A SURVEY ON ANT COLONY OPTIMIZATION ALGORITHM

A novel Ant Colony Optimization algorithm (ACO) combined for the hierarchical multi- label classification problem of protein function prediction. This kind of problem is mainly focused on biometric area, given the large increase in the number of uncharacterized proteins available for analysis and the importance of determining their functions in order to improve the current biological knowledge. Because it is known that a protein can perform more than one function and many protein functional-definition schemes are organized in a hierarchical structure, the classification problem in this case is an instance of a hierarchical multi-label problem. In this classification method, each class might have multiple class labels and class labels are represented in a hierarchical structure—either a tree or a directed acyclic graph (DAG) structure. A more difficult problem than conventional flat classification in this approach, given that the classification algorithm has to take into account hierarchical relationships between class labels and be able to predict multiple class labels for the same example. The proposed ACO algorithm discovers an ordered list of hierarchical multi-label classification rules

Temporal - spatial recognizer for multi-label data

Pattern recognition is an important artificial intelligence task with practical applications in many fields such as medical and species distribution. Such application involves overlapping data points which are demonstrated in the multi- label dataset. Hence, there is a need for a recognition algorithm that can separate the overlapping data points in order to recognize the correct pattern. Existing recognition methods suffer from sensitivity to noise and overlapping points as they could not recognize a pattern when there is a shift in the position of the data points. Furthermore, the methods do not implicate temporal information in the process of recognition, which leads to low quality of data clustering. In this study, an improved pattern recognition method based on Hierarchical Temporal Memory (HTM) is proposed to solve the overlapping in data points of multi- label dataset. The imHTM (Improved HTM) method includes improvement in two of its components; feature extraction and data clustering. The first improvement is realized as TS-Layer Neocognitron algorithm which solves the shift in position problem in feature extraction phase. On the other hand, the data clustering step, has two improvements, TFCM and cFCM (TFCM with limit- Chebyshev distance metric) that allows the overlapped data points which occur in patterns to be separated correctly into the relevant clusters by temporal clustering. Experiments on five datasets were conducted to compare the proposed method (imHTM) against statistical, template and structural pattern recognition methods. The results showed that the percentage of success in recognition accuracy is 99% as compared with the template matching method (Featured-Based Approach, Area-Based Approach), statistical method (Principal Component Analysis, Linear Discriminant Analysis, Support Vector Machines and Neural Network) and structural method (original HTM). The findings indicate that the improved HTM can give an optimum pattern recognition accuracy, especially the ones in multi- label dataset

Mitmekesiste bioloogiliste andmete ühendamine ja analüüs

Väitekirja elektrooniline versioon ei sisalda publikatsiooneTänu tehnoloogiate arengule on bioloogiliste andmete maht viimastel aastatel mitmekordistunud. Need andmed katavad erinevaid bioloogia valdkondi. Piirdudes vaid ühe andmestikuga saab bioloogilisi protsesse või haigusi uurida vaid ühest aspektist korraga. Seetõttu on tekkinud üha suurem vajadus masinõppe meetodite järele, mis aitavad kombineerida eri valdkondade andmeid, et uurida bioloogilisi protsesse tervikuna. Lisaks on nõudlus usaldusväärsete haigusspetsiifiliste andmestike kogude järele, mis võimaldaks vastavaid analüüse efektiivsemalt läbi viia. Käesolev väitekiri kirjeldab, kuidas rakendada masinõppel põhinevaid integratsiooni meetodeid erinevate bioloogiliste küsimuste uurimiseks. Me näitame kuidas integreeritud andmetel põhinev analüüs võimaldab paremini aru saada bioloogilistes protsessidest kolmes valdkonnas: Alzheimeri tõbi, toksikoloogia ja immunoloogia. Alzheimeri tõbi on vanusega seotud neurodegeneratiivne haigus millel puudub efektiivne ravi. Väitekirjas näitame, kuidas integreerida erinevaid Alzheimeri tõve spetsiifilisi andmestikke, et moodustada heterogeenne graafil põhinev Alzheimeri spetsiifiline andmestik HENA. Seejärel demonstreerime süvaõppe meetodi, graafi konvolutsioonilise tehisnärvivõrgu, rakendamist HENA-le, et leida potentsiaalseid haigusega seotuid geene. Teiseks uurisime kroonilist immuunpõletikulist haigust psoriaasi. Selleks kombineerisime patsientide verest ja nahast pärinevad laboratoorsed mõõtmised kliinilise infoga ning integreerisime vastavad analüüside tulemused tuginedes valdkonnaspetsiifilistel teadmistel. Töö viimane osa keskendub toksilisuse testimise strateegiate edasiarendusele. Toksilisuse testimine on protsess, mille käigus hinnatakse, kas uuritavatel kemikaalidel esineb organismile kahjulikke toimeid. See on vajalik näiteks ravimite ohutuse hindamisel. Töös me tuvastasime sarnase toimemehhanismiga toksiliste ühendite rühmad. Lisaks arendasime klassifikatsiooni mudeli, mis võimaldab hinnata uute ühendite toksilisust.A fast advance in biotechnological innovation and decreasing production costs led to explosion of experimental data being produced in laboratories around the world. Individual experiments allow to understand biological processes, e.g. diseases, from different angles. However, in order to get a systematic view on disease it is necessary to combine these heterogeneous data. The large amounts of diverse data requires building machine learning models that can help, e.g. to identify which genes are related to disease. Additionally, there is a need to compose reliable integrated data sets that researchers could effectively work with. In this thesis we demonstrate how to combine and analyze different types of biological data in the example of three biological domains: Alzheimer’s disease, immunology, and toxicology. More specifically, we combine data sets related to Alzheimer’s disease into a novel heterogeneous network-based data set for Alzheimer’s disease (HENA). We then apply graph convolutional networks, state-of-the-art deep learning methods, to node classification task in HENA to find genes that are potentially associated with the disease. Combining patient’s data related to immune disease helps to uncover its pathological mechanisms and to find better treatments in the future. We analyse laboratory data from patients’ skin and blood samples by combining them with clinical information. Subsequently, we bring together the results of individual analyses using available domain knowledge to form a more systematic view on the disease pathogenesis. Toxicity testing is the process of defining harmful effects of the substances for the living organisms. One of its applications is safety assessment of drugs or other chemicals for a human organism. In this work we identify groups of toxicants that have similar mechanism of actions. Additionally, we develop a classification model that allows to assess toxic actions of unknown compounds.https://www.ester.ee/record=b523255

Fitness Proportionate Niching: Harnessing The Power Of Evolutionary Algorithms For Evolving Cooperative Populations And Dynamic Clustering

Evolutionary algorithms work on the notion of best fit will survive criteria. This makes evolving a cooperative and diverse population in a competing environment via evolutionary algorithms a challenging task. Analogies to species interactions in natural ecological systems have been used to develop methods for maintaining diversity in a population. One such area that mimics species interactions in natural systems is the use of niching. Niching methods extend the application of EAs to areas that seeks to embrace multiple solutions to a given problem. The conventional fitness sharing technique has limitations when the multimodal fitness landscape has unequal peaks. Higher peaks are strong population attractors. And this technique suffers from the curse of population size in attempting to discover all optimum points. The use of high population size makes the technique computationally complex, especially when there is a big jump in fitness values of the peaks. This work introduces a novel bio-inspired niching technique, termed Fitness Proportionate Niching (FPN), based on the analogy of finite resource model where individuals share the resource of a niche in proportion to their actual fitness. FPN makes the search algorithm unbiased to the variation in fitness values of the peaks and hence mitigates the drawbacks of conventional fitness sharing. FPN extends the global search ability of Genetic Algorithms (GAs) for evolving hierarchical cooperation in genetics-based machine learning and dynamic clustering. To this end, this work introduces FPN based resource sharing which leads to the formation of a viable default hierarchy in classifiers for the first time. It results in the co-evolution of default and exception rules, which lead to a robust and concise model description. The work also explores the feasibility and success of FPN for dynamic clustering. Unlike most other clustering techniques, FPN based clustering does not require any a priori information on the distribution of the data

Water filtration by using apple and banana peels as activated carbon

Water filter is an important devices for reducing the contaminants in raw water. Activated from charcoal is used to absorb the contaminants. Fruit peels are some of the suitable alternative carbon to substitute the charcoal. Determining the role of fruit peels which were apple and banana peels powder as activated carbon in water filter is the main goal. Drying and blending the peels till they become powder is the way to allow them to absorb the contaminants. Comparing the results for raw water before and after filtering is the observation. After filtering the raw water, the reading for pH was 6.8 which is in normal pH and turbidity reading recorded was 658 NTU. As for the colour, the water becomes more clear compared to the raw water. This study has found that fruit peels such as banana and apple are an effective substitute to charcoal as natural absorbent

Machine learning and applications in microbiology

To understand the intricacies of microorganisms at the molecular level requires making sense of copious volumes of data such that it may now be humanly impossible to detect insightful data patterns without an artificial intelligence application called machine learning. Applying machine learning to address biological problems is expected to grow at an unprecedented rate, yet it is perceived by the uninitiated as a mysterious and daunting entity entrusted to the domain of mathematicians and computer scientists. The aim of this review is to identify key points required to start the journey of becoming an effective machine learning practitioner. These key points are further reinforced with an evaluation of how machine learning has been applied so far in a broad scope of real-life microbiology examples. This includes predicting drug targets or vaccine candidates, diagnosing microorganisms causing infectious diseases, classifying drug resistance against antimicrobial medicines, predicting disease outbreaks and exploring microbial interactions. Our hope is to inspire microbiologists and other related researchers to join the emerging machine learning revolution