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arXiv 2018年

作者： Bansal, Kanika Medaglia, John D. Bassett, Danielle S. Vettel, Jean M. Muldoon, Sarah F. Department of Mathematics University at Buffalo BuffaloNY United States U.S. Army Research Laboratory Aberdeen Proving GroundMD United States Department of Biomedical Engineering Columbia University New YorkNY United States Department of Psychology Drexel University PhiladelphiaPA United States Department of Neurology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Biomedical Engineering University of Pennsylvania PhiladelphiaPA United States Department of Electrical and Systems Engineering University of Pennsylvania PhiladelphiaPA United States Department of Physics and Astronomy University of Pennsylvania PhiladelphiaPA United States Department of Psychological and Brain Sciences University of California Santa BarbaraCA United States Computational and Data-Enabled Science and Engineering Program University at Buffalo-SUNY BuffaloNY United States

The relationship between brain structure and function has been probed using a variety of approaches, but how the underlying structural connectivity of the human brain drives behavior is far from understood. To investigate the effect of anatomical brain organization on human task performance, we use a data-driven computational modeling approach and explore the functional effects of naturally occurring structural differences in brain networks. We construct personalized brain network models by combining anatomical connectivity estimated from diffusion spectrum imaging of individual subjects with a nonlinear model of brain dynamics. By performing computational experiments in which we measure the excitability of the global brain network and spread of synchronization following a targeted computational stimulation, we quantify how individual variation in the underlying connectivity impacts both local and global brain dynamics. We further relate the computational results to individual variability in the subjects' performance of three language-demanding tasks both before and after transcranial magnetic stimulation to the left-inferior frontal gyrus. Our results show that task performance correlates with either local or global measures of functional activity, depending on the complexity of the task. By emphasizing differences in the underlying structural connectivity, our model serves as a powerful tool to predict individual differences in task performances, to dissociate the effect of targeted stimulation in tasks that differ in cognitive complexity, and to pave the way for the development of personalized therapeutics. Copyright © 2018, The Authors. All rights reserved.

关键词： Digital storage

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Signed iterative random forests to identify enhancer-associated transcription factor binding

arXiv

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arXiv 2018年

作者： Kumbier, Karl Basu, Sumanta Frise, Erwin Celniker, Susan E. Brown, James B. Yu, Bin University of California San Francisco Department of Pharmaceutical Chemistry San Francisco94158 United States Cornell University Department of Statistics and Data Science Ithaca14853 United States Lawrence Berkeley National Biological Systems and Engineering Division Berkeley94720 United States Lawrence Berkeley National Laboratory Division of Environmental Genomics and Systems Biology Berkeley94720 United States University of California Berkeley Department of Statistics Berkeley94720 United States University of California Berkeley Department of Electrical Engineering and Computer Science Berkeley94720 United States University of California Berkeley Center for Computational Biology Berkeley94720 United States

Standard ChIP-seq peak calling pipelines seek to differentiate biochemically reproducible signals of individual genomic elements from background noise. However, reproducibility alone does not imply functional regulation (e.g., enhancer activation, alternative splicing). Here we present a general-purpose, interpretable machine learning method: signed iterative random forests (siRF), which we use to infer regulatory interactions among transcription factors and functional binding signatures surrounding enhancer elements in Drosophila melanogaster. Copyright © 2018, The Authors. All rights reserved.

关键词： Transcription factors

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IDTxl: The information dynamics toolkit xl: A python package for the efficient analysis of multivariate information dynamics in networks

arXiv

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arXiv 2018年

作者： Wollstadt, Patricia Lizier, Joseph T. Vicente, Raul Finn, Conor Martinez-Zarzuela, Mario Mediano, Pedro Novelli, Leonardo Wibral, Michael MEG Unit Brain Imaging Center Goethe-University Frankfurt Fankfurt am Main Germany Centre for Complex Systems Faculty of Engineering and IT University of Sydney SydneyNSW Australia Computational Neuroscience Lab Institute of Computer Science Tartu Estonia Data61 CSIRO EppingNSW Australia Communications and Signal Theory and Telematics Engineering University of Valladolid Valladolid Spain Computational Neurodynamics Group Department of Computing Imperial College London London United Kingdom Max Planck Institute for Dynamics and Self-Organization Göttingen Germany Campus Institute for Dynamics of Biological Networks Georg-August Universität Göttingen Germany

We present IDTxl (the Information Dynamics Toolkit xl), a new open source Python toolbox for effective network inference from multivariate time series using information theory, available from GitHub (https://***/pwollstadt/IDTxl). Information theory (Cover & Thomas, 2006;MacKay, 2003;Shannon, 1948) is the mathematical theory of information and its transmission over communication channels. Information theory provides quantitative measures of the information content of a single random variable (entropy) and of the information shared between two variables (mutual information). The defined measures build on probability theory and solely depend on the probability distributions of the variables involved. As a consequence, the dependence between two variables can be quantified as the information shared between them, without the need to explicitly model a specific type of dependence. Hence, mutual information is a model-free measure of dependence, which makes it a popular choice for the analysis of systems other than communication channels. Transfer entropy (TE) (Schreiber, 2000) is an extension of mutual information that measures the directed information transfer between time series of a source and a target variable. TE has become popular in many scientific disciplines to infer dependencies and whole networks from data. Notable application domains include neuroscience (Wibral, Vicente, & Lindner, 2014) and dynamical systems analysis (Lizier, Prokopenko, & Zomaya, 2014) (see Bossomaier, Barnett, Harré, & Lizier (2016) for an introduction to TE and a comprehensive discussion of its application). In the majority of the applications, TE is used in a bivariate fashion, where information transfer is quantified between all sourcetarget pairs. In a multivariate setting, however, such a bivariate analysis may infer spurious or redundant interactions, where multiple sources provide the same information about the target. Conversely, bivariate analysis may also miss synergistic

关键词： High level languages

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GRINS: A multiphysics framework based on the libMesh finite element library

GRINS: A multiphysics framework based on the libMesh finite ...

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作者： Bauman, Paul T. Stogner, Roy H. Mechanical and Aerospace Engineering Computational and Data-Enabled Science and Engineering University at Buffalo State University of New York BuffaloNY14260-4400 United States Institute for Computational Engineering and Sciences University of Texas at Austin AustinTX78712 United States

This paper describes a flexible C++ software framework, called GRINS, for simulating complex multiphysics systems of partial differential equations using the finite element method. GRINS is designed to facilitate the rapid development and reuse of finite element formulation code as well as other features of complex simulations, including quantity-of-interest functionals, solvers, boundary conditions, initial conditions, and postprocessing. GRINS is built on the FEMSystem framework that is part of the libMesh finite element library. GRINS, through FEMSystem and libMesh, supports a number of contemporary algorithms and computing features including hybrid distributed and shared memory parallelism, parallel adaptive mesh refinement on unstructured grids, goal-oriented refinement driven by dual-weighted residual error estimates in quantities of interest, and adjoint-based parameter sensitivities. GRINS is deployed both as an application binary, allowing immediate use of existing features, and as a library to which the user may build and link a stand-alone application, extending the framework to their needs. Several examples demonstrate the effectiveness of the design, including uncertainty quantification applications. Planned developments are also discussed. © 2016 Society for Industrial and Applied Mathematics.

关键词： Multiphysics

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Structure-based Fitness Prediction for the Variable-structure DANNA Neuromorphic Architecture

Structure-based Fitness Prediction for the Variable-structur...

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International Joint Conference on Neural Networks

作者： Aleksander Klibisz Grant Bruer James S. Plank Catherine D. Schuman Department of Electrical Engineering and Computer Science University of Tennessee Knoxville Tennessee USA 37996 Computational Data Analytics Oak Ridge National Laboratory Oak Ridge Tennessee USA 37831

ISBN: (纸本)9781509061839

In recent years, research on neuromporphic computing platforms has focused on variable-structure, spiking network models. An important methodology for programming these networks is evoluationary optimization (EO), where thousands of networks are generated and then evaluated by determining fitness scores on specific tasks. Fitness scores guide the generation of new networks until a target fitness is achieved. One source of performance overhead during EO is the simulation of the task on each network to determing its fitness. To mitigate this source of overhead, we formulate the Static Fitness Prediction Task (SFPT), for predicting a network's fitness without direct simulation. Our hypothesis is that we can use SFPT to predict a network's fitness sufficiently accurately to reject a significant portion of networks during EO without having to simulate them, thereby making the EO more efficient. We propose a data-driven approach to the SFPT on the neuromorphic model DANNA [1]. Our approach transforms networks into directed graphs and extracts structural features to train an ancillary model for predicting the fitness of new networks. We analyze the extracted features and evaluate several predictive models to predict the fitness of networks for five tasks. Our results demonstrate a predictive capacity in these features and models. Our primary contribution is to demonstrate the utility of graph-level features extracted from variable-structure networks to predict network fitness and circumvent expensive simulations.

关键词： Predictive models Feature extraction computational modeling Neurons Training Reservoirs Genetic algorithms

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The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI

arXiv

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arXiv 2023年

作者： Moawad, Ahmed W. Janas, Anastasia Baid, Ujjwal Ramakrishnan, Divya Saluja, Rachit Ashraf, Nader Jekel, Leon Amiruddin, Raisa Adewole, Maruf Albrecht, Jake Anazodo, Udunna Aneja, Sanjay Anwar, Syed Muhammad Bergquist, Timothy Calabrese, Evan Chiang, Veronica Chung, Verena Conte, Gian Marco Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Kazerooni, Anahita Fathi Kofler, Florian Krantchev, Kiril LaBella, Dominic Van Leemput, Koen Li, Hongwei Bran Linguraru, Marius George Link, Katherine E. Liu, Xinyang Maleki, Nazanin Meier, Zeke Menze, Bjoern H. Moy, Harrison Osenberg, Klara Piraud, Marie Reitman, Zachary Shinohara, Russel Takeshi Tahon, Nourel hoda Nada, Ayman Velichko, Yuri S. Wang, Chunhao Wiestler, Benedikt Wiggins, Walter Shafique, Umber Willms, Klara Avesta, Arman Bousabarah, Khaled Chakrabarty, Satrajit Gennaro, Nicolo Holler, Wolfgang Kaur, Manpreet LaMontagne, Pamela Lin, MingDe Lost, Jan Marcus, Daniel S. Maresca, Ryan Merkaj, Sarah Nada, Ayaman Pedersen, Gabriel Cassinelli von Reppert, Marc Sotiras, Aristeidis Teytelboym, Oleg Tillmans, Niklas Westerhoff, Malte Youssef, Ayda Godfrey, Devon Floyd, Scott Rauschecker, Andreas Villanueva-Meyer, Javier Pflüger, Irada Cho, Jaeyoung Bendszus, Martin Brugnara, Gianluca Cramer, Justin Perez-Carillo, Gloria Guzman J. Johnson, Derek R. Kam, Anthony Kwan, Benjamin Yin Ming Lai, Lillian Lall, Neil U. Memon, Fatima Patro, Satya Narayana Petrovic, Bojan So, Tiffany Y. Thompson, Gerard Wu, Lei Schrickel, E. Brooke Bansal, Anu Barkhof, Frederik Besada, Cristina Chu, Sammy Druzgal, Jason Dusoi, Alexandru Farage, Luciano Feltrin, Fabricio Fong, Amy Fung, Steve H. Gray, R. Ian Ikuta, Ichiro Iv, Michael Postma, Alida A. Mahajan, Amit Joyner, David Krumpelman, Chase Letourneau-Guillon, Laurent Lincoln, Christie M. Maros, Mate E. Miller, Elka Morón, Fanny Nimchinsky, Esther A. Ozsarlak, Ozkan Patel, Uresh Rohatgi, Saurabh Saha, Atin Sayah, Anousheh Schwartz, Eric D. Shih, Robert Shiroishi, Mark Trinity health Mid Atlantic Hosiptals DarbyPA United States Department of Radiology and Biomedical Imaging Yale School of Medicine New HavenCT United States Division of Computational Pathology Department of Pathology and Laboratory Medicine School of Medicine Indiana University IndianapolisIN United States Department of Electical and Computer Engineering Cornell University Cornell Tech New YorkNY United States Department of Radiology Weill Cornell Medicine New YorkNY United States ImagineQuant Children’s Hospital of Philadelphia PhiladelphiaPA United States College of Medicine Alfaisal University Riyadh Saudi Arabia DKFZ Division of Translational Neurooncology The WTZ German Cancer Consortium DKTK Partner Site University Hospital Essen Essen Germany Medical Artificial Intelligence Lab Crestview Radiology Lagos Nigeria Sage Bionetworks SeattleWA United States Montreal Neurological Institute McGill University Montreal Canada lab Crestview Radiology Lagos Nigeria Department of Therapeutic Radiology Yale School of Medicine New HavenCT United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Radiology Mayo Clinic RochesterMN United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Neurosurgery Yale School of Medicine New HavenCT United States Center for Global Health Perelman School of Medicine University of Pennsylvania PA United States Department of Informatics Technical University Munich Germany Children’s Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Children’s National Hospital WashingtonDC United States PrecisionFDA U.S. Food and Drug Administration S

The translation of AI-generated brain metastases (BM) segmentation into clinical practice relies heavily on diverse, high-quality annotated medical imaging datasets. The BraTS-METS 2023 challenge has gained momentum for testing and benchmarking algorithms using rigorously annotated internationally compiled real-world datasets. This study presents the results of the segmentation challenge and characterizes the challenging cases that impacted the performance of the winning algorithms. Untreated brain metastases on standard anatomic MRI sequences (T1, T2, FLAIR, T1PG) from eight contributed international datasets were annotated in stepwise method: published UNET algorithms, student, neuroradiologist, final approver neuroradiologist. Segmentations were ranked based on lesion-wise Dice and Hausdorff distance (HD95) scores. False positives (FP) and false negatives (FN) were rigorously penalized, receiving a score of 0 for Dice and a fixed penalty of 374 for HD95. The mean scores for the teams were calculated. Eight datasets comprising 1303 studies were annotated, with 402 studies (3076 lesions) released on Synapse as publicly available datasets to challenge competitors. Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing. Segmentation accuracy was measured as rank across subjects, with the winning team achieving a LesionWise mean score of 7.9. The Dice score for the winning team was 0.65 ± 0.25. Common errors among the leading teams included false negatives for small lesions and misregistration of masks in space. The Dice scores and lesion detection rates of all algorithms diminished with decreasing tumor size, particularly for tumors smaller than 100 mm3. In conclusion, algorithms for BM segmentation require further refinement to balance high sensitivity in lesion detection with the minimization of false positives and negatives. The BraTS-METS 2023 challenge successfully curated well-annotated, diverse d

关键词： Image segmentation

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computer-aided whole-cell design: Taking a holistic approach by integrating synthetic with systems biology

arXiv

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arXiv 2020年

作者： Marucci, Lucia Barberis, Matteo Karr, Jonathan Ray, Oliver Race, Paul R. de Souza Andrade, Miguel Grierson, Claire Hoffmann, Stefan Andreas Landon, Sophie Rech, Elibio Rees-Garbutt, Joshua Seabrook, Richard Shaw, William Woods, Christopher Department of Engineering Mathematics University of Bristol BristolBS81UB United Kingdom School of Cellular and Molecular Medicine University of Bristol BS81TD Bristol United Kingdom University of Bristol BS81TQ Bristol United Kingdom Systems Biology School of Biosciences and Medicine Faculty of Health and Medical Sciences University of Surrey Guildford SurreyGU2 7XH United Kingdom Centre for Mathematical and Computational Biology CMCB University of Surrey Guildford SurreyGU2 7XH United Kingdom Synthetic Systems Biology and Nuclear Organization Swammerdam Institute for Life Sciences University of Amsterdam Amsterdam1098 XH Netherlands Icahn Institute for Data Science and Genomic Technology Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai 1255 5th Avenue Suite C2 New York10029 United States Department of Computer Science University of Bristol BristolBS81UB United Kingdom School of Biochemistry University of Bristol BristolBS8 1TD United Kingdom Brazilian Agriculture Research Corporation National Institute of Science and Technology - Synthetic Biology BrasíliaDF70770-917 Brazil Universidade de Brasília DF Brazil School of Biological Sciences University of Bristol BristolBS8 1TQ United Kingdom Manchester Institute of Biotechnology University of Manchester 131 Princess Street ManchesterM1 7DN United Kingdom University of Bristol BristolBS8 1UH United Kingdom Department of Bioengineering Imperial College London LondonSW7 2AZ United Kingdom School of Chemistry University of Bristol BristolBS8 1TS United Kingdom

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Stability of stationary inverse transport equation in diffusion scaling

arXiv

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arXiv 2017年

作者： Chen, Ke Li, Qin Wang, Li Mathematics Department University of Wisconsin-Madison 480 Lincoln Dr. MadisonWI53705 United States Department of Mathematics Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo 244 Mathematics Building BuffaloNY14206 United States

We consider the inverse problem of reconstructing the optical parameters for stationary radiative transfer equation (RTE) from velocity-averaged measurement. The RTE often contains multiple scales characterized by the magnitude of a dimensionless parameter-the Knudsen number (Kn). In the diffusive scaling (Kn 1), the stationary RTE is well approximated by an elliptic equation in the forward setting. However, the inverse problem for the elliptic equation is acknowledged to be severely ill-posed as compared to the well-posedness of inverse transport equation, which raises the question of how uniqueness being lost as Kn → 0. We tackle this problem by examining the stability of inverse problem with varying Kn. We show that, the discrepancy in two measurements is amplified in the reconstructed parameters at the order of Knp (p = 1 or 2), and as a result lead to ill-posedness in the zero limit of Kn. Our results apply to both continuous and discrete settings. Some numerical tests are performed in the end to validate these theoretical findings. Copyright © 2017, The Authors. All rights reserved.

关键词： Parameter estimation

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An accurate front capturing scheme for tumor growth models with a free boundary limit

arXiv

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arXiv 2017年

作者： Liu, Jian-Guo Tang, Min Wang, Li Zhou, Zhennan Department of Mathematics Department of Physics Duke University Department of Mathematics Institute of Natural Sciences MOE LSC Shanghai Jiao Tong University Department of Mathematics Computational and Data-Enabled Science and Engineering Program State University of New York Buffalo United States Department of Mathematics Duke University

We consider a class of tumor growth models under the combined effects of density-dependent pressure and cell multiplication, with a free boundary model as its singular limit when the pressure-density relationship becomes highly nonlinear. In particular, the constitutive law connecting pressure p and density ρ is p(ρ) = mm−1 ρm−1, and when m 1, the cell density ρ may evolve its support due to a pressure-driven geometric motion with sharp interface along the boundary of its support. The nonlinearity and degeneracy in the diffusion bring great challenges in numerical simulations, let alone the capturing of the singular free boundary limit. Prior to the present paper, there is lack of standard mechanism to numerically capture the front propagation speed as m 1. In this paper, we develope a numerical scheme based on a novel prediction-correction reformulation that can accurately approximate the front propagation even when the nonlinearity is extremely strong. We show that the semi-discrete scheme naturally connects to the free boundary limit equation as m → ∞, and with proper spacial discretization, the fully discrete scheme has improved stability, preserves positivity, and implements without nonlinear solvers. Finally, extensive numerical examples in both one and two dimensions are provided to verify the claimed properties and showcase good performance in various applications.35K55, 35B25, 76D27, 92C50 Copyright © 2017, The Authors. All rights reserved.

关键词： Tumors

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Personality traits and ego-network dynamics

arXiv

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arXiv 2017年

作者： Centellegher, Simone López, Eduardo Saramäki, Jari Lepri, Bruno Department of Information Engineering and Computer Science University of Trento Trento Italy Trento Italy CABDyN Complexity Center Saïd Business School University of Oxford Oxford United Kingdom Department of Computational and Data Sciences College of Science George Mason University FairfaxVA United States Department of Computer Science Aalto University School of Science Espoo Finland

Strong and supportive social relationships are fundamental to our well-being. However, there are costs to their maintenance, resulting in a trade-off between quality and quantity, a typical strategy being to put a lot of effort on a few high-intensity relationships while maintaining larger numbers of less close relationships. It has also been shown that there are persistent individual differences in this pattern;some individuals allocate their efforts more uniformly across their networks, while others strongly focus on their closest relationships. Furthermore, some individuals maintain more stable networks than others. Here, we focus on how personality traits of individuals affect this picture, using mobile phone calls records and survey data from the Mobile Territorial Lab (MTL) study. In particular, we look at the relationship between personality traits and the (i) persistence of social signatures, namely the similarity of the social signature shape of an individual measured in different time intervals;(ii) the turnover in egocentric networks, that is, differences in the set of alters present at two consecutive temporal intervals;and (iii) the rank dynamics defined as the variation of alter rankings in egocentric networks in consecutive intervals. We observe that some traits have effects on the stability of the social signatures as well as network turnover and rank dynamics. As an example, individuals who score highly in the Openness to Experience trait tend to have higher levels of network turnover and larger alter rank variations. On broader terms, our study shows that personality traits clearly affect the ways in which individuals maintain their personal networks. Copyright © 2017, The Authors. All rights reserved.

关键词： Dynamics

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