4,914 research outputs found
Knowledge Extraction from Textual Resources through Semantic Web Tools and Advanced Machine Learning Algorithms for Applications in Various Domains
Nowadays there is a tremendous amount of unstructured data, often represented by texts, which is created and stored in variety of forms in many domains such as patients' health records, social networks comments, scientific publications, and so on. This volume of data represents an invaluable source of knowledge, but unfortunately it is challenging its mining for machines. At the same time, novel tools as well as advanced methodologies have been introduced in several domains, improving the efficacy and the efficiency of data-based services.
Following this trend, this thesis shows how to parse data from text with Semantic Web based tools, feed data into Machine Learning methodologies, and produce services or resources to facilitate the execution of some tasks. More precisely, the use of Semantic Web technologies powered by Machine Learning algorithms has been investigated in the Healthcare and E-Learning domains through not yet experimented methodologies. Furthermore, this thesis investigates the use of some state-of-the-art tools to move data from texts to graphs for representing the knowledge contained in scientific literature. Finally, the use of a Semantic Web ontology and novel heuristics to detect insights from biological data in form of graph are presented. The thesis contributes to the scientific literature in terms of results and resources. Most of the material presented in this thesis derives from research papers published in international journals or conference proceedings
DeepHTLV: a Deep Learning Framework for Detecting Human T-Lymphotrophic Virus 1 Integration Sites
In the 1980s, researchers found the first human oncogenic retrovirus called human T-lymphotrophic virus type 1 (HTLV-1). Since then, HTLV-1 has been identified as the causative agent behind several diseases such as adult T-cell leukemia/lymphoma (ATL) and a HTLV-1 associated myelopathy or tropical spastic paraparesis (HAM/TSP). As part of its normal replication cycle, the genome is converted into DNA and integrated into the genome. With several hundreds to thousands of unique viral integration sites (VISs) distributed with indeterminate preference throughout the genome, detection of HTLV-1 VISs is a challenging task. Experimental studies typically use molecular biology techniques such as fluorescent in-situ hybridization (FISH) or using rt-qPCR (reverse transcriptase quantitative PCR) to detect VISs. While these methods are accurate, they cannot be applied in a high throughput manner. Next generation sequencing (NGS) has generated vast amounts of data, resulting in the development of several computational methods for VIS detection such as VERSE, VirusFinder, or DeepVISP for the task of rapid detection VIS across an entire genome. However, no such model exists for predicting HTLV-1 VISs. In this study, we have developed DeepHTLV: the first deep neural network for accurate detection of HTLV-1 insertion sites. We focused on 1) accurately predicting HTLV-1 VISs by extracting and generating superior feature representations and 2) uncovering the cis-regulatory features surrounding the insertion sites. DeepHTLV was implemented as a deep convolutional neural network (CNN) with self-attention architecture after comparing with several other deep neural network structures. To improve model accuracy, we trained the model using a bootstrap balanced sampling method with 10-fold CV. Furthermore, we demonstrated that this model has higher accuracy than several traditional machine learning models, with a modest improvement in area under the curve (AUC) values by 3-10%. To study the cis-regulatory features around HTLV-1 insertion sites, we extracted informative motifs from convolutional layer. Clustering of these motifs yielded eight unique consensus sequence motifs that represented potential integration sites in humans. The informative motif sequences were matched with a known transcription factor (TF) binding profile database, JASPAR2020, with the sequence matching tool TOMTOM. 79 TFs associations were enriched in regions surrounding HTLV-1 VISs. Furthermore, literature screening of HTLV-1, ATL, and HAM/TSP validated nearly half (34) of the predicted TFs interactions. This work demonstrates that DeepHTLV can accurately identify HTLV-1 VISs, elucidate surrounding features regulating these insertion sites, and make biologically meaningful predictions about cis-regulatory elements surrounding the insertion sites
Choreographic and Somatic Approaches for the Development of Expressive Robotic Systems
As robotic systems are moved out of factory work cells into human-facing
environments questions of choreography become central to their design,
placement, and application. With a human viewer or counterpart present, a
system will automatically be interpreted within context, style of movement, and
form factor by human beings as animate elements of their environment. The
interpretation by this human counterpart is critical to the success of the
system's integration: knobs on the system need to make sense to a human
counterpart; an artificial agent should have a way of notifying a human
counterpart of a change in system state, possibly through motion profiles; and
the motion of a human counterpart may have important contextual clues for task
completion. Thus, professional choreographers, dance practitioners, and
movement analysts are critical to research in robotics. They have design
methods for movement that align with human audience perception, can identify
simplified features of movement for human-robot interaction goals, and have
detailed knowledge of the capacity of human movement. This article provides
approaches employed by one research lab, specific impacts on technical and
artistic projects within, and principles that may guide future such work. The
background section reports on choreography, somatic perspectives,
improvisation, the Laban/Bartenieff Movement System, and robotics. From this
context methods including embodied exercises, writing prompts, and community
building activities have been developed to facilitate interdisciplinary
research. The results of this work is presented as an overview of a smattering
of projects in areas like high-level motion planning, software development for
rapid prototyping of movement, artistic output, and user studies that help
understand how people interpret movement. Finally, guiding principles for other
groups to adopt are posited.Comment: Under review at MDPI Arts Special Issue "The Machine as Artist (for
the 21st Century)"
http://www.mdpi.com/journal/arts/special_issues/Machine_Artis
Digital Pathology: The Time Is Now to Bridge the Gap between Medicine and Technological Singularity
Digitalization of the imaging in radiology is a reality in several healthcare institutions worldwide. The challenges of filing, confidentiality, and manipulation have been brilliantly solved in radiology. However, digitalization of hematoxylin- and eosin-stained routine histological slides has shown slow movement. Although the application for external quality assurance is a reality for a pathologist with most of the continuing medical education programs utilizing virtual microscopy, the abandonment of traditional glass slides for routine diagnostics is far from the perspectives of many departments of laboratory medicine and pathology. Digital pathology images are captured as images by scanning and whole slide imaging/virtual microscopy can be obtained by microscopy (robotic) on an entire histological (microscopic) glass slide. Since 1986, services using telepathology for the transfer of images of anatomic pathology between detached locations have benefited countless patients globally, including the University of Alberta. The purpose of specialist recertification or re-validation for the Royal College of Pathologists of Canada belonging to the Royal College of Physicians and Surgeons of Canada and College of American Pathologists is a milestone in virtual reality. Challenges, such as high bandwidth requirement, electronic platforms, the stability of the operating systems, have been targeted and are improving enormously. The encryption of digital images may be a requirement for the accreditation of laboratory services—quantum computing results in quantum-mechanical phenomena, such as superposition and entanglement. Different from binary digital electronic computers based on transistors where data are encoded into binary digits (bits) with two different states (0 and 1), quantum computing uses quantum bits (qubits), which can be in superpositions of states. The use of quantum computing protocols on encrypted data is crucial for the permanent implementation of virtual pathology in hospitals and universities. Quantum computing may well represent the technological singularity to create new classifications and taxonomic rules in medicine
Engineering Advantage, Fall 2013
https://digitalcommons.calpoly.edu/ceng_news/1015/thumbnail.jp
Current Studies and Applications of Krill Herd and Gravitational Search Algorithms in Healthcare
Nature-Inspired Computing or NIC for short is a relatively young field that
tries to discover fresh methods of computing by researching how natural
phenomena function to find solutions to complicated issues in many contexts. As
a consequence of this, ground-breaking research has been conducted in a variety
of domains, including synthetic immune functions, neural networks, the
intelligence of swarm, as well as computing of evolutionary. In the domains of
biology, physics, engineering, economics, and management, NIC techniques are
used. In real-world classification, optimization, forecasting, and clustering,
as well as engineering and science issues, meta-heuristics algorithms are
successful, efficient, and resilient. There are two active NIC patterns: the
gravitational search algorithm and the Krill herd algorithm. The study on using
the Krill Herd Algorithm (KH) and the Gravitational Search Algorithm (GSA) in
medicine and healthcare is given a worldwide and historical review in this
publication. Comprehensive surveys have been conducted on some other
nature-inspired algorithms, including KH and GSA. The various versions of the
KH and GSA algorithms and their applications in healthcare are thoroughly
reviewed in the present article. Nonetheless, no survey research on KH and GSA
in the healthcare field has been undertaken. As a result, this work conducts a
thorough review of KH and GSA to assist researchers in using them in diverse
domains or hybridizing them with other popular algorithms. It also provides an
in-depth examination of the KH and GSA in terms of application, modification,
and hybridization. It is important to note that the goal of the study is to
offer a viewpoint on GSA with KH, particularly for academics interested in
investigating the capabilities and performance of the algorithm in the
healthcare and medical domains.Comment: 35 page
Odontology & artificial intelligence
Neste trabalho avaliam-se os três fatores que fizeram da inteligência artificial uma tecnologia essencial hoje em dia, nomeadamente para a odontologia: o desempenho do computador, Big Data e avanços algorítmicos. Esta revisão da literatura avaliou todos os artigos publicados na PubMed até Abril de 2019 sobre inteligência artificial e odontologia. Ajudado com inteligência artificial, este artigo analisou 1511 artigos. Uma árvore de decisão (If/Then) foi executada para selecionar os artigos mais relevantes (217), e um algoritmo de cluster k-means para resumir e identificar oportunidades de inovação. O autor discute os artigos mais interessantes revistos e compara o que foi feito em inovação durante o International Dentistry Show, 2019 em Colónia. Concluiu, assim, de forma crítica que há uma lacuna entre tecnologia e aplicação clínica desta, sendo que a inteligência artificial fornecida pela indústria de hoje pode ser considerada um atraso para o clínico de amanhã, indicando-se um possível rumo para a aplicação clínica da inteligência artificial.There are three factors that have made artificial intelligence (AI) an essential technology today: the computer performance, Big Data and algorithmic advances. This study reviews the literature on AI and Odontology based on articles retrieved from PubMed. With the help of AI, this article analyses a large number of articles (a total of 1511). A decision tree (If/Then) was run to select the 217 most relevant articles-. Ak-means cluster algorithm was then used to summarize and identify innovation opportunities. The author discusses the most interesting articles on AI research and compares them to the innovation presented during the International Dentistry Show 2019 in Cologne. Three technologies available now are evaluated and three suggested options are been developed. The author concludes that AI provided by the industry today is a hold-up for the praticioner of tomorrow. The author gives his opinion on how to use AI for the profit of patients
- …