Search results for: sentence%20characteristics

Authors: Y. Y. Chen, O. M. Foong, S. P. Yong, Kurniawan Iwan

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Information sharing and gathering are important in the rapid advancement era of technology. The existence of WWW has caused rapid growth of information explosion. Readers are overloaded with too many lengthy text documents in which they are more interested in shorter versions. Oil and gas industry could not escape from this predicament. In this paper, we develop an Automated Text Summarization System known as AutoTextSumm to extract the salient points of oil and gas drilling articles by incorporating statistical approach, keywords identification, synonym words and sentence-s position. In this study, we have conducted interviews with Petroleum Engineering experts and English Language experts to identify the list of most commonly used keywords in the oil and gas drilling domain. The system performance of AutoTextSumm is evaluated using the formulae of precision, recall and F-score. Based on the experimental results, AutoTextSumm has produced satisfactory performance with F-score of 0.81.

Keywords: Keyword's probability, synonym sets.

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Authors: P. Heribanová, J. Polec, S. Ondrušová, M. Hosťovecký

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This paper discusses the cued speech recognition methods in videoconference. Cued speech is a specific gesture language that is used for communication between deaf people. We define the criteria for sentence intelligibility according to answers of testing subjects (deaf people). In our tests we use 30 sample videos coded by H.264 codec with various bit-rates and various speed of cued speech. Additionally, we define the criteria for consonant sign recognizability in single-handed finger alphabet (dactyl) analogically to acoustics. We use another 12 sample videos coded by H.264 codec with various bit-rates in four different video formats. To interpret the results we apply the standard scale for subjective video quality evaluation and the percentual evaluation of intelligibility as in acoustics. From the results we construct the minimum coded bit-rate recommendations for every spatial resolution.

Keywords: cued speech, inteligibility, logatom, video

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Authors: Aji P. Wibawa, Andrew Nafalski, Neil Murray, Wayan F. Mahmudy

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Parallel text alignment is proposed as a way of aligning bahasa Indonesia to words in Javanese. Since the one-to-one word translator does not have the facility to translate pragmatic aspects of Javanese, the parallel text alignment model described uses a phrase pair combination. The algorithm aligns the parallel text automatically from the beginning to the end of each sentence. Even though the results of the phrase pair combination outperform the previous algorithm, it is still inefficient. Recording all possible combinations consume more space in the database and time consuming. The original algorithm is modified by applying the edit distance coefficient to improve the data-storage efficiency. As a result, the data-storage consumption is 90% reduced as well as its learning period (42s).

Keywords: Parallel text alignment, phrase pair combination, edit distance coefficient, Javanese-Indonesian language.

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Authors: Liming Zhang

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In this paper, a new adaptive Fourier decomposition (AFD) based time-frequency speech analysis approach is proposed. Given the fact that the fundamental frequency of speech signals often undergo fluctuation, the classical short-time Fourier transform (STFT) based spectrogram analysis suffers from the difficulty of window size selection. AFD is a newly developed signal decomposition theory. It is designed to deal with time-varying non-stationary signals. Its outstanding characteristic is to provide instantaneous frequency for each decomposed component, so the time-frequency analysis becomes easier. Experiments are conducted based on the sample sentence in TIMIT Acoustic-Phonetic Continuous Speech Corpus. The results show that the AFD based time-frequency distribution outperforms the STFT based one.

Keywords: Adaptive fourier decomposition, instantaneous frequency, speech analysis, time-frequency distribution.

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Authors: Theologos Athanaselis, Stelios Bakamidis, Ioannis Dologlou

Abstract:

There are multiple reasons to expect that detecting the word order errors in a text will be a difficult problem, and detection rates reported in the literature are in fact low. Although grammatical rules constructed by computer linguists improve the performance of grammar checker in word order diagnosis, the repairing task is still very difficult. This paper presents an approach for repairing word order errors in English text by reordering words in a sentence and choosing the version that maximizes the number of trigram hits according to a language model. The novelty of this method concerns the use of an efficient confusion matrix technique for reordering the words. The comparative advantage of this method is that works with a large set of words, and avoids the laborious and costly process of collecting word order errors for creating error patterns.

Keywords: Permutations filtering, Statistical languagemodel N-grams, Word order errors

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Authors: Hee-Jeong Ahn, Kee-Won Kim, Seung-Hoon Kim

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The knowledge of the relationship between characters can help readers to understand the overall story or plot of the literary fiction. In this paper, we present a method for extracting the specific relationship between characters from a Korean literary fiction. Generally, methods for extracting relationships between characters in text are statistical or computational methods based on the sentence distance between characters without considering Korean linguistic features. Furthermore, it is difficult to extract the relationship with direction from text, such as one-sided love, because they consider only the weight of relationship, without considering the direction of the relationship. Therefore, in order to identify specific relationships between characters, we propose a statistical method considering linguistic features, such as syntactic patterns and speech verbs in Korean. The result of our method is represented by a weighted directed graph of the relationship between the characters. Furthermore, we expect that proposed method could be applied to the relationship analysis between characters of other content like movie or TV drama.

Keywords: Data mining, Korean linguistic feature, literary fiction, relationship extraction.

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Authors: L. H. Chong, Y. Y. Chen

Abstract:

Information is increasing in volumes; companies are overloaded with information that they may lose track in getting the intended information. It is a time consuming task to scan through each of the lengthy document. A shorter version of the document which contains only the gist information is more favourable for most information seekers. Therefore, in this paper, we implement a text summarization system to produce a summary that contains gist information of oil and gas news articles. The summarization is intended to provide important information for oil and gas companies to monitor their competitor-s behaviour in enhancing them in formulating business strategies. The system integrated statistical approach with three underlying concepts: keyword occurrences, title of the news article and location of the sentence. The generated summaries were compared with human generated summaries from an oil and gas company. Precision and recall ratio are used to evaluate the accuracy of the generated summary. Based on the experimental results, the system is able to produce an effective summary with the average recall value of 83% at the compression rate of 25%.

Keywords: Information retrieval, text summarization, statistical approach.

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Authors: Vadivel Ayyasamy

Abstract:

The present approach deals with the identification of Emotions and classification of Emotional patterns at Phrase-level with respect to Positive and Negative Orientation. The proposed approach considers emotion triggered terms, its co-occurrence terms and also associated sentences for recognizing emotions. The proposed approach uses Part of Speech Tagging and Emotion Actifiers for classification. Here sentence patterns are broken into phrases and Neuro-Fuzzy model is used to classify which results in 16 patterns of emotional phrases. Suitable intensities are assigned for capturing the degree of emotion contents that exist in semantics of patterns. These emotional phrases are assigned weights which supports in deciding the Positive and Negative Orientation of emotions. The approach uses web documents for experimental purpose and the proposed classification approach performs well and achieves good F-Scores.

Keywords: Emotions, sentences, phrases, classification, patterns, fuzzy, positive orientation, negative orientation.

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Authors: S. V. Kogilavani, C. S. Kanimozhiselvi, S. Malliga

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Fast changing knowledge systems on the Internet can be accessed more efficiently with the help of automatic document summarization and updating techniques. The aim of multi-document update summary generation is to construct a summary unfolding the mainstream of data from a collection of documents based on the hypothesis that the user has already read a set of previous documents. In order to provide a lot of semantic information from the documents, deeper linguistic or semantic analysis of the source documents were used instead of relying only on document word frequencies to select important concepts. In order to produce a responsive summary, meaning oriented structural analysis is needed. To address this issue, the proposed system presents a document summarization approach based on sentence annotation with aspects, prepositions and named entities. Semantic element extraction strategy is used to select important concepts from documents which are used to generate enhanced semantic summary.

Keywords: Aspects, named entities, prepositions, update summary.

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Authors: Hu Haibo, Tu Chunmei, Fu Chunlei, Fu Li, Mao Fan, Ma Yuan

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Chinese Idioms are a type of traditional Chinese idiomatic expressions with specific meanings and stereotypes structure which are widely used in classical Chinese and are still common in vernacular written and spoken Chinese today. Currently, Chinese Idioms are retrieved in glossary with key character or key word in morphology or pronunciation index that can not meet the need of searching semantically. OCIRS is proposed to search the desired idiom in the case of users only knowing its meaning without any key character or key word. The user-s request in a sentence or phrase will be grammatically analyzed in advance by word segmentation, key word extraction and semantic similarity computation, thus can be mapped to the idiom domain ontology which is constructed to provide ample semantic relations and to facilitate description logics-based reasoning for idiom retrieval. The experimental evaluation shows that OCIRS realizes the function of searching idioms via semantics, obtaining preliminary achievement as requested by the users.

Keywords: Chinese idiom, idiom retrieval, semantic searching, ontology, semantics similarity.

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Authors: Jerneja Žganec Gros, Aleš Mihelič, Nikola Pavešić, Mario Žganec, Stanislav Gruden

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The paper presents the design concept of a unitselection text-to-speech synthesis system for the Slovenian language. Due to its modular and upgradable architecture, the system can be used in a variety of speech user interface applications, ranging from server carrier-grade voice portal applications, desktop user interfaces to specialized embedded devices. Since memory and processing power requirements are important factors for a possible implementation in embedded devices, lexica and speech corpora need to be reduced. We describe a simple and efficient implementation of a greedy subset selection algorithm that extracts a compact subset of high coverage text sentences. The experiment on a reference text corpus showed that the subset selection algorithm produced a compact sentence subset with a small redundancy. The adequacy of the spoken output was evaluated by several subjective tests as they are recommended by the International Telecommunication Union ITU.

Keywords: text-to-speech synthesis, prosody modeling, speech user interface.

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Authors: Meltem Serhatli, Ferda N. Alpaslan

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Processing the data by computers and performing reasoning tasks is an important aim in Computer Science. Semantic Web is one step towards it. The use of ontologies to enhance the information by semantically is the current trend. Huge amount of domain specific, unstructured on-line data needs to be expressed in machine understandable and semantically searchable format. Currently users are often forced to search manually in the results returned by the keyword-based search services. They also want to use their native languages to express what they search. In this paper, an ontology-based automated question answering system on software test documents domain is presented. The system allows users to enter a question about the domain by means of natural language and returns exact answer of the questions. Conversion of the natural language question into the ontology based query is the challenging part of the system. To be able to achieve this, a new algorithm regarding free text to ontology based search engine query conversion is proposed. The algorithm is based on investigation of suitable question type and parsing the words of the question sentence.

Keywords: Description Logics, ontology, question answering, reasoning.

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Authors: Ismail Celik, Ismail Sahin, Fetah Eren

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The computer, among the most important inventions of the twentieth century, has become an increasingly important component in our everyday lives. Computer games also have become increasingly popular among people day-by-day, owing to their features based on realistic virtual environments, audio and visual features, and the roles they offer players. In the present study, the metaphors students have for computer games are investigated, as well as an effort to fill the gap in the literature. Students were asked to complete the sentence—‘Computer game is like/similar to….because….’— to determine the middle school students’ metaphorical images of the concept for ‘computer game’. The metaphors created by the students were grouped in six categories, based on the source of the metaphor. These categories were ordered as ‘computer game as a means of entertainment’, ‘computer game as a beneficial means’, ‘computer game as a basic need’, ‘computer game as a source of evil’, ‘computer game as a means of withdrawal’, and ‘computer game as a source of addiction’, according to the number of metaphors they included.

Keywords: Computer game, metaphor, middle school students.

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Authors: A. M. H. Elyasir, K. S. M. Anbananthen

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The internet is growing larger and becoming the most popular platform for the people to share their opinion in different interests. We choose the education domain specifically comparing some Malaysian universities against each other. This comparison produces benchmark based on different criteria shared by the online users in various online resources including Twitter, Facebook and web pages. The comparison is accomplished using opinion mining framework to extract, process the unstructured text and classify the result to positive, negative or neutral (polarity). Hence, we divide our framework to three main stages; opinion collection (extraction), unstructured text processing and polarity classification. The extraction stage includes web crawling, HTML parsing, Sentence segmentation for punctuation classification, Part of Speech (POS) tagging, the second stage processes the unstructured text with stemming and stop words removal and finally prepare the raw text for classification using Named Entity Recognition (NER). Last phase is to classify the polarity and present overall result for the comparison among the Malaysian universities. The final result is useful for those who are interested to study in Malaysia, in which our final output declares clear winners based on the public opinions all over the web.

Keywords: Entity Recognition, Education Domain, Opinion Mining, Unstructured Text.

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Authors: Maya Lisa Aryanti, S. S. M. Hum

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To improve students’ skill, writing is the most challenging skill to be developed. The reason is that besides helping the students to develop their skill, this activity also helps them to express themselves. This paper depicts how paraphrasing is very helpful to interpret students’ writing. Syntactic units, used tenses and meanings will indeed change once the writings were paraphrased. The objectives of this research are to reveal the inappropriate structure of syntactic units, to show what types of sentences the students often make, and to show how paraphrasing can help to infer the message. The methodology of this research is descriptive qualitative research. In addition, theories of linguistics are also included. This includes theory of Syntax to describe syntactic units and tenses and theory of Semantics to describe theories of meaning and how paraphrasing works. The theories of general linguistics, grammar and writing are also provided to support the theories of Syntax and Semantics. The results of this research are concerned with how the message is received in the end. The message written in the students’ essay is not clear because of the improper structure of syntactic units and use of incorrect of tenses. The students tend to use simple sentences, compound sentences and complex sentences with a few mistakes in their writing. In addition, they tend to create unnecessary phrases. The last point is that this research shows how paraphrase works to attain complete meaning of a sentence.

Keywords: Paraphrase, meanings, syntactic units and tenses.

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Authors: Wernhuar Tarng, Yuan-Yuan Chen, Chien-Lung Li, Kun-Rong Hsie, Mingteh Chen

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An emotional speech recognition system for the applications on smart phones was proposed in this study to combine with 3G mobile communications and social networks to provide users and their groups with more interaction and care. This study developed a mechanism using the support vector machines (SVM) to recognize the emotions of speech such as happiness, anger, sadness and normal. The mechanism uses a hierarchical classifier to adjust the weights of acoustic features and divides various parameters into the categories of energy and frequency for training. In this study, 28 commonly used acoustic features including pitch and volume were proposed for training. In addition, a time-frequency parameter obtained by continuous wavelet transforms was also used to identify the accent and intonation in a sentence during the recognition process. The Berlin Database of Emotional Speech was used by dividing the speech into male and female data sets for training. According to the experimental results, the accuracies of male and female test sets were increased by 4.6% and 5.2% respectively after using the time-frequency parameter for classifying happy and angry emotions. For the classification of all emotions, the average accuracy, including male and female data, was 63.5% for the test set and 90.9% for the whole data set.

Keywords: Smart phones, emotional speech recognition, socialnetworks, support vector machines, time-frequency parameter, Mel-scale frequency cepstral coefficients (MFCC).

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Authors: Tahani Aljohani, Jialin Yu, Alexandra. I. Cristea

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The more an educational system knows about a learner, the more personalised interaction it can provide, which leads to better learning. However, asking a learner directly is potentially disruptive, and often ignored by learners. Especially in the booming realm of MOOC Massive Online Learning platforms, only a very low percentage of users disclose demographic information about themselves. Thus, in this paper, we aim to predict learners’ demographic characteristics, by proposing an approach using linguistically motivated Deep Learning Architectures for Learner Profiling, particularly targeting gender prediction on a FutureLearn MOOC platform. Additionally, we tackle here the difficult problem of predicting the gender of learners based on their comments only – which are often available across MOOCs. The most common current approaches to text classification use the Long Short-Term Memory (LSTM) model, considering sentences as sequences. However, human language also has structures. In this research, rather than considering sentences as plain sequences, we hypothesise that higher semantic - and syntactic level sentence processing based on linguistics will render a richer representation. We thus evaluate, the traditional LSTM versus other bleeding edge models, which take into account syntactic structure, such as tree-structured LSTM, Stack-augmented Parser-Interpreter Neural Network (SPINN) and the Structure-Aware Tag Augmented model (SATA). Additionally, we explore using different word-level encoding functions. We have implemented these methods on Our MOOC dataset, which is the most performant one comparing with a public dataset on sentiment analysis that is further used as a cross-examining for the models' results.

Keywords: Deep learning, data mining, gender predication, MOOCs.

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Authors: Sugandhi, Parteek Kumar, Sanmeet Kaur

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Sign Language (SL) is used by deaf and other people who cannot speak but can hear or have a problem with spoken languages due to some disability. It is a visual gesture language that makes use of either one hand or both hands, arms, face, body to convey meanings and thoughts. SL automation system is an effective way which provides an interface to communicate with normal people using a computer. In this paper, an avatar based dictionary has been proposed for text to Indian Sign Language (ISL) generation system. This research work will also depict a literature review on SL corpus available for various SL s over the years. For ISL generation system, a written form of SL is required and there are certain techniques available for writing the SL. The system uses Hamburg sign language Notation System (HamNoSys) and Signing Gesture Mark-up Language (SiGML) for ISL generation. It is developed in PHP using Web Graphics Library (WebGL) technology for 3D avatar animation. A multilingual ISL dictionary is developed using HamNoSys for both English and Hindi Language. This dictionary will be used as a database to associate signs with words or phrases of a spoken language. It provides an interface for admin panel to manage the dictionary, i.e., modification, addition, or deletion of a word. Through this interface, HamNoSys can be developed and stored in a database and these notations can be converted into its corresponding SiGML file manually. The system takes natural language input sentence in English and Hindi language and generate 3D sign animation using an avatar. SL generation systems have potential applications in many domains such as healthcare sector, media, educational institutes, commercial sectors, transportation services etc. This research work will help the researchers to understand various techniques used for writing SL and generation of Sign Language systems.

Keywords: Avatar, dictionary, HamNoSys, hearing-impaired, Indian Sign Language, sign language.

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Authors: Anja Kurz, Marc Flynn, Tobias Good, Marco Caversaccio, Martin Kompis

Abstract:

Bone Anchored Hearing Implants (BAHI) are  routinely used in patients with conductive or mixed hearing loss, e.g.  if conventional air conduction hearing aids cannot be used. New  sound processors and new fitting software now allow the adjustment  of parameters such as loudness compression ratios or maximum  power output separately. Today it is unclear, how the choice of these  parameters influences aided speech understanding in BAHI users.  In this prospective experimental study, the effect of varying the  compression ratio and lowering the maximum power output in a  BAHI were investigated.  Twelve experienced adult subjects with a mixed hearing loss  participated in this study. Four different compression ratios (1.0; 1.3;  1.6; 2.0) were tested along with two different maximum power output  settings, resulting in a total of eight different programs. Each  participant tested each program during two weeks. A blinded Latin  square design was used to minimize bias.  For each of the eight programs, speech understanding in quiet and  in noise was assessed. For speech in quiet, the Freiburg number test  and the Freiburg monosyllabic word test at 50, 65, and 80 dB SPL  were used. For speech in noise, the Oldenburg sentence test was  administered.  Speech understanding in quiet and in noise was improved  significantly in the aided condition in any program, when compared  to the unaided condition. However, no significant differences were  found between any of the eight programs. In contrast, on a subjective  level there was a significant preference for medium compression  ratios of 1.3 to 1.6 and higher maximum power output.

 

Keywords: Bone Anchored Hearing Implant, Compression, Maximum Power Output, Speech understanding.

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Authors: Dini Dewi Heniarti

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The importance of this study is to understand how Indonesian military court asserts its jurisdiction over military members who commit general crimes within the Indonesian military judiciary system in comparison to other countries. This research employs a normative-juridical approach in combination with historical and comparative-juridical approaches. The research specification is analytical-descriptive in nature, i.e. describing or outlining the principles, basic concepts, and norms related to military judiciary system, which are further analyzed within the context of implementation and as the inputs for military justice regulation under the Indonesian legal system. Main data used in this research are secondary data, including primary, secondary and tertiary legal sources. The research focuses on secondary data, while primary data are supplementary in nature. The validity of data is checked using multi-methods commonly known as triangulation, i.e. to reflect the efforts to gain an in-depth understanding of phenomena being studied. Here, the military element is kept intact in the judiciary process with due observance of the Military Criminal Justice System and the Military Command Development Principle. The Indonesian military judiciary jurisdiction over military members committing general crimes is based on national legal system and global development while taking into account the structure, composition and position of military forces within the state structure. Jurisdiction is formulated by setting forth the substantive norm of crimes that are military in nature. At the level of adjudication jurisdiction, the military court has a jurisdiction to adjudicate military personnel who commit general offences. At the level of execution jurisdiction, the military court has a jurisdiction to execute the sentence against military members who have been convicted with a final and binding judgement. Military court's jurisdiction needs to be expanded when the country is in the state of war.

Keywords: Military courts, Jurisdiction, Military members, Military justice system.

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Authors: Ebipatei Victoria Tunyan, T. A. Cao, Cheol Young Ock

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Detecting subjectively biased statements is a vital task. This is because this kind of bias, when present in the text or other forms of information dissemination media such as news, social media, scientific texts, and encyclopedias, can weaken trust in the information and stir conflicts amongst consumers. Subjective bias detection is also critical for many Natural Language Processing (NLP) tasks like sentiment analysis, opinion identification, and bias neutralization. Having a system that can adequately detect subjectivity in text will boost research in the above-mentioned areas significantly. It can also come in handy for platforms like Wikipedia, where the use of neutral language is of importance. The goal of this work is to identify the subjectively biased language in text on a sentence level. With machine learning, we can solve complex AI problems, making it a good fit for the problem of subjective bias detection. A key step in this approach is to train a classifier based on BERT (Bidirectional Encoder Representations from Transformers) as upstream model. BERT by itself can be used as a classifier; however, in this study, we use BERT as data preprocessor as well as an embedding generator for a Bi-LSTM (Bidirectional Long Short-Term Memory) network incorporated with attention mechanism. This approach produces a deeper and better classifier. We evaluate the effectiveness of our model using the Wiki Neutrality Corpus (WNC), which was compiled from Wikipedia edits that removed various biased instances from sentences as a benchmark dataset, with which we also compare our model to existing approaches. Experimental analysis indicates an improved performance, as our model achieved state-of-the-art accuracy in detecting subjective bias. This study focuses on the English language, but the model can be fine-tuned to accommodate other languages.

Keywords: Subjective bias detection, machine learning, BERT–BiLSTM–Attention, text classification, natural language processing.

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Authors: Vishal Raj, Noorhan Abbas

Abstract:

Ambiguity in NLP (Natural Language Processing) refers to the ability of a word, phrase, sentence, or text to have multiple meanings. This results in various kinds of ambiguities such as lexical, syntactic, semantic, anaphoric and referential. This study is focused mainly on solving the issue of Lexical ambiguity. Word Sense Disambiguation (WSD) is an NLP technique that aims to resolve lexical ambiguity by determining the correct meaning of a word within a given context. Most WSD solutions rely on words for training and testing, but we have used lemma and Part of Speech (POS) tokens of words for training and testing. Lemma adds generality and POS adds properties of word into token. We have designed a method to create an affinity matrix to calculate the affinity between any pair of lemma_POS (a token where lemma and POS of word are joined by underscore) of given training set. Additionally, we have devised an algorithm to create the sense clusters of tokens using affinity matrix under hierarchy of POS of lemma. Furthermore, three different mechanisms to predict the sense of target word using the affinity/similarity value are devised. Each contextual token contributes to the sense of target word with some value and whichever sense gets higher value becomes the sense of target word. So, contextual tokens play a key role in creating sense clusters and predicting the sense of target word, hence, the model is named Contextual SenSe Model (CSM). CSM exhibits a noteworthy simplicity and explication lucidity in contrast to contemporary deep learning models characterized by intricacy, time-intensive processes, and challenging explication. CSM is trained on SemCor training data and evaluated on SemEval test dataset. The results indicate that despite the naivety of the method, it achieves promising results when compared to the Most Frequent Sense (MFS) model.

Keywords: Word Sense Disambiguation, WSD, Contextual SenSe Model, Most Frequent Sense, part of speech, POS, Natural Language Processing, NLP, OOV, out of vocabulary, ELMo, Embeddings from Language Model, BERT, Bidirectional Encoder Representations from Transformers, Word2Vec, lemma_POS, Algorithm.

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Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

Abstract:

Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: Metagenomics, phenotype prediction, deep learning, embeddings, multiple instance learning.

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