iATC-NRAKEL: an efficient multi-label classifier for recognizing anatomical therapeutic chemical classes of drugs

Abstract Motivation The anatomical therapeutic chemical (ATC) classification system plays an increasingly important role in drug repositioning and discovery. The correct identification of classes in each level of such system that a given drug may belong to is an essential problem. Several multi-label classifiers have been proposed in this regard. Although they provided satisfactory performance, the feature extraction procedures were still rough. More refined features may further improve the predicted quality. Results In this article, we provide a novel multi-label classifier, called iATC-NRAKEL, to predict drug ATC classes in the first level. To obtain more informative drug features, we employed the drug association information in STITCH and KEGG, which was organized by seven drug networks. The powerful network embedding algorithm, Mashup, was adopted to extract informative drug features. The obtained features were fed into the RAndom k-labELsets (RAKEL) algorithm with support vector machine as the basic classification algorithm to construct the classifier. The 10-fold cross-validation of the benchmark dataset with 3883 drugs showed that the accuracy and absolute true were 76.56 and 74.51%, respectively. The comparison results indicated that iATC-NRAKEL was much superior to all previous reported classifiers. Finally, the contribution of each network was analyzed. Availability and implementation The codes of iATC-NRAKEL are available at https://github.com/zhou256/iATC-NRAKEL.

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Hierarchy-Based File Fragment Classification

Machine Learning and Knowledge Extraction ◽

10.3390/make2030012 ◽

2020 ◽

Vol 2 (3) ◽

pp. 216-232

Author(s):

Manish Bhatt ◽

Avdesh Mishra ◽

Md Wasi Ul Kabir ◽

S. E. Blake-Gatto ◽

Rishav Rajendra ◽

...

Keyword(s):

Cross Validation ◽

Hierarchical Classification ◽

Future Research ◽

Support Vector ◽

Challenging Problem ◽

Fine Grain ◽

Average Accuracy ◽

Vector Machines ◽

Essential Problem ◽

Fold Cross Validation

File fragment classification is an essential problem in digital forensics. Although several attempts had been made to solve this challenging problem, a general solution has not been found. In this work, we propose a hierarchical machine-learning-based approach with optimized support vector machines (SVM) as the base classifiers for file fragment classification. This approach consists of more general classifiers at the top level and more specialized fine-grain classifiers at the lower levels of the hierarchy. We also propose a primitive taxonomy for file types that can be used to perform hierarchical classification. We evaluate our model with a dataset of 14 file types, with 1000 fragments measuring 512 bytes from each file type derived from a subset of the publicly available Digital Corpora, the govdocs1 corpus. Our experiment shows comparable results to the present literature, with an average accuracy of 67.78% and an F1-measure of 65% using 10-fold cross-validation. We then improve on the hierarchy and find better results, with an increase in the F1-measure of 1%. Finally, we make our assessment and observations, then conclude the paper by discussing the scope of future research.

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Drug repositioning by prediction of drug’s anatomical therapeutic chemical code via network-based inference approaches

Briefings in Bioinformatics ◽

10.1093/bib/bbaa027 ◽

2020 ◽

Cited By ~ 4

Author(s):

Yayuan Peng ◽

Manjiong Wang ◽

Yixiang Xu ◽

Zengrui Wu ◽

Jiye Wang ◽

...

Keyword(s):

Cross Validation ◽

Drug Repositioning ◽

Anatomical Therapeutic Chemical ◽

External Validation ◽

Chemical Properties ◽

Glucose Deprivation ◽

Target Drug ◽

Validation Set ◽

Fold Cross Validation

Abstract Drug discovery and development is a time-consuming and costly process. Therefore, drug repositioning has become an effective approach to address the issues by identifying new therapeutic or pharmacological actions for existing drugs. The drug’s anatomical therapeutic chemical (ATC) code is a hierarchical classification system categorized as five levels according to the organs or systems that drugs act and the pharmacology, therapeutic and chemical properties of drugs. The 2nd-, 3rd- and 4th-level ATC codes reserved the therapeutic and pharmacological information of drugs. With the hypothesis that drugs with similar structures or targets would possess similar ATC codes, we exploited a network-based approach to predict the 2nd-, 3rd- and 4th-level ATC codes by constructing substructure drug-ATC (SD-ATC), target drug-ATC (TD-ATC) and Substructure&Target drug-ATC (STD-ATC) networks. After 10-fold cross validation and two external validations, the STD-ATC models outperformed the SD-ATC and TD-ATC ones. Furthermore, with KR as fingerprint, the STD-ATC model was identified as the optimal model with AUC values at 0.899 ± 0.015, 0.916 and 0.893 for 10-fold cross validation, external validation set 1 and external validation set 2, respectively. To illustrate the predictive capability of the STD-ATC model with KR fingerprint, as a case study, we predicted 25 FDA-approved drugs (22 drugs were actually purchased) to have potential activities on heart failure using that model. Experiments in vitro confirmed that 8 of the 22 old drugs have shown mild to potent cardioprotective activities on both hypoxia model and oxygen–glucose deprivation model, which demonstrated that our STD-ATC prediction model would be an effective tool for drug repositioning.

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Combination of Support Vector Machine and K-Fold cross-validation for prediction of long-term degradation of the compressive strength of marine concrete

International Journal of Computational Physics Series ◽

10.29167/a1i1p120-130 ◽

2018 ◽

Vol 1 (1) ◽

pp. 120-130 ◽

Cited By ~ 1

Author(s):

Chunxiang Qian ◽

Wence Kang ◽

Hao Ling ◽

Hua Dong ◽

Chengyao Liang ◽

...

Keyword(s):

Support Vector Machine ◽

Environmental Factors ◽

Cross Validation ◽

Concrete Strength ◽

Simulation Method ◽

Support Vector ◽

Svm Model ◽

Artificial Neural Network Ann ◽

Influence Degree ◽

Fold Cross Validation

Support Vector Machine (SVM) model optimized by K-Fold cross-validation was built to predict and evaluate the degradation of concrete strength in a complicated marine environment. Meanwhile, several mathematical models, such as Artificial Neural Network (ANN) and Decision Tree (DT), were also built and compared with SVM to determine which one could make the most accurate predictions. The material factors and environmental factors that influence the results were considered. The materials factors mainly involved the original concrete strength, the amount of cement replaced by fly ash and slag. The environmental factors consisted of the concentration of Mg2+, SO42-, Cl-, temperature and exposing time. It was concluded from the prediction results that the optimized SVM model appeared to perform better than other models in predicting the concrete strength. Based on SVM model, a simulation method of variables limitation was used to determine the sensitivity of various factors and the influence degree of these factors on the degradation of concrete strength.

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Pengenalan Wajah Manusia berbasis Algoritma Local Binary Pattern

Emitor: Jurnal Teknik Elektro ◽

10.23917/emitor.v17i2.6232 ◽

2017 ◽

Vol 17 (2) ◽

pp. 29-38

Author(s):

Ratih Purwati ◽

Gunawan Ariyanto

Keyword(s):

Computer Vision ◽

Support Vector Machine ◽

Face Recognition ◽

Local Binary Pattern ◽

Cross Validation ◽

Support Vector ◽

Fold Cross Validation

Face Recognition merupakan teknologi komputer untuk mengidentifikasi wajah manusia melalui gambar digital yang tersimpan di database. Wajah manusia dapat berubah bentuk sesuai dengan ekspresi yang dimilikinya. Wajah manusia dapat berubah bentuk sesuai dengan eskpresi yang dimilikinya. Ekspresi wajah manusia memiliki kemiripan satu sama lain sehingga untuk mengenali suatu ekspresi adalah kepunyaan siapa akan sedikit sulit. Pengenalan wajah terus menjadi topik aktif di zaman sekarang pada penelitian bidang computer vision. Penggunaan wajah manusia sering kita jumpai pada fitur-fitur aplikasi media sosial seperti Snapchat, Snapgram dari Instagram dan banyak aplikasi sosial media lainnya yang menggunakan teknologi tersebut. Pada penelitian ini dilakukan analisa pengenalan ekpresi wajah manusia dengan pendekatan fitur alogaritma Local Binary Pattern dan mencari pengembangan alogaritma dasar Local Binary Pattern yang paling optimal dengan cara menggabungkan metode Hisogram Equalization, Support Vector Machine, dan K-fold cross validation sehingga dapat meningkatkan pengenalan gambar wajah manusia pada hasil yang terbaik. Penelitian ini menginput beberapa database wajah manusia seperti JAFFE yang merupakan gambar wajah manusia wanita jepang yang berjumlah 10 orang dengan 7 ekspresi emosional seperti marah, sedih, bahagia, jijik, kaget, takut dan netral ke dalam sistem. YALE yaitu merupakan gambar wajah manusia orang Amerika. Serta menggunakan dataset CALTECH yang merupakan gambar manusia yang terdiri dari 450 gambar dengan ukuran 896 x 592 piksel dan disimpan dalam format JPEG. Kemudian data tersebut di sesuaikan dengan bentuk tekstur wajah masing-masing. Dari hasil penggabungan ketiga metode diatas dan percobaan-percobaan yang sudah dilakukan, didapatkan hasil yang paling optimal dalam pengenalan wajah manusia yaitu menggunakan dataset JAFFE dengan resolusi 92 x 112 piksel dan dengan tingkat penggunaan processor yang tinggi dapat mempengaruhi waktu kecepatan komputasi dalam proses menjalankan sistem sehingga menghasilkan prediksi yang lebih tepat.

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Abstract 473: Identification of Apolipoproteins Using Feature Selection Technique

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.36.suppl_1.473 ◽

2016 ◽

Vol 36 (suppl_1) ◽

Author(s):

Hua Tang ◽

Hao Lin

Keyword(s):

Support Vector Machine ◽

Cross Validation ◽

Support Vector ◽

Feature Subset ◽

Risk Markers ◽

Dipeptide Composition ◽

Accurate Identification ◽

Feature Selection Technique ◽

Physiological Importance ◽

Fold Cross Validation

Objective: Apolipoproteins are of great physiological importance and are associated with different diseases such as dyslipidemia, thrombogenesis and angiocardiopathy. Apolipoproteins have therefore emerged as key risk markers and important research targets yet the types of apolipoproteins has not been fully elucidated. Accurate identification of the apoliproproteins is very crucial to the comprehension of cardiovascular diseases and drug design. The aim of this study is to develop a powerful model to precisely identify apolipoproteins. Approach and Results: We manually collected a non-redundant dataset of 53 apoliproproteins and 136 non-apoliproproteins with the sequence identify of less than 40% from UniProt. After formulating the protein sequence samples with g -gap dipeptide composition (here g =1~10), the analysis of various (ANOVA) was adopted to find out the best feature subset which can achieve the best accuracy. Support Vector Machine (SVM) was then used to perform classification. The predictive model was evaluated using a five-fold cross-validation which yielded a sensitivity of 96.2%, a specificity of 99.3%, and an accuracy of 98.4%. The study indicated that the proposed method could be a feasible means of conducting preliminary analyses of apoliproproteins. Conclusion: We demonstrated that apoliproproteins can be predicted from their primary sequences. Also we discovered the special dipeptide distribution in apoliproproteins. These findings open new perspectives to improve apoliproproteins prediction by considering the specific dipeptides. We expect that these findings will help to improve drug development in anti-angiocardiopathy disease. Key words: Apoliproproteins Angiocardiopathy Support Vector Machine

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The Animal Classification: An Evaluation of Different Transfer Learning Pipeline

Mekatronika ◽

10.15282/mekatronika.v3i1.6680 ◽

2021 ◽

Vol 3 (1) ◽

pp. 27-31

Author(s):

Ken-ji Ee ◽

Ahmad Fakhri Bin Ab. Nasir ◽

Anwar P. P. Abdul Majeed ◽

Mohd Azraai Mohd Razman ◽

Nur Hafieza Ismail

Keyword(s):

Transfer Learning ◽

Classification System ◽

Cross Validation ◽

Support Vector ◽

Svm Classifier ◽

Average Classification Accuracy ◽

Validation Technique ◽

Search Approach ◽

Fold Cross Validation

The animal classification system is a technology to classify the animal class (type) automatically and useful in many applications. There are many types of learning models applied to this technology recently. Nonetheless, it is worth noting that the extraction of the features and the classification of the animal features is non-trivial, particularly in the deep learning approach for a successful animal classification system. The use of Transfer Learning (TL) has been demonstrated to be a powerful tool in the extraction of essential features. However, the employment of such a method towards animal classification applications are somewhat limited. The present study aims to determine a suitable TL-conventional classifier pipeline for animal classification. The VGG16 and VGG19 were used in extracting features and then coupled with either k-Nearest Neighbour (k-NN) or Support Vector Machine (SVM) classifier. Prior to that, a total of 4000 images were gathered consisting of a total of five classes which are cows, goats, buffalos, dogs, and cats. The data was split into the ratio of 80:20 for train and test. The classifiers hyper parameters are tuned by the Grids Search approach that utilises the five-fold cross-validation technique. It was demonstrated from the study that the best TL pipeline identified is the VGG16 along with an optimised SVM, as it was able to yield an average classification accuracy of 0.975. The findings of the present investigation could facilitate animal classification application, i.e. for monitoring animals in wildlife.

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A novel computational model for predicting potential LncRNA-disease associations based on both direct and indirect features of LncRNA-disease pairs

BMC Bioinformatics ◽

10.1186/s12859-020-03906-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Yubin Xiao ◽

Zheng Xiao ◽

Xiang Feng ◽

Zhiping Chen ◽

Linai Kuang ◽

...

Keyword(s):

Computational Model ◽

Cross Validation ◽

State Of The Art ◽

Prediction Methods ◽

Good Prediction ◽

Average Case ◽

Comparison Results ◽

Disease Associations ◽

Fold Cross Validation

Abstract Background Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships between lncRNAs and diseases. Due to the high costs and time complexity of traditional bio-experiments, in recent years, more and more computational methods have been proposed by researchers to infer potential lncRNA-disease associations. However, there exist all kinds of limitations in these state-of-the-art prediction methods as well. Results In this manuscript, a novel computational model named FVTLDA is proposed to infer potential lncRNA-disease associations. In FVTLDA, its major novelty lies in the integration of direct and indirect features related to lncRNA-disease associations such as the feature vectors of lncRNA-disease pairs and their corresponding association probability fractions, which guarantees that FVTLDA can be utilized to predict diseases without known related-lncRNAs and lncRNAs without known related-diseases. Moreover, FVTLDA neither relies solely on known lncRNA-disease nor requires any negative samples, which guarantee that it can infer potential lncRNA-disease associations more equitably and effectively than traditional state-of-the-art prediction methods. Additionally, to avoid the limitations of single model prediction techniques, we combine FVTLDA with the Multiple Linear Regression (MLR) and the Artificial Neural Network (ANN) for data analysis respectively. Simulation experiment results show that FVTLDA with MLR can achieve reliable AUCs of 0.8909, 0.8936 and 0.8970 in 5-Fold Cross Validation (fivefold CV), 10-Fold Cross Validation (tenfold CV) and Leave-One-Out Cross Validation (LOOCV), separately, while FVTLDA with ANN can achieve reliable AUCs of 0.8766, 0.8830 and 0.8807 in fivefold CV, tenfold CV, and LOOCV respectively. Furthermore, in case studies of gastric cancer, leukemia and lung cancer, experiment results show that there are 8, 8 and 8 out of top 10 candidate lncRNAs predicted by FVTLDA with MLR, and 8, 7 and 8 out of top 10 candidate lncRNAs predicted by FVTLDA with ANN, having been verified by recent literature. Comparing with the representative prediction model of KATZLDA, comparison results illustrate that FVTLDA with MLR and FVTLDA with ANN can achieve the average case study contrast scores of 0.8429 and 0.8515 respectively, which are both notably higher than the average case study contrast score of 0.6375 achieved by KATZLDA. Conclusion The simulation results show that FVTLDA has good prediction performance, which is a good supplement to future bioinformatics research.

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Predictor Selection for Bacterial Vaginosis Diagnosis Using Decision Tree and Relief Algorithms

Applied Sciences ◽

10.3390/app10093291 ◽

2020 ◽

Vol 10 (9) ◽

pp. 3291

Author(s):

Jesús F. Pérez-Gómez ◽

Juana Canul-Reich ◽

José Hernández-Torruco ◽

Betania Hernández-Ocaña

Keyword(s):

Feature Selection ◽

Decision Tree ◽

Bacterial Vaginosis ◽

Cross Validation ◽

Performance Comparison ◽

Support Vector ◽

Ongoing Research ◽

Selection For ◽

Comparison Of The Results ◽

Fold Cross Validation

Requiring only a few relevant characteristics from patients when diagnosing bacterial vaginosis is highly useful for physicians as it makes it less time consuming to collect these data. This would result in having a dataset of patients that can be more accurately diagnosed using only a subset of informative or relevant features in contrast to using the entire set of features. As such, this is a feature selection (FS) problem. In this work, decision tree and Relief algorithms were used as feature selectors. Experiments were conducted on a real dataset for bacterial vaginosis with 396 instances and 252 features/attributes. The dataset was obtained from universities located in Baltimore and Atlanta. The FS algorithms utilized feature rankings, from which the top fifteen features formed a new dataset that was used as input for both support vector machine (SVM) and logistic regression (LR) algorithms for classification. For performance evaluation, averages of 30 runs of 10-fold cross-validation were reported, along with balanced accuracy, sensitivity, and specificity as performance measures. A performance comparison of the results was made between using the total number of features against using the top fifteen. These results found similar attributes from our rankings compared to those reported in the literature. This study is part of ongoing research that is investigating a range of feature selection and classification methods.

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Analisis Sentimen Pada Maskapai Penerbangan di Platform Twitter Menggunakan Algoritma Support Vector Machine (SVM)

Teknika ◽

10.34148/teknika.v10i1.311 ◽

2021 ◽

Vol 10 (1) ◽

pp. 18-26

Author(s):

Hendry Cipta Husada ◽

Adi Suryaputra Paramita

Keyword(s):

Machine Learning ◽

Social Media ◽

Support Vector Machine ◽

Cross Validation ◽

Support Vector ◽

Learning Approach ◽

Social Media Platform ◽

Machine Learning Approach ◽

Media Platform ◽

Fold Cross Validation

Perkembangan teknologi saat ini telah memberikan kemudahan bagi banyak orang dalam mendapatkan dan menyebarkan informasi di berbagai social media platform. Twitter merupakan salah satu media yang kerap digunakan untuk menyampaikan opini sebagai bentuk reaksi seseorang atas suatu hal. Opini yang terdapat di Twitter dapat digunakan perusahaan maskapai penerbangan sebagai parameter kunci untuk mengetahui tingkat kepuasan publik sekaligus bahan evaluasi bagi perusahaan. Berdasarkan hal tersebut, diperlukan sebuah metode yang dapat secara otomatis melakukan klasifikasi opini ke dalam kategori positif, negatif, atau netral melalui proses analisis sentimen. Proses analisis sentimen dilakukan dengan proses data preprocessing, pembobotan kata menggunakan metode TF-IDF, penerapan algoritma, dan pembahasan atas hasil klasifikasi. Klasifikasi opini dilakukan dengan machine learning approach memanfaatkan algoritma multi-class Support Vector Machine (SVM). Data yang digunakan dalam penelitian ini adalah opini dalam bahasa Inggris dari para pengguna Twitter terhadap maskapai penerbangan. Berdasarkan pengujian yang telah dilakukan, hasil klasifikasi terbaik diperoleh menggunakan SVM kernel RBF pada nilai parameter 𝐶(complexity) = 10 dan 𝛾(gamma) = 1, dengan nilai accuracy sebesar 84,37% dan 80,41% ketika menggunakan 10-fold cross validation.

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A Novel Computational Model for Predicting Potential LncRNA-Disease Associations based on Both Direct and Indirect Features of LncRNA-Disease Pairs

10.21203/rs.2.18937/v3 ◽

2020 ◽

Author(s):

Yubin Xiao ◽

Zheng Xiao ◽

Xiang Feng ◽

Zhiping Chen ◽

Linai Kuang ◽

...

Keyword(s):

Computational Model ◽

Cross Validation ◽

State Of The Art ◽

Prediction Methods ◽

Good Prediction ◽

Average Case ◽

Comparison Results ◽

Disease Associations ◽

Fold Cross Validation

Abstract Background: Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships between lncRNAs and diseases. Due to the high costs and time complexity of traditional bio-experiments, in recent years, more and more computational methods have been proposed by researchers to infer potential lncRNA-disease associations. However, there exist all kinds of limitations in these state-of-the-art prediction methods as well.Results: In this manuscript, a novel computational model named FVTLDA is proposed to infer potential lncRNA-disease associations. In FVTLDA, its major novelty lies in the integration of direct and indirect features related to lncRNA-disease associations such as the feature vectors of lncRNA-disease pairs and their corresponding association probability fractions, which guarantees that FVTLDA can be utilized to predict diseases without known related-lncRNAs and lncRNAs without known related-diseases. Moreover, FVTLDA neither relies solely on known lncRNA-disease nor requires any negative samples, which guarantee that it can infer potential lncRNA-disease associations more equitably and effectively than traditional state-of-the-art prediction methods. Additionally, to avoid the limitations of single model prediction techniques, we combine FVTLDA with the Multiple Linear Regression (MLR) and the Artificial Neural Network (ANN) for data analysis respectively. Simulation experiment results show that FVTLDA with MLR can achieve reliable AUCs of 0.8909, 0.8936 and 0.8970 in 5-Fold Cross Validation (5-fold CV), 10-Fold Cross Validation (10-fold CV) and Leave-One-Out Cross Validation (LOOCV), separately, while FVTLDA with ANN can achieve reliable AUCs of 0.8766, 0.8830 and 0.8807 in 5-fold CV, 10-fold CV, and LOOCV respectively. Furthermore, in case studies of gastric cancer, leukemia and lung cancer, experiment results show that there are 8, 8 and 8 out of top 10 candidate lncRNAs predicted by FVTLDA with MLR, and 8, 7 and 8 out of top 10 candidate lncRNAs predicted by FVTLDA with ANN, having been verified by recent literature. Comparing with the representative prediction model of KATZLDA, comparison results illustrate that FVTLDA with MLR and FVTLDA with ANN can achieve the average case study contrast scores of 0.8429 and 0.8515 respectively, which are both notably higher than the average case study contrast score of 0.6375 achieved by KATZLDA.Conclusion: The simulation results show that FVTLDA has good prediction performance, which is a good supplement to future bioinformatics research.

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