Development of an efficient Computational Model for classification of Tissue remodeling

Tissue remodeling is one of the most important and crucial biological process. Process in which tissue reorganization and renovation takes place is called tissue remodeling. Mean of recovery in human beings is tissue remodeling in which damaged tissue are replaced completely with new tissue or through tissue repairmen types physiological and pathological tissue remodeling are two derivatives of Tissue remodeling. Normal Tissue remodeling is referred to as Physiological tissue remodeling, however abnormal process which may lead to a disease is known as pathological tissue remodeling. From past till now different techniques like histopathology and chemicals were being used to identify abnormality in tissues. Which is a time taking and costly processes. There is no such computational method which can be used for the identification of the physiological and pathological tissue remodeling. The current article aims to develop a classification model which has ability to classify weather the given sequence is physiological or pathological process. Three classifiers RF, ANN and SVM will be used for practice and evaluation of proposed classification model

Identification of Phage Viral Proteins With Hybrid Sequence Features

The uniqueness of bacteriophages plays an important role in bioinformatics research. In real applications, the function of the bacteriophage virion proteins is the main area of interest. Therefore, it is very important to classify bacteriophage virion proteins and non-phage virion proteins accurately. Extracting comprehensive and effective sequence features from proteins plays a vital role in protein classification. In order to more fully represent protein information, this paper is more comprehensive and effective by combining the features extracted by the feature information representation algorithm based on sequence information (CCPA) and the feature representation algorithm based on sequence and structure information. After extracting features, the Max-Relevance-Max-Distance (MRMD) algorithm is used to select the optimal feature set with the strongest correlation between class labels and low redundancy between features. Given the randomness of the samples selected by the random forest classification algorithm and the randomness features for producing each node variable, a random forest method is employed to perform 10-fold cross-validation on the bacteriophage protein classification. The accuracy of this model is as high as 93.5% in the classification of phage proteins in this study. This study also found that, among the eight physicochemical properties considered, the charge property has the greatest impact on the classification of bacteriophage proteins These results indicate that the model discussed in this paper is an important tool in bacteriophage protein research

Naïve Bayes Classifier with Feature Selection to Identify Phage Virion Proteins

Knowledge about the protein composition of phage virions is a key step to understand the functions of phage virion proteins. However, the experimental method to identify virion proteins is time consuming and expensive. Thus, it is highly desirable to develop novel computational methods for phage virion protein identification. In this study, a Naïve Bayes based method was proposed to predict phage virion proteins using amino acid composition and dipeptide composition. In order to remove redundant information, a novel feature selection technique was employed to single out optimized features. In the jackknife test, the proposed method achieved an accuracy of 79.15% for phage virion and nonvirion proteins classification, which are superior to that of other state-of-the-art classifiers. These results indicate that the proposed method could be as an effective and promising high-throughput method in phage proteomics research

Optimisation Method for Training Deep Neural Networks in Classification of Non- functional Requirements

Non-functional requirements (NFRs) are regarded critical to a software system's success. The majority of NFR detection and classification solutions have relied on supervised machine learning models. It is hindered by the lack of labelled data for training and necessitate a significant amount of time spent on feature engineering. In this work we explore emerging deep learning techniques to reduce the burden of feature engineering. The goal of this study is to develop an autonomous system that can classify NFRs into multiple classes based on a labelled corpus. In the first section of the thesis, we standardise the NFRs ontology and annotations to produce a corpus based on five attributes: usability, reliability, efficiency, maintainability, and portability. In the second section, the design and implementation of four neural networks, including the artificial neural network, convolutional neural network, long short-term memory, and gated recurrent unit are examined to classify NFRs. These models, necessitate a large corpus. To overcome this limitation, we proposed a new paradigm for data augmentation. This method uses a sort and concatenates strategy to combine two phrases from the same class, resulting in a two-fold increase in data size while keeping the domain vocabulary intact. We compared our method to a baseline (no augmentation) and an existing approach Easy data augmentation (EDA) with pre-trained word embeddings. All training has been performed under two modifications to the data; augmentation on the entire data before train/validation split vs augmentation on train set only. Our findings show that as compared to EDA and baseline, NFRs classification model improved greatly, and CNN outperformed when trained using our suggested technique in the first setting. However, we saw a slight boost in the second experimental setup with just train set augmentation. As a result, we can determine that augmentation of the validation is required in order to achieve acceptable results with our proposed approach. We hope that our ideas will inspire new data augmentation techniques, whether they are generic or task specific. Furthermore, it would also be useful to implement this strategy in other languages

Predictive models as early warning systems for student academic performance in introductory programming

Computer programming is fundamental to Computer Science and IT curricula. At the novice level it covers programming concepts that are essential for subsequent advanced programming courses. However, introductory programming courses are among the most challenging courses for novices and high failure and attrition rates continue even as computer science education has seen improvements in pedagogy. Consequently, the quest to identify factors that affect student learning and academic performance in introductory computer programming courses has been a long-standing activity. Specifically, weak novice learners of programming need to be identified and assisted early in the semester in order to alleviate any potential risk of failing or withdrawing from their course. Hence, it is essential to identify at-risk programming students early, in order to plan (early) interventions. The goal of this thesis was to develop a validated, predictive model(s) with suitable predictors of student academic performance in introductory programming courses. The proposed model utilises the Naïve Bayes classification machine learning algorithm to analyse student performance data, based on the principle of parsimony. Furthermore, an additional objective was to propose this validated predictive model as an early warning system (EWS), to predict at-risk students early in the semester and, in turn, to potentially inform instructors (and students) for early interventions. We obtained data from two introductory programming courses in our study to develop and test the predictive models. The models were built with student presage and in progress-data for which instructors may easily collect or access despite the nature of pedagogy of educational settings. In addition, our work analysed the predictability of selected data sources and looked for the combination of predictors, which yields the highest prediction accuracy to predict student academic performance. The prediction accuracies of the models were computed by using confusion matrix data including overall model prediction accuracy, prediction accuracy sensitivity and specificity, balanced accuracy and the area under the ROC curve (AUC) score for generalisation. On average, the models developed with formative assessment tasks, which were partially assisted by the instructor in the classroom, returned higher at-risk prediction accuracies than the models developed with take-home assessment task only as predictors. The unknown data test results of this study showed that it is possible to predict 83% of students that need support as early as Week 3 in a 12-week introductory programming course. The ensemble method-based results suggest that it is possible to improve overall at-risk prediction performance with low false positives and to incorporate this in early warning systems to identify students that need support, in order to provide early intervention before they reach critical stages (at-risk of failing). The proposed model(s) of this study were developed on the basis of the principle of parsimony as well as previous research findings, which accounted for variations in academic settings, such as academic environment, and student demography. The predictive model could potentially provide early warning indicators to facilitate early warning intervention strategies for at-risk students in programming that allow for early interventions. The main contribution of this thesis is a model that may be applied to other programming and non-programming courses, which have both continuous formative and a final exam summative assessment, to predict final student performance early in the semester.Ohjelmointi on informaatioteknologian ja tietojenkäsittelytieteen opinto-ohjelmien olennainen osa. Aloittelijatasolla opetus kattaa jatkokurssien kannalta keskeisiä ohjelmoinnin käsitteitä. Tästä huolimatta ohjelmoinnin peruskurssit ovat eräitä haasteellisimmista kursseista aloittelijoille. Korkea keskeyttämisprosentti ja opiskelijoiden asteittainen pois jättäytyminen ovat vieläkin tunnusomaisia piirteitä näille kursseille, vaikka ohjelmoinnin opetuksen pedagogiikka onkin kehittynyt. Näin ollen vaikuttavia syitä opiskelijoiden heikkoon suoriutumiseen on etsitty jo pitkään. Erityisesti heikot, aloittelevat ohjelmoijat tulisi tunnistaa mahdollisimman pian, jotta heille voitaisiin tarjota tukea ja pienentää opiskelijan riskiä epäonnistua kurssin läpäimisessä ja riskiä jättää kurssi kesken. Heikkojen opiskelijoiden tunnistaminen on tärkeää, jotta voidaan suunnitella aikainen väliintulo. Tämän väitöskirjatyön tarkoituksena oli kehittää todennettu, ennustava malli tai malleja sopivilla ennnustusfunktioilla koskien opiskelijan akateemista suoriutumista ohjelmoinnin peruskursseilla. Kehitetty malli käyttää koneoppivaa naiivia bayesilaista luokittelualgoritmia analysoimaan opiskelijoiden suoriutumisesta kertynyttä aineistoa. Lähestymistapa perustuu yksinkertaisimpien mahdollisten selittävien mallien periaatteeseen. Lisäksi, tavoitteena oli ehdottaa tätä validoitua ennustavaa mallia varhaiseksi varoitusjärjestelmäksi, jolla ennustetaan putoamisvaarassa olevat opiskelijat opintojakson alkuvaiheessa sekä informoidaan ohjaajia (ja opiskelijaa) aikaisen väliintulon tarpeellisuudesta. Keräsimme aineistoa kahdelta ohjelmoinnin peruskurssilta, jonka pohjalta ennustavaa mallia kehitettiin ja testattiin. Mallit on rakennettu opiskelijoiden ennakkotietojen ja kurssin kestäessä kerättyjen suoriutumistietojen perusteella, joita ohjaajat voivat helposti kerätä tai joihin he voivat päästä käsiksi oppilaitoksesta tai muusta ympäristöstä huolimatta. Lisäksi väitöskirjatyö analysoi valittujen datalähteiden ennustettavuutta ja sitä, mitkä mallien muuttujista ja niiden kombinaatioista tuottivat kannaltamme korkeimman ennustetarkkuuden opiskelijoiden akateemisessa suoriutumisessa. Mallien ennustusten tarkkuuksia laskettiin käyttämällä sekaannusmatriisia, josta saadaan laskettua ennusteen tarkkuus, ennusteen spesifisyys, sensitiivisyys, tasapainotettu tarkkuus sekä luokitteluvastekäyriä (receiver operating characteristics (ROC)) ja näiden luokitteluvastepinta-ala (area under curve (AUC)) Mallit, jotka kehitettiin formatiivisilla tehtävillä, ja joissa ohjaaja saattoi osittain auttaa luokkahuonetilanteessa, antoivat keskimäärin tarkemman ennustuksen putoamisvaarassa olevista opiskelijoista kuin mallit, joissa käytettiin kotiin vietäviä tehtäviä ainoina ennusteina. Tuntemattomalla testiaineistolla tehdyt mallinnukset osoittavat, että voimme tunnistaa jo 3. viikon kohdalla 83% niistä opiskelijoista, jotka tarvitsevat lisätukea 12 viikkoa kestävällä ohjelmoinnin kurssilla. Tulosten perusteella vaikuttaisi, että yhdistämällä metodeja voidaan saavuttaa parempi yleinen ennustettavuus putoamisvaarassa olevien opiskelijoiden suhteen pienemmällä määrällä väärin luokiteltuja epätositapauksia. Tulokset viittaavat myös siihen, että on mahdollista sisällyttää yhdistelmämalli varoitusjärjestelmiin, jotta voidaan tunnistaa avuntarpeessa olevia opiskelijoita ja tarjota täten varhaisessa vaiheessa tukea ennen kuin on liian myöhäistä. Tässä tutkimuksessa esitellyt mallit on kehitetty nojautuen yksinkertaisimman selittävän mallin periaatteeseen ja myös aiempiin tutkimustuloksiin, joissa huomioidaan erilaiset akateemiset ympäristöt ja opiskelijoiden tausta. Ennustava malli voi tarjota indikaattoreita, jotka voivat mahdollisesti toimia pohjana väliintulostrategioihin kurssilta putoamisvaarassa olevien opiskelijoiden tukemiseksi. Tämän tutkimuksen keskeisin anti on malli, jolla opiskelijoiden suoriutumista voidaan arvioida muilla ohjelmointia ja muita aihepiirejä käsittelevillä kursseilla, jotka sisältävät sekä jatkuvaa arviointia että loppukokeen. Malli ennustaisi näillä kursseilla lopullisen opiskelijan suoritustason opetusjakson alkuvaiheessa