Search results for: semantic web annotation

Authors: Fateh Adhnouss, Husam El-Asfour, Kenneth McIsaac, AbdulMutalib Wahaishi, Idris El-Feghia

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Conceptualization is an essential component of semantic ontology-based approaches. There have been several approaches that rely on extensional structure and extensional reduction structure in order to construct conceptualization. In this paper, several limitations are highlighted relating to their applicability to the construction of conceptualizations in dynamic and open environments. These limitations arise from a number of strong assumptions that do not apply to such environments. An intensional structure is strongly argued to be a natural and adequate modeling approach. This paper presents a conceptualization structure based on property relations and propositions theory (PRP) to the model ontology that is suitable for open environments. The model extends the First-Order Logic (FOL) notation and defines the formal representation that enables interoperability between software systems and supports semantic integration for software systems in open, dynamic environments.

Keywords: conceptualization, ontology, extensional structure, intensional structure

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Authors: Chen Wang, Chun Liang

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Microsatellite instability (MSI) is characterized by high degree of polymorphism in microsatellite (MS) length due to a deficiency in mismatch repair (MMR) system. MSI is associated with several tumor types and its status can be considered as an important indicator for tumor prognostic. Conventional clinical diagnosis of MSI examines PCR products of a panel of MS markers using electrophoresis (MSI-PCR) which is laborious, time consuming, and less reliable. MSIpred, a python 2 package for automatic classification of MSI was released by this study. It computes important somatic mutation features from files in mutation annotation format (MAF) generated from paired tumor-normal exome sequencing data, subsequently using these to predict tumor MSI status with a support vector machine (SVM) classifier trained by MAF files of 1074 tumors belonging to four types. Evaluation of MSIpred on an independent 358-tumor test set achieved overall accuracy of over 98% and area under receiver operating characteristic (ROC) curve of 0.967. These results indicated that MSIpred is a robust pan-cancer MSI classification tool and can serve as a complementary diagnostic to MSI-PCR in MSI diagnosis.

Keywords: microsatellite instability, pan-cancer classification, somatic mutation, support vector machine

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Authors: Simiao Ren, En Wei

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Drowning is a significant safety issue worldwide, and a robust computer vision-based alert system can easily prevent such tragedies in swimming pools. However, due to domain shift caused by the visual gap (potentially due to lighting, indoor scene change, pool floor color etc.) between the training swimming pool and the test swimming pool, the robustness of such algorithms has been questionable. The annotation cost for labeling each new swimming pool is too expensive for mass adoption of such a technique. To address this issue, we propose a domain-aware data augmentation pipeline based on Gaussian Poisson Generative Adversarial Network (GP-GAN). Combined with YOLOv8, we demonstrate that such a domain adaptation technique can significantly improve the model performance (from 0.24 mAP to 0.82 mAP) on new test scenes. As the augmentation method only require background imagery from the new domain (no annotation needed), we believe this is a promising, practical route for preventing swimming pool drowning.

Keywords: computer vision, deep learning, YOLOv8, detection, swimming pool, drowning, domain adaptation, generative adversarial network, GAN, GP-GAN

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Authors: Narmina Mammadova

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In modern linguistics, the comparative study of languages is becoming increasingly popular, the typology and comparison of languages that have different structures is expanding and deepening. Of particular interest is the study of phraseological units, which makes it possible to identify the specific features of the compared languages in all their national identity. This paper gives a brief analysis of the comparative study of somatic phraseological units (SFU) of the Spanish and Turkish languages with the component "hand" in the semantic aspect; identification of equivalents, analogs and non-equivalent units, as well as a description of methods of translation of non-equivalent somatic phraseological units. Comparative study of the phraseology of unrelated languages is of particular relevance since it allows us to identify both general, universal features and differential and specific features characteristic of a particular language. Based on the results of the generalization of the study, it can be assumed that phraseological units containing a somatic component have a high interlingual phraseological activity, which contributes to an increase in the degree of interlingual equivalence.

Keywords: Linguoculturology, Turkish, Spanish, language picture of the world, phraseological units, semantic microfield

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Authors: Qiong Hu, Ming Yue

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Language variation signals the newest usage of language community, which might become the developmental trend of that language. However, language textbooks cannot keep up with these emergent usages. Most Chinese English learners nowadays are still exposed to traditional grammar prescribed in the textbook so that some variational usages cannot be acquired. The personal pronoun we is prescribed as a plural pronoun in the textbook grammar, but its number value is more flexible in actual use. Based on the Chinese Learner English Corpus (CLEC), and with the homemade Friends corpus as reference, the present research explores the number value of the first person pronoun we used by Chinese English learners. With consideration of the subjectivity of we, this paper annotated the number value of all the wes in “we+ PCU (Perception-cognation-utterance) verbs” collocations. Results show that though exposed to traditional textbooks which prescribe the plural reference of we, there still exists some unconventional usage (singular or vague in reference) in the writings of Chinese English learners, which is less frequent than that of the native speeches. Corpus data and results from manual semantic annotation show that this could be due to the impact of formulaic sequence on the learners and the positive transfer from their native language. An improved SLA model of native language, target language and interlanguage is put forward to recognize the existence of variation in second language acquisition, which should be given more attention during teaching.

Keywords: Chinese English learners, number, PCU verbs, Personal pronoun we

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Authors: Lucia Rottava

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The present study focuses on academic literacy and addresses the impact of semantic-discursive resources on the constitution of genres that are produced in such context. The research considers the development of writing in the academic context in Portuguese. Researches that address academic literacy and the characteristics of the texts produced in this context are rare, mainly with focus on the development of writing, considering three variables: the constitution of the writer, the perception of the reader/interlocutor and the organization of the informational text flow. The research aims to map the semantic-discursive resources of the written register in texts of several genres and produced by students in the first semester of the undergraduate course in letters. The hypothesis raised is that writing in the academic environment is not a recurrent literacy practice for these learners and can be explained by the ontogenetic and phylogenetic nature of language development. Qualitative in nature, the present research has as empirical data texts produced in a half-yearly course of Reading and Textual Production; these data result from the proposition of four different writing proposals, in a total of 600 texts. The corpus is analyzed based on semantic-discursive resources, seeking to contemplate relevant aspects of language (grammar, discourse and social context) that reveal the choices made in the reader/writer interrelationship and the organizational flow of the text. Among the semantic-discursive resources, the analysis includes three resources, including (a) appraisal and negotiation to understand the attitudes negotiated (roles of the participants of the discourse and their relationship with the other); (b) ideation to explain the construction of the experience (activities performed and participants); and (c) periodicity to outline the flow of information in the organization of the text according to the genre it instantiates. The results indicate the organizational difficulties of the flow of the text information. Cartography contributes to the understanding of the way writers use language in an effort to present themselves, evaluate someone else’s work, and communicate with readers.

Keywords: academic writing, portuguese mother tongue, semantic-discursive resources, sistemic funcional linguistic

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Authors: Linda Smail, Zineb Azouz

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Given a Bayesian network relative to a set I of discrete random variables, we are interested in computing the probability distribution P(S) where S is a subset of I. The general idea is to write the expression of P(S) in the form of a product of factors where each factor is easy to compute. More importantly, it will be very useful to give an interpretation of each of the factors in terms of conditional probabilities. This paper considers a semantic interpretation of the factors involved in computing marginal probabilities in Bayesian networks. Establishing such a semantic interpretations is indeed interesting and relevant in the case of large Bayesian networks.

Keywords: Bayesian networks, D-Separation, level two Bayesian networks, factorization of computation

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Authors: Mesnan Silalahi, Dana Indra Sensuse, Indra Budi

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Many research have revealed the fact of the complexity of ontology building process that there is a need to have a new approach which addresses the socio-technical aspects in the collaboration to reach a consensus. Meta-design approach is considered applicable as a method in the methodological model in a socio-technical ontology engineering. Principles in the meta-design framework is applied in the construction phases on the ontology. A portal is developed to support the meta-design principles requirements. To validate the methodological model semantic web applications were developed and integrated in the portal and also used as a way to show the usefulness of the ontology. The knowledge based system will be filled with data of Indonesian medicinal plants. By showing the usefulness of the developed ontology in a web semantic application, we motivate all stakeholders to participate in the development of knowledge based system of medicinal plants in Indonesia.

Keywords: socio-technical, metadesign, ontology engineering methodology, semantic web application

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Authors: M. A. T. AlSudairi, T. G. K. Vasista

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The concept of social media is becoming the top of the agenda for many business executives and public sector executives today. Decision makers as well as consultants, try to identify ways in which firms and enterprises can make profitable use of social media and network related applications such as Wikipedia, Face book, YouTube, Google+, Twitter. While it is fun and useful to participating in this media and network for achieving the communication effectively and efficiently, semantic and sentiment analysis and interpretation becomes a crucial issue. So, the objective of this paper is to provide literature review on social media, network and related technology related to semantics and sentiment or opinion analysis covering business and governance perspectives. In this regard, a case study on the use and adoption of Social media in Saudi Arabia has been discussed. It is concluded that semantic web technology play a significant role in analyzing the social networks and social media content for extracting the interpretational knowledge towards strategic decision support.

Keywords: CRASP methodology, formative assessment, literature review, semantic web services, social media, social networks

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Authors: Hui Shi

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This study investigates a newly emerged usage of Chinese numeral classifier mei (枚) in the cyberspace. In modern Chinese grammar, mei as a classifier should occupy the pre-nominal position, and its valid accompanying nouns are restricted to small, flat, fragile inanimate objects rather than humans. To examine the semantic change of mei, two types of data from Weibo.com were collected. First, 500 mei-included Weibo posts constructed a corpus for analyzing this classifier's word order distribution (post-nominal or pre-nominal) as well as its accompanying nouns' semantics (inanimate or human). Second, considering that mei accompanies a remarkable number of human nouns in the first corpus, the second corpus is composed of mei-involved Weibo IDs from users located in first and third-tier cities (n=8 respectively). The findings show that in the cyber community, mei frequently classifies human-related neologisms at the archaic post-normal position. Besides, the 23 to 29-year-old females as well as Weibo users from third-tier cities are the major populations who adopt mei in their user IDs for self-description and identity expression. This paper argues that the creative usage of mei gains popularity in the Chinese internet due to a humor effect. The marked word order switch and semantic misapplication combined to trigger incongruity and jocularity. This study has significance for research on Chinese cyber neologism. It may also lay a foundation for further studies on Chinese classifier change and Chinese internet communication.

Keywords: Chinese classifier, humor, neologism, semantic change

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Authors: Yogendra Sisodia

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Researchers are becoming more interested in extracting useful information from legal documents thanks to the development of large-scale language models in natural language processing (NLP), and deep learning has accelerated the creation of powerful text mining models. Legal fields like contracts benefit greatly from semantic text search since it makes it quick and easy to find related clauses. After collecting sentence embeddings, it is relatively simple to locate sentences with a comparable meaning throughout the entire legal corpus. The author of this research investigated two pre-trained language models for this task: MiniLM and Roberta, and further fine-tuned them on Legal Contracts. The author used Multiple Negative Ranking Loss for the creation of sentence transformers. The fine-tuned language models and sentence transformers showed promising results.

Keywords: legal contracts, multiple negative ranking loss, natural language inference, sentence transformers, semantic textual similarity

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Authors: Phumelele Kubheka, Pius Owolawi, Gbolahan Aiyetoro

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Twitter is one of the most popular social media platforms where users can share their opinions on different subjects. As of 2010, The Twitter platform generates more than 12 Terabytes of data daily, ~ 4.3 petabytes in a single year. For this reason, Twitter is a great source for big mining data. Many industries such as Telecommunication companies can leverage the availability of Twitter data to better understand their markets and make an appropriate business decision. This study performs topic modeling on Twitter data using Latent Dirichlet Allocation (LDA). The obtained results are benchmarked with another topic modeling technique, Latent Semantic Indexing (LSI). The study aims to retrieve topics on a Twitter dataset containing user tweets on South African Telcos. Results from this study show that LSI is much faster than LDA. However, LDA yields better results with higher topic coherence by 8% for the best-performing model represented in Table 1. A higher topic coherence score indicates better performance of the model.

Keywords: big data, latent Dirichlet allocation, latent semantic indexing, telco, topic modeling, twitter

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Authors: Xiaoxing Ye

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To investigate complex rumen microbial communities, 16S ribosomal RNA (rRNA) sequencing is widely used. Here, we evaluated the impact of bioinformatics pipelines on the observation of OTUs and taxonomic classification of 750 cattle rumen microbial samples by comparing three commonly used pipelines (LotuS, UPARSE, and QIIME) with Usearch. In LotuS-based analyses, 189 archaeal and 3894 bacterial OTUs were observed. The observed OTUs for the Usearch analysis were significantly larger than the LotuS results. We discovered 1495 OTUs for archaea and 92665 OTUs for bacteria using Usearch analysis. In addition, taxonomic assignments were made for the rumen microbial samples. All pipelines had consistent taxonomic annotations from the phylum to the genus level. A difference in relative abundance was calculated for all microbial levels, including Bacteroidetes (QIIME: 72.2%, Usearch: 74.09%), Firmicutes (QIIME: 18.3%, Usearch: 20.20%) for the bacterial phylum, Methanobacteriales (QIIME: 64.2%, Usearch: 45.7%) for the archaeal class, Methanobacteriaceae (QIIME: 35%, Usearch: 45.7%) and Methanomassiliicoccaceae (QIIME: 35%, Usearch: 31.13%) for archaeal family. However, the most prevalent archaeal class varied between these two annotation pipelines. The Thermoplasmata was the top class according to the QIIME annotation, whereas Methanobacteria was the top class according to Usearch.

Keywords: cattle rumen, rumen microbial, 16S rRNA gene sequencing, bioinformatics pipeline

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Authors: Mohammad Alqahtani, Eric Atwell

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This paper reviews and classifies most of the important types of search techniques that have been applied on the holy Quran. Then, it addresses the limitations in these techniques. Additionally, this paper surveys most existing Quranic ontologies and what are their deficiencies. Finally, it explains a new search tool called: A semantic search tool for Al Quran based on Qur’anic ontologies. This tool will overcome all limitations in the existing Quranic search applications.

Keywords: holy Quran, natural language processing (NLP), semantic search, information retrieval (IR), ontology

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Authors: Farzaneh Badinlou, Reza Kormi-Nouri, Monika Knopf, Kamal Kharazi

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Research into long-term memory has demonstrated that the richness of the knowledge base cues in memory tasks improves retrieval process, which in turn influences learning and memory performance. The present research investigated the idea that adding cues connected to knowledge can affect memory performance in the context of action memory in children. In action memory studies, participants are instructed to learn a series of verb–object phrases as verbal learning and experience-based learning (learning by doing and learning by observation). It is well established that executing action phrases is a more memorable way to learn than verbally repeating the phrases, a finding called enactment effect. In the present study, a total of 410 students from four grade groups—2nd, 4th, 6th, and 8th—participated in this study. During the study, participants listened to verbal action phrases (VTs), performed the phrases (SPTs: subject-performed tasks), and observed the experimenter perform the phrases (EPTs: experimenter-performed tasks). During the test phase, cued recall test was administered. Semantic relational cues (i.e., well-integrated vs. poorly integrated items) were manipulated in the present study. In that, the participants were presented two lists of action phrases with high semantic integration between verb and noun, e.g., “write with the pen” and with low semantic integration between verb and noun, e.g., “pick up the glass”. Results revealed that experience-based learning had a better results than verbal learning for both well-integrated and poorly integrated items, though manipulations of semantic relational cues can moderate the enactment effect. In addition, children of different grade groups outperformed for well- than poorly integrated items, in flavour of older children. The results were discussed in relation to the effect of knowledge-based information in facilitating retrieval process in children.

Keywords: action memory, enactment effect, knowledge-based cues, school-aged children, semantic relational cues

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Authors: Rofida Gamal, Mostafa Mohammed, Mariam Adel, Marwa Gamal, Marwa kamal, Ayat Saber, Maha Mamdouh, Amira Emad, Mai Ramadan

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Lynch Syndrome is an inherited genetic condition associated with an increased risk of colorectal and other cancers. Detecting Lynch Syndrome in individuals is crucial for early intervention and preventive measures. This study proposes a computational pipeline for Lynch Syndrome detection by integrating alignment, variant calling, and annotation. The pipeline leverages popular tools such as FastQC, Trimmomatic, BWA, bcftools, and ANNOVAR to process the input FASTQ file, perform quality trimming, align reads to the reference genome, call variants, and annotate them. It is believed that the computational pipeline was applied to a dataset of Lynch Syndrome cases, and its performance was evaluated. It is believed that the quality check step ensured the integrity of the sequencing data, while the trimming process is thought to have removed low-quality bases and adaptors. In the alignment step, it is believed that the reads were accurately mapped to the reference genome, and the subsequent variant calling step is believed to have identified potential genetic variants. The annotation step is believed to have provided functional insights into the detected variants, including their effects on known Lynch Syndrome-associated genes. The results obtained from the pipeline revealed Lynch Syndrome-related positions in the genome, providing valuable information for further investigation and clinical decision-making. The pipeline's effectiveness was demonstrated through its ability to streamline the analysis workflow and identify potential genetic markers associated with Lynch Syndrome. It is believed that the computational pipeline presents a comprehensive and efficient approach to Lynch Syndrome detection, contributing to early diagnosis and intervention. The modularity and flexibility of the pipeline are believed to enable customization and adaptation to various datasets and research settings. Further optimization and validation are believed to be necessary to enhance performance and applicability across diverse populations.

Keywords: Lynch Syndrome, computational pipeline, alignment, variant calling, annotation, genetic markers

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Authors: Thomas Ousterhout

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In an effort to test the ability of a commercial grade EEG headset to effectively measure the N400 ERP, a replication study was conducted to see if similar results could be produced as that which used a medical grade EEG. Pictures of meaningful and meaningless hand postures were borrowed from the original author and subjects were required to perform a semantic discrimination task. The N400 was detected indicating semantic processing of the meaningfulness of the hand postures. The results corroborate those of the original author and support the use of some commercial grade EEG headsets for non-critical research applications.

Keywords: EEG, ERP, N400, semantics, congruency, gestures, emotiv

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Authors: Aaron Zhang, Alimire Kahaer, Gerald Weber, Nalin Arachchilage

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Access control is an essential safeguard for the security of enterprise data, which controls users’ access to information resources and ensures the confidentiality and integrity of information resources [1]. Research shows that the more common types of access control now have shortcomings [2]. In this direction, to improve the existing access control, we have studied the current technologies in the field of data security, deeply investigated the previous data access control policies and their problems, identified the existing deficiencies, and proposed a new extension structure of SPBAC. SPBAC extension proposed in this paper aims to combine Policy-Based Access Control (PBAC) with semantics to provide logically connected, real-time data access functionality by establishing associations between enterprise data through semantics. Our design combines policies with linked data through semantics to create a "Semantic link" so that access control is no longer per-database and determines that users in each role should be granted access based on the instance policy, and improves the SPBAC implementation by constructing policies and defined attributes through the XACML specification, which is designed to extend on the original XACML model. While providing relevant design solutions, this paper hopes to continue to study the feasibility and subsequent implementation of related work at a later stage.

Keywords: access control, semantic policy-based access control, semantic link, access control model, instance policy, XACML

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Authors: Jessevel Montes

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This study explored on the culture of journal writing among the Senior High School Manobo students. The purpose of this qualitative morpho-semantic and syntactic study was to discover the morphological, semantic, and syntactic features of the written output through morphological, semantic, and syntactic categories present in their journal writings. Also, beliefs and practices embedded in the norms, values, and ideologies were identified. The study was conducted among the Manobo students in the Senior High Schools of Central Mindanao, particularly in the Division of North Cotabato. Findings revealed that morphologically, the features that flourished are the following: subject-verb concordance, tenses, pronouns, prepositions, articles, and the use of adjectives. Semantically, the features are the following: word choice, idiomatic expression, borrowing, and vernacular. Syntactically, the features are the types of sentences according to structure and function; and the dominance of code switching and run-on sentences. Lastly, as to the beliefs and practices embedded in the norms, values, and ideologies of their journal writing, the major themes are: valuing education, family, and friends as treasure, preservation of culture, and emancipation from the bondage of poverty. This study has shed light on the writing capabilities and weaknesses of the Manobo students when it comes to English language. Further, such an insight into language learning problems is useful to teachers because it provides information on common trouble-spots in language learning, which can be used in the preparation of effective teaching materials.

Keywords: applied linguistics, culture, morpho-semantic and syntactic analysis, Manobo Senior High School, Philippines

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Authors: K. P. Valdés García, E. I. Rodríguez Fonseca, L. G. Juárez Cantú

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Suicide is a global, multidimensional and dynamic problem of mental health, which requires a constant study for its understanding and prevention. When research of this phenomenon is done, it is necessary to consider the different characteristics it may have because of the individual and sociocultural variables, the importance of this consideration is related to the generation of effective treatments and interventions. Adolescents are a vulnerable population due to the characteristics of the development stage. The investigation was carried out with the objective of identifying and describing the conceptualization of adolescents of suicide, and in this process, we find possible differences between men and women. The study was carried out in Saltillo, Coahuila, Mexico. The sample was composed of 418 volunteer students aged between 11 and 18 years. The ethical aspects of the research were reviewed and considered in all the processes of the investigation with the participants, their parents and the schools to which they belonged, psychological attention was offered to the participants and preventive workshops were carried in the educational institutions. Natural semantic networks were the instrument used, since this hybrid method allows to find and analyze the social concept of a phenomenon; in this case, the word suicide was used as an evocative stimulus and participants were asked to evoke at least five words and a maximum 10 that they thought were related to suicide, and then hierarchize them according to the closeness with the construct. The subsequent analysis was carried with Excel, yielding the semantic weights, affective loads and the distances between each of the semantic fields established according to the words reported by the subjects. The results showed similarities in the conceptualization of suicide in adolescents, men and women. Seven semantic fields were generated; the words were related in the discourse analysis: 1) death, 2) possible triggering factors, 3) associated moods, 4) methods used to carry it out, 5) psychological symptomatology that could affect, 6) words associated with a rejection of suicide, and finally, 7) specific objects to carry it out. One of the necessary aspects to consider in the investigations of complex issues such as suicide is to have a diversity of instruments and techniques that adjust to the characteristics of the population and that allow to understand the phenomena from the social constructs and not only theoretical. The constant study of suicide is a pressing need, the loss of a life from emotional difficulties that can be solved through psychiatry and psychological methods requires governments and professionals to pay attention and work with the risk population.

Keywords: adolescents, psychological construct, semantic networks, suicide

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Authors: Mohsen Maraoui

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In the aim of natural language processing applications improvement, such as information retrieval, machine translation, lexical disambiguation, we focus on statistical approach to semantic indexing for multilingual text documents based on conceptual network formalism. We propose to use this formalism as an indexing language to represent the descriptive concepts and their weighting. These concepts represent the content of the document. Our contribution is based on two steps. In the first step, we propose the extraction of index terms using the multilingual lexical resource Euro WordNet (EWN). In the second step, we pass from the representation of index terms to the representation of index concepts through conceptual network formalism. This network is generated using the EWN resource and pass by a classification step based on association rules model (in attempt to discover the non-taxonomic relations or contextual relations between the concepts of a document). These relations are latent relations buried in the text and carried by the semantic context of the co-occurrence of concepts in the document. Our proposed indexing approach can be applied to text documents in various languages because it is based on a linguistic method adapted to the language through a multilingual thesaurus. Next, we apply the same statistical process regardless of the language in order to extract the significant concepts and their associated weights. We prove that the proposed indexing approach provides encouraging results.

Keywords: concept extraction, conceptual network formalism, fuzzy association rules, multilingual thesaurus, semantic indexing

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Authors: Akrem Sellami, Imed Riadh Farah

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Hyperspectral imagery (HSI) typically provides a wealth of information captured in a wide range of the electromagnetic spectrum for each pixel in the image. Hence, a pixel in HSI is a high-dimensional vector of intensities with a large spectral range and a high spectral resolution. Therefore, the semantic interpretation is a challenging task of HSI analysis. We focused in this paper on object classification as HSI semantic interpretation. However, HSI classification still faces some issues, among which are the following: The spatial variability of spectral signatures, the high number of spectral bands, and the high cost of true sample labeling. Therefore, the high number of spectral bands and the low number of training samples pose the problem of the curse of dimensionality. In order to resolve this problem, we propose to introduce the process of dimensionality reduction trying to improve the classification of HSI. The presented approach is a semi-supervised band selection method based on spatial hypergraph embedding model to represent higher order relationships with different weights of the spatial neighbors corresponding to the centroid of pixel. This semi-supervised band selection has been developed to select useful bands for object classification. The presented approach is evaluated on AVIRIS and ROSIS HSIs and compared to other dimensionality reduction methods. The experimental results demonstrate the efficacy of our approach compared to many existing dimensionality reduction methods for HSI classification.

Keywords: dimensionality reduction, hyperspectral image, semantic interpretation, spatial hypergraph

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Authors: Munaf Rashid

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For content-based human action retrieval systems, search accuracy is often inferior because of the following two reasons 1) global information pertaining to videos is totally ignored, only low level motion descriptors are considered as a significant feature to match the similarity between query and database videos, and 2) the semantic gap between the high level user concept and low level visual features. Hence, in this paper, we propose a method that will address these two issues and in doing so, this paper contributes in two ways. Firstly, we introduce a method that uses both global and local information in one framework for an action retrieval task. Secondly, to minimize the semantic gap, a user concept is involved by incorporating features weight updating (FWU) Relevance Feedback (RF) approach. We use statistical characteristics to dynamically update weights of the feature descriptors so that after every RF iteration feature space is modified accordingly. For testing and validation purpose two human action recognition datasets have been utilized, namely Weizmann and UCF. Results show that even with a number of visual challenges the proposed approach performs well.

Keywords: relevance feedback (RF), action retrieval, semantic gap, feature descriptor, codebook

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Authors: Jae-Hyung Jin, Kyung-Tae Lee, Yee-Seul So, Eunji Jeong, Yeonseon Lee, Dongpil Lee, Dong-Gi Lee, Yong-Sun Bahn

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Cryptococcus neoformans causes cryptococcal meningoencephalitis mainly in immunocompromised patients as well as immunocompetent people. But therapeutic options are limited to treat cryptococcosis. Some signaling pathways including cyclic AMP pathway, MAPK pathway, and calcineurin pathway play a central role in the regulation of the growth, differentiation, and virulence of C. neoformans. To understand signaling networks regulating the virulence of C. neoformans, we selected the 114 putative phosphatase genes, one of the major components of signaling networks, in the genome of C. neoformans. We identified putative phosphatases based on annotation in C. neoformans var. grubii genome database provided by the Broad Institute and National Center for Biotechnology Information (NCBI) and performed a BLAST search of phosphatases of Saccharomyces cerevisiae, Aspergillus nidulans, Candida albicans and Fusarium graminearum to Cryptococcus neoformans. We classified putative phosphatases into 14 groups based on InterPro phosphatase domain annotation. Here, we constructed 170 signature-tagged gene-deletion strains through homologous recombination methods for 91 putative phosphatases. We examined their phenotypic traits under 30 different in vitro conditions, including growth, differentiation, stress response, antifungal resistance and virulence-factor production.

Keywords: human fungal pathogen, phosphatase, deletion library, functional genomics

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Authors: Paul Shize Li, Frank Alber

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A fundamental task of clinical genomics is to unravel the functions of genes and their associations with disorders. Although experimental biology has made efforts to discover and elucidate the molecular mechanisms of individual genes in the past decades, still about 40% of human genes have unknown functions, not to mention the diseases they may be related to. For those biologists who are interested in a particular gene with unknown functions, a powerful computational method tailored for inferring the functions and disease relevance of uncharacterized genes is strongly needed. Studies have shown that genes strongly linked to each other in multiple biological networks are more likely to have similar functions. This indicates that the densely connected subgraphs in multiple biological networks are useful in the functional and phenotypic annotation of uncharacterized genes. Therefore, in this work, we have developed an integrative network approach to identify the frequent local clusters, which are defined as those densely connected subgraphs that frequently occur in multiple biological networks and consist of the query gene that has few or no disease or function annotations. This is a local clustering algorithm that models multiple biological networks sharing the same gene set as a three-dimensional matrix, the so-called tensor, and employs the tensor-based optimization method to efficiently find the frequent local clusters. Specifically, massive public gene expression data sets that comprehensively cover dynamic, physiological, and environmental conditions are used to generate hundreds of gene co-expression networks. By integrating these gene co-expression networks, for a given uncharacterized gene that is of biologist’s interest, the proposed method can be applied to identify the frequent local clusters that consist of this uncharacterized gene. Finally, those frequent local clusters are used for function and disease annotation of this uncharacterized gene. This local tensor clustering algorithm outperformed the competing tensor-based algorithm in both module discovery and running time. We also demonstrated the use of the proposed method on real data of hundreds of gene co-expression data and showed that it can comprehensively characterize the query gene. Therefore, this study provides a new tool for annotating the uncharacterized genes and has great potential to assist clinical genomic diagnostics.

Keywords: local tensor clustering, query gene, gene co-expression network, gene annotation

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Authors: Ian Walsh, Terry Nguyen-Khuong, Christopher H. Taron, Pauline M. Rudd

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Glycoproteins and their covalently bonded glycans play critical roles in the immune system, cell communication, disease and disease prognosis. Ultra performance liquid chromatography (UPLC) coupled with mass spectrometry is conventionally used to qualitatively and quantitatively characterise glycan structures in a given sample. Exoglycosidases are enzymes that catalyze sequential removal of monosaccharides from the non-reducing end of glycans. They naturally have specificity for a particular type of sugar, its stereochemistry (α or β anomer) and its position of attachment to an adjacent sugar on the glycan. Thus, monitoring the peak movements (both in the UPLC and MS1) after application of exoglycosidases provides a unique and effective way to annotate sugars with high detail - i.e. differentiating positional and linkage isomers. Manual annotation of an exoglycosidase experiment is difficult and time consuming. As such, with increasing sample complexity and the number of exoglycosidases, the analysis could result in manually interpreting hundreds of peak movements. Recently, we have implemented pattern recognition software for automated interpretation of UPLC-MS1 exoglycosidase digestions. In this work, we explain the software, indicate how much time it will save and provide example usage showing the annotation of positional and linkage isomers in Immunoglobulin G, apolipoprotein J, and simple glycan standards.

Keywords: bioinformatics, automated glycan assignment, liquid chromatography, mass spectrometry

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Authors: Marrone Silverio Melo Dantas Pedro Henrique Dreyer, Gabriel Fonseca Reis de Souza, Daniel Bezerra, Ricardo Souza, Silvia Lins, Judith Kelner, Djamel Fawzi Hadj Sadok

Abstract:

The creation of a dataset is time-consuming and often discourages researchers from pursuing their goals. To overcome this problem, we present and discuss two solutions adopted for the automation of this process. Both optimize valuable user time and resources and support video object segmentation with object tracking and 3D projection. In our scenario, we acquire images from a moving robotic arm and, for each approach, generate distinct annotated datasets. We evaluated the precision of the annotations by comparing these with a manually annotated dataset, as well as the efficiency in the context of detection and classification problems. For detection support, we used YOLO and obtained for the projection dataset an F1-Score, accuracy, and mAP values of 0.846, 0.924, and 0.875, respectively. Concerning the tracking dataset, we achieved an F1-Score of 0.861, an accuracy of 0.932, whereas mAP reached 0.894. In order to evaluate the quality of the annotated images used for classification problems, we employed deep learning architectures. We adopted metrics accuracy and F1-Score, for VGG, DenseNet, MobileNet, Inception, and ResNet. The VGG architecture outperformed the others for both projection and tracking datasets. It reached an accuracy and F1-score of 0.997 and 0.993, respectively. Similarly, for the tracking dataset, it achieved an accuracy of 0.991 and an F1-Score of 0.981.

Keywords: RJ45, automatic annotation, object tracking, 3D projection

Procedia PDF Downloads 133

Authors: Kowit Pimpuang

Abstract:

Through analysis of the Pali-Sanskrit (PL-SKT) terms and their uses in reflecting political society of Thailand, the objectives of this study were to explore PL-SKT word formation and its semantic changes employed in the political society of Thailand and to explore the political reflection of Thai society through their uses. Conceptual framework of this study consists of (1) use of PL-SKT word formation namely, primary derivative (Kitaka), secondary derivative (Tathita), compound (Samasa) and prefix (Upasagga), (2) semantic changes namely; widening, narrowing and transferring of meaning, and (3) political reflection of Thai society. Qualitative method was employed in this study and data were collected from Thai Newspapers. It was found that there were uses of the four kinds of word formation in formatting the new political terms concerned namely, primary derivative, secondary derivative, compound and prefix leading by compound through the following three semantic changes; widening, narrowing and transferring, in order to make clear in understanding. Furthermore, PL-SKT terms were employed in reflecting Thai politics caused by democratic conflicts through the bureaucracy, plutocracy, businessocracy and juristocracy respectively. Later, there have been political business groups and their corruption problems in political society of Thailand.

Keywords: Pali, Sanskrit, reflection, politics, Thailand

Procedia PDF Downloads 248

Authors: Chryssa Thermolia, Ekaterini S. Bei, Stelios Sotiriadis, Kostas Stravoskoufos, Euripides G. M. Petrakis

Abstract:

Moving into a new era of healthcare, new tools and devices are developed to extend and improve health services, such as remote patient monitoring and risk prevention. In this concept, Internet of Things (IoT) and Cloud Computing present great advantages by providing remote and efficient services, as well as cooperation between patients, clinicians, researchers and other health professionals. This paper focuses on patients suffering from bipolar disorder, a brain disorder that belongs to a group of conditions called effective disorders, which is characterized by great mood swings.We exploit the advantages of Semantic Web and Cloud Technologies to develop a patient monitoring system to support clinicians. Based on intelligently filtering of evidence-knowledge and individual-specific information we aim to provide treatment notifications and recommended function tests at appropriate times or concluding into alerts for serious mood changes and patient’s non-response to treatment. We propose an architecture, as the back-end part of a cloud platform for IoT, intertwining intelligence devices with patients’ daily routine and clinicians’ support.

Keywords: bipolar disorder, intelligent systems patient monitoring, semantic web technologies, healthcare

Procedia PDF Downloads 479

Authors: Hazel P. Atilano

Abstract:

In this age of AI-assisted teaching and learning, there seems to be a dearth of research literature on the linguistic analysis of English as a Second Language (ESL) student-generated paraphrased academic texts. This study sought to examine the lexico-semantic, morphosyntactic features of paraphrased academic texts generated by ESL students. Employing a descriptive qualitative design, specifically linguistic analysis, the study involved a total of 85 students from senior high school, college, and graduate school enrolled in research courses. Data collection consisted of a 60-minute real-time, on-site paraphrasing practice exercise using excerpts from discipline-specific literature reviews of 150 to 200 words. A focus group discussion (FGD) was conducted to probe into the challenges experienced by the participants. The writing exercise yielded a total of 516 paraphrase pairs. A total of 176 paraphrase units (PUs) and 340 non-paraphrase pairs (NPPs) were detected. Findings from the linguistic analysis of PUs reveal that the modifications made to the original texts are predominantly syntax-based (Diathesis Alterations and Coordination Changes) and a combination of Miscellaneous Changes (Change of Order, Change of Format, and Addition/Deletion). Results of the analysis of paraphrase extremes (PE) show that Identical Structures resulting from the use of synonymous substitutions, with no significant change in the structural features of the original, is the most frequently occurring instance of PE. The analysis of paraphrase errors reveals that synonymous substitutions resulting in identical structures are the most frequently occurring error that leads to PE. Another type of paraphrasing error involves semantic and content loss resulting from the deletion or addition of meaning-altering content. Three major themes emerged from the FGD: (1) The Challenge of Preserving Semantic Content and Fidelity; (2) The Best Words in the Best Order: Grappling with the Lexico-semantic and Morphosyntactic Demands of Paraphrasing; and (3) Contending with Limited Vocabulary, Poor Comprehension, and Lack of Practice. A pedagogical paradigm was designed based on the major findings of the study for a sustainable instructional intervention.

Keywords: academic text, lexico-semantic analysis, linguistic analysis, morphosyntactic analysis, paraphrasing

Procedia PDF Downloads 28