Improving rule-based classification using Harmony Search.
Ontology highlight
ABSTRACT:
SUBMITTER: Hasanpour H
PROVIDER: S-EPMC7924428 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Relating chemical features to bioactivities is critical in molecular design and is used extensively in the lead discovery and optimization process. A variety of techniques from statistics, data mining and machine learning have been applied to this process. In this study, we utilize a collection of methods, called associative classification mining (ACM), which are popular in the data mining community, but so far have not been applied widely in cheminformatics. More specifically, classification based on predictive association rules (CPAR), classification based on multiple association rules (CMAR) and classification based on association rules (CBA) are employed on three datasets using various descriptor sets. Experimental evaluations on anti-tuberculosis (antiTB), mutagenicity and hERG (the human Ether-a-go-go-Related Gene) blocker datasets show that these three methods are computationally scalable and appropriate for high speed mining. Additionally, they provide comparable accuracy and efficiency to the commonly used Bayesian and support vector machines (SVM) methods, and produce highly interpretable models.
| S-EPMC3515428 | biostudies-literature
Project description:With the rapid increase in social networks and blogs, the social media services are increasingly being used by online communities to share their views and experiences about a particular product, policy and event. Due to economic importance of these reviews, there is growing trend of writing user reviews to promote a product. Nowadays, users prefer online blogs and review sites to purchase products. Therefore, user reviews are considered as an important source of information in Sentiment Analysis (SA) applications for decision making. In this work, we exploit the wealth of user reviews, available through the online forums, to analyze the semantic orientation of words by categorizing them into +ive and -ive classes to identify and classify emoticons, modifiers, general-purpose and domain-specific words expressed in the public's feedback about the products. However, the un-supervised learning approach employed in previous studies is becoming less efficient due to data sparseness, low accuracy due to non-consideration of emoticons, modifiers, and presence of domain specific words, as they may result in inaccurate classification of users' reviews. Lexicon-enhanced sentiment analysis based on Rule-based classification scheme is an alternative approach for improving sentiment classification of users' reviews in online communities. In addition to the sentiment terms used in general purpose sentiment analysis, we integrate emoticons, modifiers and domain specific terms to analyze the reviews posted in online communities. To test the effectiveness of the proposed method, we considered users reviews in three domains. The results obtained from different experiments demonstrate that the proposed method overcomes limitations of previous methods and the performance of the sentiment analysis is improved after considering emoticons, modifiers, negations, and domain specific terms when compared to baseline methods.
| S-EPMC5322980 | biostudies-literature
Project description:BackgroundProtein-protein interactions (PPI) can be classified according to their characteristics into, for example obligate or transient interactions. The identification and characterization of these PPI types may help in the functional annotation of new protein complexes and in the prediction of protein interaction partners by knowledge driven approaches.ResultsThis work addresses pattern discovery of the interaction sites for four different interaction types to characterize and uses them for the prediction of PPI types employing Association Rule Based Classification (ARBC) which includes association rule generation and posterior classification. We incorporated domain information from protein complexes in SCOP proteins and identified 354 domain-interaction sites. 14 interface properties were calculated from amino acid and secondary structure composition and then used to generate a set of association rules characterizing these domain-interaction sites employing the APRIORI algorithm. Our results regarding the classification of PPI types based on a set of discovered association rules shows that the discriminative ability of association rules can significantly impact on the prediction power of classification models. We also showed that the accuracy of the classification can be improved through the use of structural domain information and also the use of secondary structure content.ConclusionThe advantage of our approach is that we can extract biologically significant information from the interpretation of the discovered association rules in terms of understandability and interpretability of rules. A web application based on our method can be found at http://bioinfo.ssu.ac.kr/~shpark/picasso/
| S-EPMC2667511 | biostudies-literature
Project description:In the i2b2 Medication Extraction Challenge, medication names together with details of their administration were to be extracted from medical discharge summaries.The task of the challenge was decomposed into three pipelined components: named entity identification, context-aware filtering and relation extraction. For named entity identification, first a rule-based (RB) method that was used in our overall fifth place-ranked solution at the challenge was investigated. Second, a conditional random fields (CRF) approach is presented for named entity identification (NEI) developed after the completion of the challenge. The CRF models are trained on the 17 ground truth documents, the output of the rule-based NEI component on all documents, a larger but potentially inaccurate training dataset. For both NEI approaches their effect on relation extraction performance was investigated. The filtering and relation extraction components are both rule-based.In addition to the official entry level evaluation of the challenge, entity level analysis is also provided.On the test data an entry level F(1)-score of 80% was achieved for exact matching and 81% for inexact matching with the RB-NEI component. The CRF produces a significantly weaker result, but CRF outperforms the rule-based model with 81% exact and 82% inexact F(1)-score (p<0.02).This study shows that a simple rule-based method is on a par with more complicated machine learners; CRF models can benefit from the addition of the potentially inaccurate training data, when only very few training documents are available. Such training data could be generated using the outputs of rule-based methods.
| S-EPMC2995683 | biostudies-other
Project description:Constructing a robust emotion-aware analytical framework using non-invasively recorded electroencephalogram (EEG) signals has gained intensive attentions nowadays. However, as deploying a laboratory-oriented proof-of-concept study toward real-world applications, researchers are now facing an ecological challenge that the EEG patterns recorded in real life substantially change across days (i.e., day-to-day variability), arguably making the pre-defined predictive model vulnerable to the given EEG signals of a separate day. The present work addressed how to mitigate the inter-day EEG variability of emotional responses with an attempt to facilitate cross-day emotion classification, which was less concerned in the literature. This study proposed a robust principal component analysis (RPCA)-based signal filtering strategy and validated its neurophysiological validity and machine-learning practicability on a binary emotion classification task (happiness vs. sadness) using a five-day EEG dataset of 12 subjects when participated in a music-listening task. The empirical results showed that the RPCA-decomposed sparse signals (RPCA-S) enabled filtering off the background EEG activity that contributed more to the inter-day variability, and predominately captured the EEG oscillations of emotional responses that behaved relatively consistent along days. Through applying a realistic add-day-in classification validation scheme, the RPCA-S progressively exploited more informative features (from 12.67 ± 5.99 to 20.83 ± 7.18) and improved the cross-day binary emotion-classification accuracy (from 58.31 ± 12.33% to 64.03 ± 8.40%) as trained the EEG signals from one to four recording days and tested against one unseen subsequent day. The original EEG features (prior to RPCA processing) neither achieved the cross-day classification (the accuracy was around chance level) nor replicated the encouraging improvement due to the inter-day EEG variability. This result demonstrated the effectiveness of the proposed method and may shed some light on developing a realistic emotion-classification analytical framework alleviating day-to-day variability.
| S-EPMC5515900 | biostudies-other
Project description:Background: Adverse events (AEs) can be caused not only by one drug but also by the interaction between two or more drugs. Therefore, clarifying whether an AE is due to a specific suspect drug or drug-drug interaction (DDI) is useful information for proper use of drugs. Whereas previous reports on the search for drug-induced AEs with signal detection using spontaneous reporting systems (SRSs) are numerous, reports on drug interactions are limited. This is because in methods that use "a safety signal indicator" (signal), which is frequently used in pharmacovigilance, a huge number of combinations must be prepared when signal detection is performed, and each risk index must be calculated, which makes interaction search appear unrealistic. Objective: In this paper, we propose association rule mining (AR) using large dataset analysis as an alternative to the conventional methods (additive interaction model (AI) and multiplicative interaction model (MI)). Methods: The data source used was the Japanese Adverse Drug Event Report database. The combination of drugs for which the risk index is detected by the "combination risk ratio (CR)" as the target was assumed to be true data, and the accuracy of signal detection using the AR methods was evaluated in terms of sensitivity, specificity, Youden's index, F-score. Results: Our experimental results targeting Stevens-Johnson syndrome indicate that AR has a sensitivity of 99.05%, specificity of 92.60%, Youden's index of 0.917, F-score of 0.876, AI has a sensitivity of 95.62%, specificity of 96.92%, Youden's index of 0.925, and F-score of 0.924, and MI has a sensitivity of 65.46%, specificity of 98.78%, Youden's index of 0.642, and F-score of 0.771. This result was about the same level as or higher than the conventional method. Conclusions: If you use similar calculation methods to create combinations from the database, not only for SJS, but for all AEs, the number of combinations would be so enormous that it would be difficult to perform the calculations. However, in the AR method, the "Apriori algorithm" is used to reduce the number of calculations. Thus, the proposed method has the same detection power as the conventional methods, with the significant advantage that its calculation process is simple.
| S-EPMC5854950 | biostudies-literature
Project description:Advances in high-throughput sequencing technologies have made it possible to access millions of measurements from thousands of people. Single nucleotide polymorphisms (SNPs), the most common type of mutation in the human genome, have been shown to play a significant role in the development of complex and multifactorial diseases. However, studying the synergistic interactions between different SNPs in explaining multifactorial diseases is challenging due to the high dimensionality of the data and methodological complexities. Existing solutions often use a multi-objective approach based on metaheuristic optimization algorithms such as harmony search. However, previous studies have shown that using a multi-objective approach is not sufficient to address complex disease models with no or low marginal effect. In this research, we introduce a locus-driven harmony search (LDHS), an improved harmony search algorithm that focuses on using SNP locus information and genetic inheritance patterns to initialize harmony memories. The proposed method integrates biological knowledge to improve harmony memory initialization by adding SNP combinations that are likely candidates for interaction and disease causation. Using a SNP grouping process, LDHS generates harmonies that include SNPs with a higher potential for interaction, resulting in greater power in detecting disease-causing SNP combinations. The performance of the proposed algorithm was evaluated on 200 synthesized datasets for disease models with and without marginal effect. The results show significant improvement in the power of the algorithm to find disease-related SNP sets while decreasing computational cost compared to state-of-the-art algorithms. The proposed algorithm also demonstrated notable performance on real breast cancer data, showing that integrating prior knowledge can significantly improve the process of detecting disease-related SNPs in both real and synthesized data.
| S-EPMC10575495 | biostudies-literature
Project description:BackgroundA variety of key activities within life sciences research involves integrating and intelligently managing large amounts of biochemical information. Semantic technologies provide an intuitive way to organise and sift through these rapidly growing datasets via the design and maintenance of ontology-supported knowledge bases. To this end, OWL-a W3C standard declarative language- has been extensively used in the deployment of biochemical ontologies that can be conveniently organised using the classification facilities of OWL-based tools. One of the most established ontologies for the chemical domain is ChEBI, an open-access dictionary of molecular entities that supplies high quality annotation and taxonomical information for biologically relevant compounds. However, ChEBI is being manually expanded which hinders its potential to grow due to the limited availability of human resources.ResultsIn this work, we describe a prototype that performs automatic classification of chemical compounds. The software we present implements a sound and complete reasoning procedure of a formalism that extends datalog and builds upon an off-the-shelf deductive database system. We capture a wide range of chemical classes that are not expressible with OWL-based formalisms such as cyclic molecules, saturated molecules and alkanes. Furthermore, we describe a surface 'less-logician-like' syntax that allows application experts to create ontological descriptions of complex biochemical objects without prior knowledge of logic. In terms of performance, a noticeable improvement is observed in comparison with previous approaches. Our evaluation has discovered subsumptions that are missing from the manually curated ChEBI ontology as well as discrepancies with respect to existing subclass relations. We illustrate thus the potential of an ontology language suitable for the life sciences domain that exhibits a favourable balance between expressive power and practical feasibility.ConclusionsOur proposed methodology can form the basis of an ontology-mediated application to assist biocurators in the production of complete and error-free taxonomies. Moreover, such a tool could contribute to a more rapid development of the ChEBI ontology and to the efforts of the ChEBI team to make annotated chemical datasets available to the public. From a modelling point of view, our approach could stimulate the adoption of a different and expressive reasoning paradigm based on rules for which state-of-the-art and highly optimised reasoners are available; it could thus pave the way for the representation of a broader spectrum of life sciences and biomedical knowledge.
| S-EPMC4040517 | biostudies-literature
Project description:Fake news is a complex problem that leads to different approaches used to identify them. In our paper, we focus on identifying fake news using its content. The used dataset containing fake and real news was pre-processed using syntactic analysis. Dependency grammar methods were used for the sentences of the dataset and based on them the importance of each word within the sentence was determined. This information about the importance of words in sentences was utilized to create the input vectors for classifications. The paper aims to find out whether it is possible to use the dependency grammar to improve the classification of fake news. We compared these methods with the TfIdf method. The results show that it is possible to use the dependency grammar information with acceptable accuracy for the classification of fake news. An important finding is that the dependency grammar can improve existing techniques. We have improved the traditional TfIdf technique in our experiment.
| S-EPMC8439466 | biostudies-literature
Project description:BackgroundAccurate identification of protein complexes in protein-protein interaction (PPI) networks is crucial for understanding the principles of cellular organization. Most computational methods ignore the fact that proteins in a protein complex have a functional similarity and are co-localized and co-expressed at the same place and time, respectively. Meanwhile, the parameters of the current methods are specified by users, so these methods cannot effectively deal with different input PPI networks.ResultTo address these issues, this study proposes a new method called MP-AHSA to detect protein complexes with Multiple Properties (MP), and an Adaptation Harmony Search Algorithm is developed to optimize the parameters of the MP algorithm. First, a weighted PPI network is constructed using functional annotations, and multiple biological properties and the Markov cluster algorithm (MCL) are used to mine protein complex cores. Then, a fitness function is defined, and a protein complex forming strategy is designed to detect attachment proteins and form protein complexes. Next, a protein complex filtering strategy is formulated to filter out the protein complexes. Finally, an adaptation harmony search algorithm is developed to determine the MP algorithm's parameters automatically.ConclusionsExperimental results show that the proposed MP-AHSA method outperforms 14 state-of-the-art methods for identifying protein complexes. Also, the functional enrichment analyses reveal that the protein complexes identified by the MP-AHSA algorithm have significant biological relevance.
| S-EPMC9541083 | biostudies-literature