: Proceedings of the 25th International Conference on Artificial Intelligence and Statistics 2022 3
Tasks: parameter estimation

Modern machine learning demands a large amount of training data. Weak supervision is a promising approach to meet this demand. It aggregates multiple labeling functions (LFs)—noisy, user-provided labeling heuristics—to rapidly and cheaply curate probabilistic labels for large-scale unlabeled data. However, standard assumptions in weak supervision—such as user-specified class balance, similar accuracy of an LF in classifying different classes, and full knowledge of LF dependency at inference time—might be undesirable in practice. In response, we present Firebolt, a new weak supervision framework that seeks to operate under weaker assumptions. In particular, Firebolt learns the class balance and class-specific accuracy of LFs jointly from unlabeled data. It carries out inference in an efficient and interpretable manner. We analyze the parameter estimation error of Firebolt and characterize its impact on downstream model performance. Furthermore, we show that on five publicly available datasets, Firebolt outperforms a state-of-the-art weak supervision method by up to 5.8 points in AUC. We also provide a case study in the production setting of a tech company, where a Firebolt-supervised model outperforms the existing weakly-supervised production model by 1.3 points in AUC and speeds up label model training and inference from one hour to three minutes.
GPS-GLASS: Learning Nighttime Semantic Segmentation Using Daytime Video and GPS data
Authors: Hongjae Lee, Changwoo Han, Jun-Sang Yoo, Seung-Won Jung
Date: 2022-07-27 00:00:00
Tasks: Autonomous Driving, Dense Pixel Correspondence Estimation, Domain Adaptation, Optical Flow Estimation, Segmentation, Semantic Segmentation

Semantic segmentation for autonomous driving should be robust against various in-the-wild environments. Nighttime semantic segmentation is especially challenging due to a lack of annotated nighttime images and a large domain gap from daytime images with sufficient annotation. In this paper, we propose a novel GPS-based training framework for nighttime semantic segmentation. Given GPS-aligned pairs of daytime and nighttime images, we perform cross-domain correspondence matching to obtain pixel-level pseudo supervision. Moreover, we conduct flow estimation between daytime video frames and apply GPS-based scaling to acquire another pixel-level pseudo supervision. Using these pseudo supervisions with a confidence map, we train a nighttime semantic segmentation network without any annotation from nighttime images. Experimental results demonstrate the effectiveness of the proposed method on several nighttime semantic segmentation datasets. Our source code is available at https://github.com/jimmy9704/GPS-GLASS.