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Full-Text Articles in Computer Sciences

A Comparative Study On Out Of Scope Detection For Chest X-Ray Images, Nuttapol Kamolkunasiri Jan 2022

A Comparative Study On Out Of Scope Detection For Chest X-Ray Images, Nuttapol Kamolkunasiri

Chulalongkorn University Theses and Dissertations (Chula ETD)

Image classification models in actual applications may receive input outside the intended data distribution. For crucial applications such as clinical decision-making, it is critical that a model can recognize and describe such out-of-distribution (OOD) inputs. The objective of this study is to investigate the efficacy of several approaches for OOD identification in medical images. We examine three classes of OOD detection methods (Classification models, Confidence-based models, and Generative models) on the data of X-ray images. We found that simple classification methods and HealthyGAN perform the best overall. However, HealthyGAN cannot generalize to unseen scenarios, while classification models still retain some …

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Xgboost For Prediction Of Ethereum Short-Term Returns Based On Technical Factor, Wipawee Nayam Jan 2022

Xgboost For Prediction Of Ethereum Short-Term Returns Based On Technical Factor, Wipawee Nayam

Chulalongkorn University Theses and Dissertations (Chula ETD)

Unlike traditional currencies that rely on centralized such as banks or governments, cryptocurrencies today have become popular due to its decentralized transactions. Decentralization takes advantage of no requirement for intermediaries, thus reducing transaction fees and processing time. However, investing in cryptocurrencies incurs risks and uncertainties due to price volatility and rapid changes. The fact that prediction of asset prices is complex due to the influence of multiple factors on price movements. This paper studied the technical factor to analyze the short-term returns of Ethereum in the periods of 1-10 days. The historical data containing Ethereum closing price are collected from …

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Class-Level And Token-Level Approaches For Test Impact Analysis, Alon Basin Jan 2022

Class-Level And Token-Level Approaches For Test Impact Analysis, Alon Basin

Chulalongkorn University Theses and Dissertations (Chula ETD)

The objective of the thesis is to examine the efficacy of test impact analysis in a setting of continuous testing, where automated test cases are routinely run to guarantee the integration of high-quality codes. While continuous testing can enhance code quality and minimize maintenance workload, it also leads to a notable rise in overhead for test execution. In our study on test impact analysis, we developed a novel static class level technique that utilizes JavaParser to create a dependency graph between test cases and source code classes based on abstract syntax trees. We applied this technique to seven Java systems …

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Y-X-Y Encoding For Identifying Types Of Sentence Similarity, Thanaporn Jinnovart Jan 2022

Y-X-Y Encoding For Identifying Types Of Sentence Similarity, Thanaporn Jinnovart

Chulalongkorn University Theses and Dissertations (Chula ETD)

The task of finding semantic similarity of any two arbitrary sentences consists of two main steps, which are encoding sentences to produce feature vectors of equal length and measuring the similarity, respectively. The quality of an encoding technique can determine the degree of success a model can achieve in measuring the similarity. This is because a good representation is subjected to how finely established the spectrum of similarities is. The clearer the definition of similarity is, the better the representations can be constructed. This, in turn, helps distinguish between types of sentences. Generally, all existing methods for measuring similarity were …

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การสร้างคำถามไวยากรณ์ภาษาอังกฤษแบบปรนัยโดยใช้ทรานส์ฟอร์เมอร์ถ่ายทอดชนิดข้อความถึงข้อความ, พีรวัชน์ ชมภูยอด Jan 2022

การสร้างคำถามไวยากรณ์ภาษาอังกฤษแบบปรนัยโดยใช้ทรานส์ฟอร์เมอร์ถ่ายทอดชนิดข้อความถึงข้อความ, พีรวัชน์ ชมภูยอด

Chulalongkorn University Theses and Dissertations (Chula ETD)

คำถามปรนัยสำหรับทดสอบไวยากรณ์ภาษาอังกฤษสามารถสร้างแบบอัตโนมัติเพื่อลดระยะเวลาในการสร้างคำถาม ในอดีตงานวิจัยด้านนี้มุ่งเน้นไปที่การสร้างคำถามแบบกึ่งอัตโนมัติ โดยนำข้อความที่สร้างโดยมนุษย์มาแปลงให้เป็นคำถามปรนัย ส่งผลให้จำนวนคำถามที่สร้างได้ขึ้นอยู่กับจำนวนข้อความในคลังข้อมูลเท่านั้น วิทยานิพนธ์ฉบับนี้นำเสนอระบบสร้างคำถามปรนัยแบบอัตโนมัติที่นำเทคโนโลยีปัญญาประดิษฐ์มาประยุกต์ใช้ โดยนำปัญญาประดิษฐ์มาฝึกสอนให้สามารถสร้างข้อความอัตโนมัติแบบควบคุมคุณสมบัติของข้อความได้ แบบจำลองการเรียนรู้ของเครื่องที่นำมาฝึกในงานวิจัยนี้คือแบบจำลองทรานส์ฟอร์มเมอร์ชนิดข้อความถึงข้อความหรือทีไฟว์ ซึ่งเป็นแบบจำลองที่มีประสิทธิภาพในการสร้างข้อความอัตโนมัติ คุณลักษณะที่ใช้ฝึกแบบจำลองได้แก่ คำสำคัญ และแม่แบบ เพื่อควบคุมเนื้อหาและชนิดคำของข้อความที่สร้างขึ้น นอกจากการสร้างข้อความอัตโนมัติ วิทยานิพนธ์ฉบับนี้ได้เสนอกลวิธีแบบกฎเพื่อแปลงข้อความให้เป็นคำถามปรนัยสำหรับ 10 หัวข้อไวยากรณ์ ผลการทดลองของงานวิจัยนี้ชี้ให้เห็นว่าเมื่อนำคำถามที่สร้างขี้น มาประเมินผลด้วยผู้เชี่ยวชาญด้านภาษาอังกฤษแล้ว มีการยอมรับได้อยู่ที่ร้อยละ 86 ถึงแม้ว่าคำถามที่ถูกสร้างขึ้นทั้งหมดไม่สามารถนำไปทดสอบนักเรียนได้โดยตรง แต่ระบบสร้างคำถามอัตโนมัตินี้สามารถช่วยสนับสนุนคุณครูให้จัดเตรียมข้อสอบได้รวดเร็วขึ้น

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Hashtag Recommendation Based On Neural Topic Model, Thunchanok Tangpong Jan 2022

Hashtag Recommendation Based On Neural Topic Model, Thunchanok Tangpong

Chulalongkorn University Theses and Dissertations (Chula ETD)

Hashtag recommendation is a method that aims to recommend the relevant hashtag to the target microblog. The previous work applies a topic model for discovering the topic of users, words, and hashtags. Despite their progress, two problems remain unresolved. Firstly, the previous work infers topic distribution by using a non-neural network framework which is a non-linear function, limiting the model's ability to capture topic distribution complexly. Secondly, the representation of words and hashtags used in the prior model is merely the frequency of words, making the model to ignore not only word context but also the relation between word and …

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High Performance Data Acquisition And Analysis Routines For The Nab Experiment, David Mathews Jan 2022

High Performance Data Acquisition And Analysis Routines For The Nab Experiment, David Mathews

Theses and Dissertations--Physics and Astronomy

Probes of the Standard Model of particle physics are pushing further and further into the so-called “precision frontier”. In order to reach the precision goals of these experiments, a combination of elegant experimental design and robust data acquisition and analysis is required. Two experiments that embody this philosophy are the Nab and Calcium-45 experiments. These experiments are probing the understanding of the weak interaction by examining the beta decay of the free neutron and Calcium-45 respectively. They both aim to measure correlation parameters in the neutron beta decay alphabet, a and b. The parameter a, the electron-neutrino correlation coefficient, is …

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Partnering For Value Perfection And Business Sustainability In The Cloud Services Brokerage Market, Richard Shang, Robert John Kauffman Jan 2022

Partnering For Value Perfection And Business Sustainability In The Cloud Services Brokerage Market, Richard Shang, Robert John Kauffman

Research Collection School Of Computing and Information Systems

The cloud computing and services market has advanced in the past ten years. They now include most IT services from fundamental computing to cutting-edge AI capabilities. With the widespread adoption of cloud services, clients are facing the fact that they are utilizing cloud resources at a sub-optimal level. Cloud services brokers (CSBs) grew from the market to fill the needs for cloud resource management and risk mitigation. Based on analysis of the cloud market and the case of cloud services brokerage and related activities in North America, we offer theoretical analysis for how value creation works, its impacts on the …

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Steps Before Syntax: Helping Novice Programmers Solve Problems Using The Pcdit Framework, Oka Kurniawan, Cyrille Jegourel, Norman Tiong Seng Lee, Matthieu De Mari, Christopher M. Poskitt Jan 2022

Steps Before Syntax: Helping Novice Programmers Solve Problems Using The Pcdit Framework, Oka Kurniawan, Cyrille Jegourel, Norman Tiong Seng Lee, Matthieu De Mari, Christopher M. Poskitt

Research Collection School Of Computing and Information Systems

Novice programmers often struggle with problem solving due to the high cognitive loads they face. Furthermore, many introductory programming courses do not explicitly teach it, assuming that problem solving skills are acquired along the way. In this paper, we present 'PCDIT', a non-linear problem solving framework that provides scaffolding to guide novice programmers through the process of transforming a problem specification into an implemented and tested solution for an imperative programming language. A key distinction of PCDIT is its focus on developing concrete cases for the problem early without actually writing test code: students are instead encouraged to think about …

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On Discovering Motifs And Frequent Patterns In Spatial Trajectories With Discrete Fréchet Distance, Bo Tang, Man Lung Yiu, Kyriakos Mouratidis, Jiahao Zhang, Kai Wang Jan 2022

On Discovering Motifs And Frequent Patterns In Spatial Trajectories With Discrete Fréchet Distance, Bo Tang, Man Lung Yiu, Kyriakos Mouratidis, Jiahao Zhang, Kai Wang

Research Collection School Of Computing and Information Systems

The discrete Fréchet distance (DFD) captures perceptual and geographical similarity between two trajectories. It has been successfully adopted in a multitude of applications, such as signature and handwriting recognition, computer graphics, as well as geographic applications. Spatial applications, e.g., sports analysis, traffic analysis, etc. require discovering similar subtrajectories within a single trajectory or across multiple trajectories. In this paper, we adopt DFD as the similarity measure, and study two representative trajectory analysis problems, namely, motif discovery and frequent pattern discovery. Due to the time complexity of DFD, these tasks are computationally challenging. We address that challenge with a suite of …

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Accessibility In Software Practice: A Practitioner's Perspective, Tingting Bi, Xin Xia, David Lo, John C. Grundy, Thomas Zimmermann, Denae Ford Jan 2022

Accessibility In Software Practice: A Practitioner's Perspective, Tingting Bi, Xin Xia, David Lo, John C. Grundy, Thomas Zimmermann, Denae Ford

Research Collection School Of Computing and Information Systems

Being able to access software in daily life is vital for everyone, and thus accessibility is a fundamental challenge for software development. However, given the number of accessibility issues reported by many users, e.g., in app reviews, it is not clear if accessibility is widely integrated into current software projects and how software projects address accessibility issues. In this article, we report a study of the critical challenges and benefits of incorporating accessibility into software development and design. We applied a mixed qualitative and quantitative approach for gathering data from 15 interviews and 365 survey respondents from 26 countries across …

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Temporal Disambiguation Of Relative Temporal Expressions In Clinical Texts Using Temporally Fine-Tuned Contextual Word Embeddings., Amy L. Olex Jan 2022

Temporal Disambiguation Of Relative Temporal Expressions In Clinical Texts Using Temporally Fine-Tuned Contextual Word Embeddings., Amy L. Olex

Theses and Dissertations

Temporal reasoning is the ability to extract and assimilate temporal information to reconstruct a series of events such that they can be reasoned over to answer questions involving time. Temporal reasoning in the clinical domain is challenging due to specialized medical terms and nomenclature, shorthand notation, fragmented text, a variety of writing styles used by different medical units, redundancy of information that has to be reconciled, and an increased number of temporal references as compared to general domain texts. Work in the area of clinical temporal reasoning has progressed, but the current state-of-the-art still has a ways to go before …

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Learning Robot Motion From Creative Human Demonstration, Charles C. Dietzel Jan 2022

Learning Robot Motion From Creative Human Demonstration, Charles C. Dietzel

Theses and Dissertations

This thesis presents a learning from demonstration framework that enables a robot to learn and perform creative motions from human demonstrations in real-time. In order to satisfy all of the functional requirements for the framework, the developed technique is comprised of two modular components, which integrate together to provide the desired functionality. The first component, called Dancing from Demonstration (DfD), is a kinesthetic learning from demonstration technique. This technique is capable of playing back newly learned motions in real-time, as well as combining multiple learned motions together in a configurable way, either to reduce trajectory error or to generate entirely …

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Smart City Management Using Machine Learning Techniques, Mostafa Zaman Jan 2022

Smart City Management Using Machine Learning Techniques, Mostafa Zaman

Theses and Dissertations

In response to the growing urban population, "smart cities" are designed to improve people's quality of life by implementing cutting-edge technologies. The concept of a "smart city" refers to an effort to enhance a city's residents' economic and environmental well-being via implementing a centralized management system. With the use of sensors and actuators, smart cities can collect massive amounts of data, which can improve people's quality of life and design cities' services. Although smart cities contain vast amounts of data, only a percentage is used due to the noise and variety of the data sources. Information and communication technology (ICT) …

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Computational Analysis Of Drug Targets And Prediction Of Protein-Compound Interactions, Sina Ghadermarzi Jan 2022

Computational Analysis Of Drug Targets And Prediction Of Protein-Compound Interactions, Sina Ghadermarzi

Theses and Dissertations

Computational prediction of compound-protein interactions generated a substantial amount of interest in the recent years owing to the importance of the knowledge of these interaction for drug discovery and drug repurposing efforts. Research suggests that the currently known drug targets constitute only a fraction of a complete set of drug targets, limiting our ability to identify suitable targets to develop new drugs or to repurpose current drugs for new diseases. These efforts are further thwarted by our limited knowledge of protein-drug (and more generally protein-compound) interactions, where only a subset of drug targets is typically known for the currently used …

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Eye Movement And Pupil Measures: A Review, Bhanuka Mahanama, Yasith Jayawardana, Sundararaman Rengarajan, Gavindya Jayawardena, Leanne Chukoskie, Joseph Snider, Sampath Jayarathna Jan 2022

Eye Movement And Pupil Measures: A Review, Bhanuka Mahanama, Yasith Jayawardana, Sundararaman Rengarajan, Gavindya Jayawardena, Leanne Chukoskie, Joseph Snider, Sampath Jayarathna

Computer Science Faculty Publications

Our subjective visual experiences involve complex interaction between our eyes, our brain, and the surrounding world. It gives us the sense of sight, color, stereopsis, distance, pattern recognition, motor coordination, and more. The increasing ubiquity of gaze-aware technology brings with it the ability to track gaze and pupil measures with varying degrees of fidelity. With this in mind, a review that considers the various gaze measures becomes increasingly relevant, especially considering our ability to make sense of these signals given different spatio-temporal sampling capacities. In this paper, we selectively review prior work on eye movements and pupil measures. We first …

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Streaminghub: Interactive Stream Analysis Workflows, Yasith Jayawardana, Vikas G. Ashok, Sampath Jayarathna Jan 2022

Streaminghub: Interactive Stream Analysis Workflows, Yasith Jayawardana, Vikas G. Ashok, Sampath Jayarathna

Computer Science Faculty Publications

Reusable data/code and reproducible analyses are foundational to quality research. This aspect, however, is often overlooked when designing interactive stream analysis workflows for time-series data (e.g., eye-tracking data). A mechanism to transmit informative metadata alongside data may allow such workflows to intelligently consume data, propagate metadata to downstream tasks, and thereby auto-generate reusable, reproducible analytic outputs with zero supervision. Moreover, a visual programming interface to design, develop, and execute such workflows may allow rapid prototyping for interdisciplinary research. Capitalizing on these ideas, we propose StreamingHub, a framework to build metadata propagating, interactive stream analysis workflows using visual programming. We conduct …

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M-Cubes: An Efficient And Portable Implementation Of Multi-Dimensional Integration For Gpus, Ioannis Sakiotis, Kamesh Arumugam, Marc Paterno, Desh Ranjan, Balŝa Terzić, Mohammad Zubair Jan 2022

M-Cubes: An Efficient And Portable Implementation Of Multi-Dimensional Integration For Gpus, Ioannis Sakiotis, Kamesh Arumugam, Marc Paterno, Desh Ranjan, Balŝa Terzić, Mohammad Zubair

Computer Science Faculty Publications

The task of multi-dimensional numerical integration is frequently encountered in physics and other scientific fields, e.g., in modeling the effects of systematic uncertainties in physical systems and in Bayesian parameter estimation. Multi-dimensional integration is often time-prohibitive on CPUs. Efficient implementation on many-core architectures is challenging as the workload across the integration space cannot be predicted a priori. We propose m-Cubes, a novel implementation of the well-known Vegas algorithm for execution on GPUs. Vegas transforms integration variables followed by calculation of a Monte Carlo integral estimate using adaptive partitioning of the resulting space. mCubes improves performance on GPUs by maintaining relatively …

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Introducing A Real-Time Advanced Eye Movements Analysis Pipeline, Gavindya Jayawardana Jan 2022

Introducing A Real-Time Advanced Eye Movements Analysis Pipeline, Gavindya Jayawardana

Computer Science Faculty Publications

Real-Time Advanced Eye Movements Analysis Pipeline (RAEMAP) is an advanced pipeline to analyze traditional positional gaze measurements as well as advanced eye gaze measurements. The proposed implementation of RAEMAP includes real-time analysis of fixations, saccades, gaze transition entropy, and low/high index of pupillary activity. RAEMAP will also provide visualizations of fixations, fixations on AOIs, heatmaps, and dynamic AOI generation in real-time. This paper outlines the proposed architecture of RAEMAP.

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Camouflaged Poisoning Attack On Graph Neural Networks, Chao Jiang, Yi He, Richard Chapman, Hongyi Wu Jan 2022

Camouflaged Poisoning Attack On Graph Neural Networks, Chao Jiang, Yi He, Richard Chapman, Hongyi Wu

Computer Science Faculty Publications

Graph neural networks (GNNs) have enabled the automation of many web applications that entail node classification on graphs, such as scam detection in social media and event prediction in service networks. Nevertheless, recent studies revealed that the GNNs are vulnerable to adversarial attacks, where feeding GNNs with poisoned data at training time can lead them to yield catastrophically devastative test accuracy. This finding heats up the frontier of attacks and defenses against GNNs. However, the prior studies mainly posit that the adversaries can enjoy free access to manipulate the original graph, while obtaining such access could be too costly in …

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Completing Single-Cell Dna Methylome Profiles Via Transfer Learning Together With Kl-Divergence, Sanjeeva Dodlapati, Zongliang Jiang, Jiangwen Sun Jan 2022

Completing Single-Cell Dna Methylome Profiles Via Transfer Learning Together With Kl-Divergence, Sanjeeva Dodlapati, Zongliang Jiang, Jiangwen Sun

Computer Science Faculty Publications

The high level of sparsity in methylome profiles obtained using whole-genome bisulfite sequencing in the case of low biological material amount limits its value in the study of systems in which large samples are difficult to assemble, such as mammalian preimplantation embryonic development. The recently developed computational methods for addressing the sparsity by imputing missing have their limits when the required minimum data coverage or profiles of the same tissue in other modalities are not available. In this study, we explored the use of transfer learning together with Kullback-Leibler (KL) divergence to train predictive models for completing methylome profiles with …

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Visual Descriptor Extraction From Patent Figure Captions: A Case Study Of Data Efficiency Between Bilstm And Transformer, Xin Wei, Jian Wu, Kehinde Ajayi, Diane Oyen Jan 2022

Visual Descriptor Extraction From Patent Figure Captions: A Case Study Of Data Efficiency Between Bilstm And Transformer, Xin Wei, Jian Wu, Kehinde Ajayi, Diane Oyen

Computer Science Faculty Publications

Technical drawings used for illustrating designs are ubiquitous in patent documents, especially design patents. Different from natural images, these drawings are usually made using black strokes with little color information, making it challenging for models trained on natural images to recognize objects. To facilitate indexing and searching, we propose an effective and efficient visual descriptor model that extracts object names and aspects from patent captions to annotate benchmark patent figure datasets. We compared two state-of-the-art named entity recognition (NER) models and found that with a limited number of annotated samples, the BiLSTM-CRF model outperforms the Transformer model by a significant …

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Multi-User Eye-Tracking, Bhanuka Mahanama Jan 2022

Multi-User Eye-Tracking, Bhanuka Mahanama

Computer Science Faculty Publications

The human gaze characteristics provide informative cues on human behavior during various activities. Using traditional eye trackers, assessing gaze characteristics in the wild requires a dedicated device per participant and therefore is not feasible for large-scale experiments. In this study, we propose a commodity hardware-based multi-user eye-tracking system. We leverage the recent advancements in Deep Neural Networks and large-scale datasets for implementing our system. Our preliminary studies provide promising results for multi-user eye-tracking on commodity hardware, providing a cost-effective solution for large-scale studies.

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Segmenting Technical Drawing Figures In Us Patents, Md Reshad Ul Hoque, Xin Wei, Muntabir Hasan Choudhury, Kehinde Ajayi, Martin Gryder, Jian Wu, Diane Oyen Jan 2022

Segmenting Technical Drawing Figures In Us Patents, Md Reshad Ul Hoque, Xin Wei, Muntabir Hasan Choudhury, Kehinde Ajayi, Martin Gryder, Jian Wu, Diane Oyen

Computer Science Faculty Publications

Image segmentation is the core computer vision problem for identifying objects within a scene. Segmentation is a challenging task because the prediction for each pixel label requires contextual information. Most recent research deals with the segmentation of natural images rather than drawings. However, there is very little research on sketched image segmentation. In this study, we introduce heuristic (point-shooting) and deep learning-based methods (U-Net, HR-Net, MedT, DETR) to segment technical drawings in US patent documents. Our proposed methods on the US Patent dataset achieved over 90% accuracy where transformer performs well with 97% segmentation accuracy, which is promising and computationally …

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D-Lib Magazine Pioneered Web-Based Scholarly Communication, Michael L. Nelson, Herbert Van De Sompel Jan 2022

D-Lib Magazine Pioneered Web-Based Scholarly Communication, Michael L. Nelson, Herbert Van De Sompel

Computer Science Faculty Publications

The web began with a vision of, as stated by Tim Berners-Lee in 1991, “that much academic information should be freely available to anyone”. For many years, the development of the web and the development of digital libraries and other scholarly communications infrastructure proceeded in tandem. A milestone occurred in July, 1995, when the first issue of D-Lib Magazine was published as an online, HTML-only, open access magazine, serving as the focal point for the then emerging digital library research community. In 2017 it ceased publication, in part due to the maturity of the community it served as well as …

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Customer Gaze Estimation In Retail Using Deep Learning, Shashimal Senarath, Primesh Pathirana, Dulani Meedeniya, Sampath Jayarathna Jan 2022

Customer Gaze Estimation In Retail Using Deep Learning, Shashimal Senarath, Primesh Pathirana, Dulani Meedeniya, Sampath Jayarathna

Computer Science Faculty Publications

At present, intelligent computing applications are widely used in different domains, including retail stores. The analysis of customer behaviour has become crucial for the benefit of both customers and retailers. In this regard, the concept of remote gaze estimation using deep learning has shown promising results in analyzing customer behaviour in retail due to its scalability, robustness, low cost, and uninterrupted nature. This study presents a three-stage, three-attention-based deep convolutional neural network for remote gaze estimation in retail using image data. In the first stage, we design a mechanism to estimate the 3D gaze of the subject using image data …

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Spaghetti Tracer: A Framework For Tracing Semiregular Filamentous Densities In 3d Tomograms, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers Jan 2022

Spaghetti Tracer: A Framework For Tracing Semiregular Filamentous Densities In 3d Tomograms, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between—or specific shape on—individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D …

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Loss Of Acta2 In Cardiac Fibroblasts Does Not Prevent The Myofibroblast Differentiation Or Affect The Cardiac Repair After Myocardial Infarction, Yuxia Li, Chaoyang Li, Qianglin Liu, Leshan Wang, Adam X. Bao, Jangwook P. Jung, Sanjeev Dodlapati, Jingwen Sun, Peidong Gao, Xujia Zhang, Joseph Francis, Jeffery D. Molkentin, Xing Fu Jan 2022

Loss Of Acta2 In Cardiac Fibroblasts Does Not Prevent The Myofibroblast Differentiation Or Affect The Cardiac Repair After Myocardial Infarction, Yuxia Li, Chaoyang Li, Qianglin Liu, Leshan Wang, Adam X. Bao, Jangwook P. Jung, Sanjeev Dodlapati, Jingwen Sun, Peidong Gao, Xujia Zhang, Joseph Francis, Jeffery D. Molkentin, Xing Fu

Computer Science Faculty Publications

In response to myocardial infarction (MI), quiescent cardiac fibroblasts differentiate into myofibroblasts mediating tissue repair. One of the most widely accepted markers of myofibroblast differentiation is the expression of Acta2 which encodes smooth muscle alpha-actin (SMαA) that is assembled into stress fibers. However, the requirement of Acta2/SMαA in the myofibroblast differentiation of cardiac fibroblasts and its role in post-MI cardiac repair remained unknown. To answer these questions, we generated a tamoxifen-inducible cardiac fibroblast-specific Acta2 knockout mouse line. Surprisingly, mice that lacked Acta2 in cardiac fibroblasts had a normal post-MI survival rate. Moreover, Acta2 deletion did …

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Machine Learning-Based Event Generator For Electron-Proton Scattering, Y. Alanazi, P. Ambrozewicz, M. Battaglieri, A.N. Hiller Blin, M. P. Kuchera, Y. Li, T. Liu, R. E. Mcclellan, W. Melnitchouk, E. Pritchard, M. Robertson, N. Sato, R. Strauss, L. Velasco Jan 2022

Machine Learning-Based Event Generator For Electron-Proton Scattering, Y. Alanazi, P. Ambrozewicz, M. Battaglieri, A.N. Hiller Blin, M. P. Kuchera, Y. Li, T. Liu, R. E. Mcclellan, W. Melnitchouk, E. Pritchard, M. Robertson, N. Sato, R. Strauss, L. Velasco

Computer Science Faculty Publications

We present a new machine learning-based Monte Carlo event generator using generative adversarial networks (GANs) that can be trained with calibrated detector simulations to construct a vertex-level event generator free of theoretical assumptions about femtometer scale physics. Our framework includes a GAN-based detector folding as a fast-surrogate model that mimics detector simulators. The framework is tested and validated on simulated inclusive deep-inelastic scattering data along with existing parametrizations for detector simulation, with uncertainty quantification based on a statistical bootstrapping technique. Our results provide for the first time a realistic proof of concept to mitigate theory bias in inferring vertex-level event …

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Refinement Of Alphafold2 Models Against Experimental And Hybrid Cryo-Em Density Maps, Maytha Alshammari, Willy Wriggers, Jiangwen Sun, Jing He Jan 2022

Refinement Of Alphafold2 Models Against Experimental And Hybrid Cryo-Em Density Maps, Maytha Alshammari, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Recent breakthroughs in deep learning-based protein structure prediction show that it is possible to obtain highly accurate models for a wide range of difficult protein targets for which only the amino acid sequence is known. The availability of accurately predicted models from sequences can potentially revolutionise many modelling approaches in structural biology, including the interpretation of cryo-EM density maps. Although atomic structures can be readily solved from cryo-EM maps of better than 4 Å resolution, it is still challenging to determine accurate models from lower-resolution density maps. Here, we report on the benefits of models predicted by AlphaFold2 (the best-performing …

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