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arXiv 2022年

作者： Gagolewski, Marek Bartoszuk, Maciej Cena, Anna Systems Research Institute Polish Academy of Sciences ul. Newelska 6 Warsaw01-447 Poland Faculty of Mathematics and Information Science Warsaw University of Technology ul. Koszykowa 75 Warsaw00-662 Poland International PhD Studies Program Institute of Computer Science Polish Academy of Sciences Poland

The time needed to apply a hierarchical clustering algorithm is most often dominated by the number of computations of a pairwise dissimilarity measure. Such a constraint, for larger data sets, puts at a disadvantage the use of all the classical linkage criteria but the single linkage one. However, it is known that the single linkage clustering algorithm is very sensitive to outliers, produces highly skewed dendrograms, and therefore usually does not reflect the true underlying data structure - unless the clusters are well-separated. To overcome its limitations, we propose a new hierarchical clustering linkage criterion called Genie. Namely, our algorithm links two clusters in such a way that a chosen economic inequity measure (e.g., the Gini- or Bonferroni-index) of the cluster sizes does not increase drastically above a given threshold. The presented benchmarks indicate a high practical usefulness of the introduced method: it most often outperforms the Ward or average linkage in terms of the clustering quality while retaining the single linkage speed. The Genie algorithm is easily parallelizable and thus may be run on multiple threads to speed up its execution further on. Its memory overhead is small: there is no need to precompute the complete distance matrix to perform the computations in order to obtain a desired clustering. It can be applied on arbitrary spaces equipped with a dissimilarity measure, e.g., on real vectors, DNA or protein sequences, images, rankings, informetric data, etc. A reference implementation of the algorithm has been included in the open source genie package for R. [See https://genieclust. gagolewski. com for a new implementation - available for both R and Python.]. © 2022, CC BY.

关键词： Clustering algorithms

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Probabilistic Genotype-Phenotype Maps Reveal Mutational Robustness of RNA Folding, Spin Glasses, and Quantum Circuits

arXiv

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arXiv 2023年

作者： Sappington, Anna Mohanty, Vaibhav Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States Program for Health Sciences and Technology Harvard Medical School BostonMA02115 United States Massachusetts Institute of Technology CambridgeMA02139 United States Harvard/MIT MD-PhD Program Harvard Medical School BostonMA02115 United States Department of Chemistry and Chemical Biology Harvard University CambridgeMA02138 United States

Recent studies of genotype-phenotype (GP) maps have reported universally enhanced phenotypic robustness to genotype mutations, a feature essential to evolution. Virtually all of these studies make a simplifying assumption that each genotype—represented as a sequence—maps deterministically to a single phenotype, such as a discrete structure. Here, we introduce probabilistic genotype-phenotype (PrGP) maps, where each genotype maps to a vector of phenotype probabilities, as a more realistic and universal language for investigating robustness in a variety of physical, biological, and computational systems. We study three model systems to show that PrGP maps offer a generalized framework which can handle uncertainty emerging from various physical sources: (1) thermal fluctuation in RNA folding, (2) external field disorder in spin glass ground state finding, and (3) superposition and entanglement in quantum circuits, which are realized experimentally on IBM quantum computers. In all three cases, we observe a novel biphasic robustness scaling which is enhanced relative to random expectation for more frequent phenotypes and approaches random expectation for less frequent phenotypes. We derive an analytical theory for the behavior of PrGP robustness, and we demonstrate that the theory is highly predictive of empirical robustness. © 2023, CC BY.

关键词： Quantum computers

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An Ordinance-Tweet Mining App to Disseminate Urban Policy Knowledge for Smart Governance 19th

An Ordinance-Tweet Mining App to Disseminate Urban Policy Kn...

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19th IFIP WG 6.11 Conference on e-Business, e-Services, and e-Society, I3E 2020

作者： Varghese, Christina Varde, Aparna S. Du, Xu Department of Computer Science Montclair State University MontclairNJ United States Department of Earth and Environmental Science Montclair State University MontclairNJ United States Environmental Science and Management PhD Program Montclair State University MontclairNJ United States

ISBN: (纸本)9783030450014

This paper focuses on how populations by the use of technology, more specifically an app, can comprehend the enactment of ordinances (local laws) in an urban area along with their public reactions expressed as tweets. Furthermore, they can understand how well the area is developing and enhancing as a Smart City. The main goal of this research is to develop an Ordinance-Tweet Mining App that disseminates the results of analyzing ordinances and tweets about them, especially related to Smart City Characteristics such as Smart Environment, Smart Mobility etc. This app would be beneficial to various users such as environmental scientists, policy makers, city committees as well as the common public in becoming more aware of legislative bodies, and possibly contributing in different aspects to make the urban area improve as a Smart City. This work fits the realm of Smart Governance due to transparency via public involvement. © 2020, IFIP International Federation for Information Processing.

关键词： Sentiment analysis

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Public participation in museums and cultural heritage sites: iCommunity mobile application

Public participation in museums and cultural heritage sites:...

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2020 AVI2CH Workshop on Advanced Visual Interfaces and Interactions in Cultural Heritage, AVI2CH 2020

作者： Nasrolahi, Ahmad Messina, Vito Gena, Cristina Tech4Culture Phd program University of Torino Turin Italy Historical Studies Dept. University of Torino Turin Italy Computer Science Dept. University of Torino Turin Italy

This paper presents iCommunity, an application that will be aimed at finding a universal method for inclusive societies in decision-making processes for cultural heritage management. iCommunity is being designed as a mobile application facilitating public participation in cultural heritage management. The main idea is to give all people, who are affected by a decision, the opportunity to be involved in the decision-making process. Any cultural heritage institution will be able to publish its activities on the application so as to evaluate users' feedback before the implementation of the activity itself. Based on the user's location, the application displays ongoing activities to the user himself. As a part of a participatory approach, users share each other's experience or data related to the posted activity. They also can show their agreement or disagreement to the activities by voting. The comments, votes and user's activities will be analysed real time for helping authorities to consider the consequence of their activities for more transparent and effective decision-making. © Copyright 2020 for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).

关键词： Decision making

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Segmenting Alzheimer's Disease MRI Slices for Hippocampal Volume Calculation

Segmenting Alzheimer's Disease MRI Slices for Hippocampal Vo...

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IEEE International Conference on Consumer Electronics-Taiwan (ICCE-TW)

作者： Hsiao-Chuan Tan Gilang Titah Ramadhan Wei-Cheng Shen Wen-Thong Chang Chih-Yang Lin Ben-Yi Liau Yih-Kuen Jan Yori Pusparani Chi-Wen Lung Department of Artificial Intelligence PhD Program Asia University Taichung Taiwan Department of Computer Science and Information Engineering Asia University Taichung Taiwan Department of Creative Product Design Asia University Taichung Taiwan Department of Mechanical Engineering National Central University Taoyuan Taiwan Department of Automatic Control Engineering Feng Chia University Taichung Taiwan Department of Kinesiology and Community Health University of Illinois Urbana America Department of Digital Media Design Asia University Taichung Taiwan

ISBN: (数字)9798350386844

ISBN: (纸本)9798350386851

Alzheimer's is a neurodegenerative disease that quietly steals human memory. This study analyzed hippocampal volume in Alzheimer's Disease (AD), Mild Cognitive Impairment (MCI), and Normal Cognition (NC) using MRI image slices from the ADNI database and YOLOv8 instance segmentation. We used 300 images to segment the left and right hippocampal. This study focused on volume calculation from five MRI image slices. The results showed 0.98 (AD), 0.92 (MCI), and 0.90 (NC) and revealed significant volumetric differences showed in the NC class (P = 0.045). This suggests early neuroanatomical changes can occur without cognitive symptoms, highlighting the potential of deep learning in the early detection of neurodegenerative diseases.

关键词： Instance segmentation Deep learning Accuracy Databases Magnetic resonance imaging Cognition Alzheimer's disease

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Cryo-EM structure of the plant 26S proteasome

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Plant Communications 2022年第3期3卷 116-126页

作者： Susanne Kandolf Irina Grishkovskaya Katarina Belacic Derek L.Bolhuis Sascha Amann Brent Foster Richard Imre Karl Mechtler Alexander Schleiffer Hemant D.Tagare Ellen D.Zhong Anton Meinhart Nicholas G.Brown David Haselbach Research Institute of Molecular Pathology(IMP) Vienna BioCenter(VBC)Campus-Vienna-BioCenter 11030 ViennaAustria Department of Radiology and Biomedical Imaging Yale UniversityNew HavenCT 06510USA Department of Pharmacology and Lineberger Comprehensive Cancer Center University of North Carolina School of MedicineChapel HillNC 27599USA Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of TechnologyCambridgeMA 02139USA Vienna BioCenter PhD Program Doctoral School of the University at Vienna and Medical University of ViennaVienna BioCenter(VBC)ViennaAustria Institute of Physical Chemistry University of FreiburgAlbertstraße 21Freiburg 79104Germany CIBSS Centre for Integrative Biological Signalling Studies University of FreiburgFreiburgGermany

Targeted proteolysis is a hallmark of *** is especially important in long-lived cells that can be found in higher eukaryotes,like *** task is mainly fulfilled by the ubiquitin–proteasome ***,proteolysis by the 26S proteasome is vital to development,immunity,and cell *** the yeast and animal proteasomes are well characterized,there is only limited information on the plant *** determined the first plant 26S proteasome structure from Spinacia oleracea by single-particle electron cryogenic microscopy at an overall resolution of 3.3 A°.We found an almost identical overall architecture of the spinach proteasome compared with the known structures from mammals and ***,we noticed a structural difference in the proteolytic active b1 ***,we uncovered an unseen compression state by characterizing the proteasome’s conformational *** suspect that this new conformation of the 20S core protease,in correlation with a partial opening of the unoccupied gate,may contribute to peptide release after *** data provide a structural basis for the plant proteasome,which is crucial for further studies.

关键词： 26S proteasome spinach UPS cryo-EM conformational landscape

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Hamiltonicity via cohomology of right-angled Artin groups

arXiv

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arXiv 2021年

作者： Flores, Ramón Kahrobaei, Delaram Koberda, Thomas Department of Geometry and Topology University of Seville Spain Department of Computer Science University of York United Kingdom New York University Tandon School of Engineering PhD Program in Computer Science CUNY Graduate Center Department of Mathematics University of Virginia CharlottesvilleVA22904 United States

Let Γ be a finite graph and let A(Γ) be the corresponding right-angled Artin group. We characterize the Hamiltonicity of Γ via the structure of the cohomology algebra of A(Γ). In doing so, we define and develop a new canonical graph associated to a matrix, which as a consequence provides a novel perspective on the matrix determinant. Copyright © 2021, The Authors. All rights reserved.

关键词： Topology

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Legal Design Through AI in Banking Contracts

Legal Design Through AI in Banking Contracts

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Metrology for Extended Reality, Artificial Intelligence and Neural Engineering (MetroXRAINE), IEEE International Conference on

作者： Lucilla Gatt Ilaria Amelia Caggiano Maria Cristina Gaeta Livia Aulino Emiliano Troisi Luigi Izzo Christian Carmine Esposito Alessandra Fabrocini Daniele Marino Research Centre of European Private Law (ReCEPL) Università degli Studi Suor Orsola Benincasa Naples Italy Research Centre of European Private Law (ReCEPL) University Suor Orsola Benincasa Naples IT University of Turin Turin IT Humanities and Technologies: an integrated research path Research Centre of European Private Law (ReCEPL) University Suor Orsola Benincasa Naples IT Computer Science University of Salerno Salerno IT Earth Observation (National PhD program) University La Sapienza - Vanvitelli Rome Caserta IT VISA Barcelona ES

ISBN: (数字)9798350378009

ISBN: (纸本)9798350378016

Consumer protection in banking is a particularly relevant issue, especially in light of the increasing complexity of banking transactions and the related legal reference cases. For this reason, the adoption of pre-contractual disclosures and contractual texts as complete as possible has been mandated to enable the consumer to be fully aware of the characteristics of the contractual relationship. This has led to the creation of contracts that are particularly detailed and full of content, with graphics designed to reduce the size of the relevant documents but inadequate to allow an understanding of these documents. It is therefore necessary to change the paradigm in the drafting of contractual texts and pre-contractual disclosures through the adoption of legal design methodologies. In particular, added value could be provided by adopting AI and metrology techniques for measuring the level of clarity of contractual texts and subsequently creating a more user-friendly version of these.

关键词： Graphics Extended reality Neural engineering Banking Metrology Particle measurements Consumer protection Complexity theory Artificial intelligence Contracts

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A Framework for Interpretability in Machine Learning for Medical Imaging

arXiv

引用

arXiv 2023年

作者： Wang, Alan Q. Karaman, Batuhan K. Kim, Heejong Rosenthal, Jacob Saluja, Rachit Young, Sean I. Sabuncu, Mert R. School of Electrical and Computer Engineering Cornell University Cornell Tech New YorkNY10044 United States Department of Radiology Weill Cornell Medical School New YorkNY10065 United States Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program New YorkNY10065 United States Martinos Center for Biomedical Imaging Harvard Medical School BostonMA02129 United States Computer Science and Artificial Intelligence Laboratory MIT CambridgeMA02139 United States

Interpretability for machine learning models in medical imaging (MLMI) is an important direction of research. However, there is a general sense of murkiness in what interpretability means. Why does the need for interpretability in MLMI arise? What goals does one actually seek to address when interpretability is needed? To answer these questions, we identify a need to formalize the goals and elements of interpretability in MLMI. By reasoning about real-world tasks and goals common in both medical image analysis and its intersection with machine learning, we identify five core elements of interpretability: localization, visual recognizability, physical attribution, model transparency, and actionability. From this, we arrive at a framework for interpretability in MLMI, which serves as a step-by-step guide to approaching interpretability in this context. Overall, this paper formalizes interpretability needs in the context of medical imaging, and our applied perspective clarifies concrete MLMI-specific goals and considerations in order to guide method design and improve real-world usage. Our goal is to provide practical and didactic information for model designers and practitioners, inspire developers of models in the medical imaging field to reason more deeply about what interpretability is achieving, and suggest future directions of interpretability research. © 2023, CC0.

关键词： Machine learning

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Statistical Power Analysis for Designing Bulk, Single-Cell, and Spatial Transcriptomics Experiments: Review, Tutorial, and Perspectives

arXiv

引用

arXiv 2023年

作者： Jeon, Hyeongseon Xie, Juan Jeon, Yeseul Jung, Kyeong Joo Gupta, Arkobrato Chang, Won Chung, Dongjun Department of Biomedical Informatics The Ohio State University ColumbusOH United States Pelotonia Institute for Immuno-Oncology The James Comprehensive Cancer Center The Ohio State University ColumbusOH43210 United States The Interdisciplinary PhD program in Biostatistics The Ohio State University ColumbusOH United States Department of Statistics and Data Science Yonsei University Seoul Korea Republic of Department of Applied Statistics Yonsei University Seoul Korea Republic of Department of Computer Science and Engineering The Ohio State University ColumbusOH United States Division of Statistics and Data Science University of Cincinnati CincinnatiOH United States

Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct characteristics. In order to guarantee biologically meaningful findings using transcriptomic experiments, it is important to consider various experimental factors in a systematic way through statistical power analysis. In this paper, we review and discuss the power analysis for three types of gene expression profiling technologies from a practical standpoint, including bulk RNA-seq, single-cell RNA-seq, and high-throughput spatial transcriptomics. Specifically, we describe the existing power analysis tools for each research objective for each of the bulk RNA-seq and scRNA-seq experiments, along with recommendations. On the other hand, since there are no power analysis tools for high-throughput spatial transcriptomics at this point, we instead investigate the factors that can influence power analysis. © 2023, CC BY-NC-ND.

关键词： RNA

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