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Inferring spatial transcriptomics markers from whole slide images to characterize metastasis-related spatial heterogeneity of colorectal tumors: A pilot study

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Journal of Pathology informatics 2023年 14卷 100308-100308页

作者： Fatemi, Michael Feng, Eric Sharma, Cyril Azher, Zarif Goel, Tarushii Ramwala, Ojas Palisoul, Scott M. Barney, Rachael E. Perreard, Laurent Kolling, Fred W. Salas, Lucas A. Christensen, Brock C. Tsongalis, Gregory J. Vaickus, Louis J. Levy, Joshua J. Department of Computer Science University of Virginia Charlottesville VA United States Thomas Jefferson High School for Science and Technology Alexandria VA United States Department of Computer Science Purdue University West Lafayette IN United States Department of Computer Science Massachusetts Institute of Technology Cambridge MA United States Department of Biomedical Informatics and Medical Education University of Washington Seattle WA United States Emerging Diagnostic and Investigative Technologies Department of Pathology and Laboratory Medicine Dartmouth Health NH United States Dartmouth Cancer Center NH United States Department of Epidemiology Dartmouth College Geisel School of Medicine Hanover NH United States Department of Molecular and Systems Biology Dartmouth College Geisel School of Medicine Hanover NH United States Integrative Neuroscience at Dartmouth (IND) graduate program Dartmouth College Geisel School of Medicine Hanover NH United States Department of Community and Family Medicine Dartmouth College Geisel School of Medicine Hanover NH United States Department of Dermatology Dartmouth Health NH United States Program in Quantitative Biomedical Sciences Dartmouth College Geisel School of Medicine Hanover NH United States

Over 150 000 Americans are diagnosed with colorectal cancer (CRC) every year, and annually over 50 000 individuals will die from CRC, necessitating improvements in screening, prognostication, disease management, and therapeutic options. Tumor metastasis is the primary factor related to the risk of recurrence and mortality. Yet, screening for nodal and distant metastasis is costly, and invasive and incomplete resection may hamper adequate assessment. Signatures of the tumor-immune microenvironment (TIME) at the primary site can provide valuable insights into the aggressiveness of the tumor and the effectiveness of various treatment options. Spatially resolved transcriptomics technologies offer an unprecedented characterization of TIME through high multiplexing, yet their scope is constrained by cost. Meanwhile, it has long been suspected that histological, cytological, and macroarchitectural tissue characteristics correlate well with molecular information (e.g., gene expression). Thus, a method for predicting transcriptomics data through inference of RNA patterns from whole slide images (WSI) is a key step in studying metastasis at scale. In this work, we collected tissue from 4 stage-III (pT3) matched colorectal cancer patients for spatial transcriptomics profiling. The Visium spatial transcriptomics (ST) assay was used to measure transcript abundance for 17 943 genes at up to 5000 55-micron (i.e., 1–10 cells) spots per patient sampled in a honeycomb pattern, co-registered with hematoxylin and eosin (H&E) stained WSI. The Visium ST assay can measure expression at these spots through tissue permeabilization of mRNAs, which are captured through spatially (i.e., x–y positional coordinates) barcoded, gene specific oligo probes. WSI subimages were extracted around each co-registered Visium spot and were used to predict the expression at these spots using machine learning models. We prototyped and compared several convolutional, transformer, and graph convolutional neural

关键词： Colorectal cancer Deep learning Graph neural network Histomorphology Spatial transcriptomics Transformers

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D-SRGAN: DEM Super-Resolution with Generative Adversarial Networks

arXiv

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arXiv 2020年

作者： Demiray, Bekir Z. Sit, Muhammed Demir, Ibrahim Department of Computer Science University of Iowa Iowa City United States Graduate Program in Informatics University of Iowa Iowa City United States Department of Civil & Environmental Engineering University of Iowa Iowa City United States

—LIDAR (light detection and ranging) is an optical remote-sensing technique that measures the distance between sensor and object, and the reflected energy from the object. Over the years, LIDAR data has been used as the primary source of Digital Elevation Models (DEMs). DEMs have been used in a variety of applications like road extraction, hydrological modeling, flood mapping, and surface analysis. A number of studies in flooding suggest the usage of high- resolution DEMs as inputs in the applications improve the overall reliability and accuracy. Despite the importance of high-resolution DEM, many areas in the United States and the world do not have access to high-resolution DEM due to technological limitations or the cost of the data collection. With recent development in Graphical Processing Units (GPU) and novel algorithms, deep learning techniques have become attractive to researchers for their performance in learning features from high-resolution datasets. Numerous new methods have been proposed such as Generative Adversarial Networks (GANs) to create intelligent models that correct and augment large-scale datasets. In this paper, a GAN based model is developed and evaluated, inspired by single image super-resolution methods, to increase the spatial resolution of a given DEM dataset up to 4 times without additional information related to data. Copyright © 2020, The Authors. All rights reserved.

关键词： Generative adversarial networks

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Determination of Giving 'Tips' Using Fuzzy Logic To Determine Restaurant Customer Service Satisfaction

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Journal of Physics: Conference Series 2021年第1期1830卷

作者： Dadang Priyanto Muhammad Zarlis Anthony Anggrawan Graduate Program Of Computer Science Department Of Computer Science Faculty Of Computer Science And Information Technology Universitas Sumatera Utara Medan Indonesia. Informatics Engineering Universitas Bumigora Mataram Indonesia Department of Computer Science Faculty of computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia.

Fuzzy logic can be used to represent obscurity based on terms such as high, old, hot, cold, and so on. Fuzzy logic can extend the range of truth values to all real numbers in intervals between 0 and 1. Numbers in this interval represent the possibility that the statement given is 'true' or 'wrong'. The use of fuzzy logic can be used in everyday life, such as in the fields of medicine, engineering, agriculture, transportation, environmental science and also in economic and business applications. As in this study, it was used to calculate the ideal amount of 'tips' for restaurant waiters based on the service provided by restaurant waiters. The method used in this study is to use Mamdani fuzzy logic with the process of defuzzyfication using the Centroid of area (COA). The results of this study are that it can be determined the value crisp of giving tips to restaurant waiters is 45 thousand rupiah provided that the service provided for service = 7 (Excellent) and food service = 8 (Delicious)..

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Literature Review of Religion Video Game

Literature Review of Religion Video Game

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2019 International Congress on Applied Information Technology, AIT 2019

作者： Wibawa, Setya Chendra Rahayu, Yuni Sri Wrahatnolo, Tri Vindy, V. Warnars, Harco Leslie Hendric Spits Hashimoto, Kiyota Universitas Negeri Surabaya Jawa Timur Informatics Department 60213 Indonesia Universitas Negeri Surabaya Jawa Timur Biology Department 60213 Indonesia Universitas Negeri Surabaya Jawa Timur Electrical Engineering Department 60213 Indonesia Game Application Technology Program School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia BINUS Graduate Program - Doctor of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Faculty of Technology and Environment Prince Songkla University Thailand

ISBN: (纸本)9781728158624

In this current digital era, the video game is favorite especially among young people. Besides widely known as a form of entertainment, some messages or lessons can be learned from a video game that may affect the players. Conscious or unconscious, games have influenced many sectors of life, and it has been recognized as a serious game and no exception to religion. Human as a living creature, like or dislike or even as an atheist should believe with something out there, and religion is as a medium which connects human with something out there. The game as a representation of entertaining, intelligent application will represent joy and happiness in human life's activities, and inevitably games will influence human religion. In the end, religion game will help the human to increase their faith in those their belief based on their religion. Similar to Information Technology which is implemented in business to increase revenue, the game as an entertaining intelligent application will increase human's faith. One kind of video game that provides it is religion video games which are the result of the incorporation between religion and video games. In this paper, we do a literature review about religion video games. We try to summarize how religious elements can be incorporated into a video game which can be seen from the parts, components, and approaches of the religion video game itself. We also try to summarize the positive side and controversies in religion video games. © 2019 IEEE.

关键词： Serious games

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Personnel System Development with Integrated Military Education Information System (MEIS) in Supporting the Personnel Position and Career

Personnel System Development with Integrated Military Educat...

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International Conference on ICT For Smart Society (ICISS)

作者： Leli Setyaningrum Suhono H. Supangkat Harco Leslie Hendric Spits Warnars Juneman Abraham Edi Abdurachman Bina Nusantara University Jakata Barat Indonesia School of Electrical Engineering and Informatics Institut Teknologi Bandung Bandung Indonesia Graduate Program Doctor of Computer Science Bina Nusantara University Jakarta Indonesia Faculty of Humanities Bina Nusantara University BINUS Jakarta Indonesia

ISBN: (数字)9781665404228

ISBN: (纸本)9781665404235

Personnel and education data very important for organizations, including the military. All data related to military personnel will give effect positions and careers in the military field. The integration of personnel and education data can assist in processing and decision making. An analysis is needed so that the developed system can be useful for the long term. Analysis with IT balanced scorecard and COBIT ® 2019, will be able to help and fill the gaps in the existing system based on the objectives of the military organization itself. It is shown that the domains BAI05 (Managed Organizational Change) and DSS02 (Managed Service Requests and Incidents) are still not being implemented well. The system developed will have the features and capabilities to support the organization in achieving its goals, including in the field of staffing and education. Besides, it provides convenience in making decisions in terms of positions related to personnel careers.

关键词： Personnel Education Organizations Task analysis Information technology Engineering profession computer science

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Implementation of Augmented Reality in Pretend Play Therapy for Children with Autism Spectrum Disorder 3

Implementation of Augmented Reality in Pretend Play Therapy ...

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3rd International Conference on Computing and Applied informatics 2018, ICCAI 2018

作者： Syahputra, M.F. Angkasih, A.P. Purnamawati, S. Andayani, U. Abdullah, D. Sriadhi, S. Iskandar, A. Rosida, T.M. Fitriany, J. Sari, I.N. Utama, M.D. Nanuru, R.F. Department of Information Technology Faculty of Computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia Department of Informatics Universitas Malikussaleh Aceh Utara Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Informatics Engineering STMIK AKBA Makassar Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Department of Pediatric Universitas Malikussaleh Aceh Utara Indonesia Departement of Social Science Education Program Post Graduate Program Universitas Kanjuruhan Malang Malang Indonesia Faculty of Social and Political Science Universitas Kristen Indonesia Maluku Indonesia Universitas Kristen Indonesia Maluku Ambon Indonesia

Autism Spectrum Disorder is a pervasive developmental disorder that will affect children in terms of interpersonal communication, social interaction, and imaginative levels in play. Many therapies to help the motor neuron performance is one of them Pretend Play. Pretend Play is a therapy that invites children in playing to demonstrate something else and tell how to use objects that are considered in the child's imagination. However, in the era of highly developed technology, many fields have used the Augmented Reality method as a visualization of various aspects. With this method researchers will present the therapeutic visualization of the block to 3D transportation tool that is useful for strengthening motor nerves and visual strength of the child. The system can run well during marker detection, marker movement, and 3D object display with the accuracy of precision angle and distance between virtual world with real world reach 100% with angle 0 at distance 31 cm and the maximum distance from the marker is 46 cm and the maximum angle is 30. © 2019 Published under licence by IOP Publishing Ltd.

关键词： Augmented reality

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Employing best input SVR robust lost function with nature-inspired metaheuristics in wind speed energy forecasting

IAENG International Journal of Computer Science

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IAENG International Journal of computer science 2020年第3期47卷 572-584页

作者： Caraka, Rezzy Eko Chen, Rung Ching Bakar, Sakhinah Abu Tahmid, Muhammad Toharudin, Toni Pardamean, Bens Huang, Su-Wen College of Informatics Chaoyang University of Technology Taichung City41349 Taiwan School of Mathematical Sciences The National University of Malaysia Bandar Baru Bangi Selangor43600 Malaysia Bioinformatics and Data Science Research Center Bina Nusantara University 11480 Indonesia Manado North Sulawesi91594 Indonesia Department of Statistics Padjadjaran University Jatinagor west java45363 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University and Computer Science Dept. BINUS Graduate Program-Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Taichung Veterans General Hospital Taiwan

Wind power has been experiencing a quick improvement. Without a doubt, wind is a variable asset that is hard to forecast. For instance, traditionally time series, extra holds are distributed to deal with this uncertainty. This paper presents a comparison of the performance of various Support Vector Regression (SVR) applied to short-term wind power forecasting. The analogy with BORUTA and multivariate adaptive regression splines (MARS) as judge best input and employ genetic algorithm and particle swarm optimization to find best parameter in Support Vector Regression with robust lost function. We measure the accuracy of this models by Symmetric means absolute percentage error (sMAPE) and we get the best model BORUTA-SVR-PSO with sMAPE 2.07155%. Moreover, we measure the energy conversion using Feedback Linearization Control (FLC). © International Association of Engineers.

关键词： Genetic algorithms

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Feasibility study of Information Technology Investment (a case study of ODOO ERP: Project Management Module Implementation in Indonesia Based Company)

Feasibility study of Information Technology Investment (a ca...

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International Conference on ICT For Smart Society (ICISS)

作者： Fredy Jingga Raymond Kosala Suhono Harso Supangkat Benny Ranti Computer Science Department BINUS Graduate Program - Doctor of Computer Science Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Doctor of Computer Science Bina Nusantara University Jakarta Indonesia School of Electrical Engineering and Informatics Bandung Institute of Technology Bandung Indonesia

IT Governance are one of the needs in managing Enterprise Level IT. This study shows part of the decision domain of IT Governance Help, which are IT Investment and Prioritization. The purpose of this study is to determine feasibility of implementation open source ERP system Odoo project management module that replaces current system based on operational, economic, and technical aspects. The method used are Fit / Gap Analysis and Cost Benefit model using economic impact worksheet. The analysis is done by comparing the requirement with features owned by current system and Odoo ERP system. This research resulted that Odoo ERP System is feasible in the 3 aspects, the operational feasibility Odoo reaching 72% Fit, the economic feasibility with ROI of 84%, and technical feasibility indicating the technical requirement can be fulfilled by leasing AWS server. The conclusion is the open source ERP system Odoo project management module is feasible to be applied in terms of 3 aspects that have been studied, those are operational, economic, and technical.

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A Step Towards a Reinforcement Learning De Novo Genome Assembler

Research Square

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Research Square 2021年

作者： Padovani, Kleber Xavier, Roberto Carvalho, André Reali, Anna Chateau, Annie Alves, Ronnie Federal University of Pará Computer Science Graduate Program Belém66.075-110 Brazil University of the State of Amazonas Itacoatiara-AM 69.101-416 Brazil Vale Technology Institute Sustainable Development Belém66.055-090 Brazil Institute of Mathematics and Computer Sciences University of São Paulo São Carlos-SP 13566-590 Brazil Polytechnic School University of São Paulo São Paulo-SP 05508-010 Brazil LIRMM-Montpellier Laboratory of Informatics Robotics and Microelectronics Univ Montpellier CNRS Montpellier France

Genome assembly is one of the most relevant and computationally complex tasks in genomics projects. It aims to reconstruct a genome through the analysis of several small textual fragments of such genome — named reads. Ideally, besides ignoring any errors contained in reads, the reconstructed genome should also optimally combine these reads, thus reaching the original genome. The quality of the genome assembly is relevant because the more reliable the genomes, the more accurate the understanding of the characteristics and functions of living beings, and it allows generating many positive impacts on society, including the prevention and treatment of diseases. The assembly becomes even more complex (and it is termed de novo in this case) when the assembler software is not supplied with a similar genome to be used as a reference. Current assemblers have predominantly used heuristic strategies on computational graphs. Despite being widely used in genomics projects, there is still no irrefutably best assembler for any genome, and the proper choice of these assemblers and their configurations depends on Bioinformatics experts. The use of reinforcement learning has proven to be very promising for solving complex activities without human supervision during their learning process. However, their successful applications are predominantly focused on fictional and entertainment problems - such as games. Based on the above, this work aims to shed light on the application of reinforcement learning to solve this relevant real-world problem, the genome assembly. By expanding the only approach found in the literature that addresses this problem, we carefully explored the aspects of intelligent agent learning, performed by the Q-learning algorithm, to understand its suitability to be applied in scenarios whose characteristics are more similar to those faced by real genome projects. The improvements proposed here include changing the previously proposed reward system and including stat

关键词： Reinforcement learning

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A Secure and Fault-Tolerant Architecture for LoRaWAN Based on Blockchain

A Secure and Fault-Tolerant Architecture for LoRaWAN Based o...

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Cyber Security in Networking Conference (CSNet)

作者： Victor Ribeiro Raimir Holanda Filho Alex Ramos Graduate Program in Applied Informatics University of Fortaleza (UNIFOR) Fortaleza Brazil Computer Science Department Federal Institute of Ceará (IFCE) Fortaleza Brazil

ISBN: (数字)9781728139494

ISBN: (纸本)9781728139500

The Internet of Things (IoT) paradigm aims to bring continuous interaction between small embedded devices and humans. The IoT has the potential to affect our daily lives and bring many benefits to society. Low-Power Wide-Area Networks (LPWAN) is a new IoT technology that offers long distance connectivity for a massive number of devices. LPWAN is a promising solution to enable complex IoT scenarios, such as smart cities and smart healthcare. LoRa is currently one of the leading LPWAN solutions available for public use. Due to the great number of connected devices and, in some cases, sensitive data transmitted in IoT networks, security is one of the main concerns in LPWAN. In this paper, we focus on the issues of key management in LoRaWAN. We propose a secure architecture for key management based on private blockchain and smart contracts in order to increase the levels of security and availability in LoRaWAN environments. In order to show the feasibility of the proposed architecture, a working prototype was implemented using open-source tools and commodity hardware.

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