Prediction of lung tumor types based on protein attributes by machine learning algorithms

Integration of machine learning models with microsatellite markers: New avenue in world grapevine germplasm characterization

Development of efficient analytical techniques is required for effective interpretation of biological data to take novel hypotheses and finding the critical predictive patterns. Machine Learning algorithms provide a novel opportunity for development of low-cost and practical solutions in biology. In this study, we proposed a new integrated analytical approach using supervised machine learning algorithms and microsatellites data of worldwide vitis populations. A total of 1378 wild (V. vinifera spp. sylvestris) and cultivated (V. vinifera spp. sativa) accessions of grapevine were investigated using 20 microsatellite markers. Data cleaning, feature selection, and supervised machine learning classification models vis, Naive Bayes, Support Vector Machine (SVM) and Tree Induction methods were implied to find most indicative and diagnostic alleles to represent wild/cultivated and originated geography of each population. Our combined approaches showed microsatellite markers with the highest differentiating capacity and proved efficiency for our pipeline of classification and prediction of vitis accessions. Moreover, our study proposed the best combination of markers for better distinguishing of populations, which can be exploited in future germplasm conservation and breeding programs.

Steroid profiling in adrenal disease

The measurement of steroid hormones in blood and urine, which reflects steroid biosynthesis and metabolism, has been recognized as a valuable tool for identifying and distinguishing steroidogenic disorders. The application of mass spectrometry enables the reliable and simultaneous analysis of large panels of steroids, ushering in a new era for diagnosing adrenal diseases. However, the interpretation of complex hormone results necessitates the expertise and experience of skilled clinicians. In this scenario, machine learning techniques are gaining worldwide attention within healthcare fields. The clinical values of combining mass spectrometry-based steroid profiles analysis with machine learning models, also known as steroid metabolomics, have been investigated for identifying and discriminating adrenal disorders such as adrenocortical carcinomas, adrenocortical adenomas, and congenital adrenal hyperplasia. This promising approach is expected to lead to enhanced clinical decision-making in the field of adrenal diseases. This review will focus on the clinical performances of steroid profiling, which is measured using mass spectrometry and analyzed by machine learning techniques, in the realm of decision-making for adrenal diseases.

Machine learning-based ensemble approach in prediction of lung cancer predisposition using XRCC1 gene polymorphism

The employment of machine learning approaches has shown promising results in predicting cancer. In the current study, polymorphisms data of five single nucleotide polymorphisms (SNPs) of DNA repair gene XRCC1 (XRCC1 399, XRCC1 194, XRCC1 206, XRCC1 632, XRCC1 280) of the north Indian population along with four smoking status data is considered as an input to the proposed ensemble model to predict the risk of individual susceptibility to the lung cancer. The prediction accuracy of the proposed ensemble model for cancer predisposition was found to be 85%. The model performance is also evaluated using sensitivity, specificity, precision and the Gini index, which is found in the range of 0.83-0.87. The proposed model also outperformed in all evaluation parameters when compared with the individual Model (LM, SVM, RF, KNN and baseline neural net). Collectively, current results suggest the potential of the proposed ensemble model in predicting the risk of cancer based on XRCC1 SNPs data.Communicated by Ramaswamy H. Sarma.

Kanser Teşhisinde Protein Haritalama Tekniklerinin Başarımlarının Derin Öğrenme Kullanılarak Karşılaştırılması

Kanser, dünya çapında çoğu insanın ölmesine neden olan ve birçok farklı alt tiplerden oluşan heterojen bir hastalıktır. Bir kanser türünün erken teşhisi ve prognozu, hastaların sonraki klinik takibini kolaylaştırabildiği için kanser araştırmalarında bir gereklilik haline gelmiştir. Bunun için en çok kullanılan yöntemlerden birisi histolojik incelemedir. Ancak bu yöntemde çok sayıda gözlemciler arası değişkenlik bulunmakta, bu ise inceleme sürecinin uzun olmasına ve zaman almasına neden olmaktadır. Bu dezavantajın önüne geçmek için araştırmacılar hesaplama-tabanlı yaklaşımlara yönelmişler ve kanserli proteinlerin belirlenmesi için protein-protein etkileşimleri, protein etkileşim ağları ve moleküler parmak izleri yöntemlerinden yararlanmaktadırlar. Bu yöntemler arasında, çeşitli çalışmalar genomik bilgilerden de kanserli hücrelerin tespit edilebildiğini göstermiştir. Kansere ait genlerin dizilimlerine göre belirli kanser türlerinin belirlenebildiği ve bu süreçte yapay öğrenme tabanlı yaklaşımların etkili olduğu görülmüştür. Bu çalışmada, derin öğrenme algoritmalarından birisi olan tekrarlayıcı sinir ağı mimarisi kullanılmış ve insana ait mesane, kolon ve prostat kanserlerinin, protein dizilimlerine göre sınıflandırılması yapılmıştır. Çalışma, verilerin elde edilmesi, protein dizilimlerinin sayısallaştırılması, derin öğrenme model uygulamasının geliştirilmesi ve protein haritalama tekniklerinin başarımının karşılaştırılması olmak üzere dört aşamadan meydana gelmektedir. Protein dizilimlerini sayısallaştırmak için AESNN1, hidrofobiklik, tam sayı, Miyazawa enerjileri ve rastgele kodlama yöntemleri ele alınmıştır. Çalışmanın sonunda, mesane kanseri için en yüksek doğruluk değeri %87.15 ile AESNN1 haritalama yöntemiyle, kolon kanseri ve prostat kanseri için ise en yüksek doğruluk değeri sırasıyla %94.40 ve %75.45 olarak Miyazawa enerjileri ve rastgele kodlama protein haritalama yöntemi ile elde edilmiştir. Bu çalışma ile yapay öğrenme ve protein haritalama tekniklerinin, kanserli protein dizilimlerinin belirlenmesinde etkili olduğu gözlemlenmiştir.

Image processing unravels the evolutionary pattern of SARS-CoV-2 against SARS and MERS through position-based pattern recognition

SARS-COV-2, Severe Acute Respiratory Syndrome (SARS), and the Middle East respiratory syndrome-related coronavirus (MERS) viruses are from the coronaviridae family; the former became a global pandemic (with low mortality rate) while the latter were confined to a limited region (with high mortality rates). To investigate the possible structural differences at basic levels for the three viruses, genomic and proteomic sequences were downloaded and converted to polynomial datasets. Seven attribute weighting (feature selection) models were employed to find the key differences in their genome's nucleotide sequence. Most attribute weighting models selected the final nucleotide sequences (from 29,000^th nucleotide positions to the end of the genome) as significantly different among the three virus classes. The genome and proteome sequences of this hot zone area (which corresponds to the 3'UTR region and encodes for nucleoprotein (N)) and Spike (S) protein sequences (as the most important viral protein) were converted into binary images and were analyzed by image processing techniques and Convolutional deep Neural Network (CNN). Although the predictive accuracy of CNN for Spike (S) proteins was low (0.48%), the machine-based learning algorithms were able to classify the three members of coronaviridae viruses with 100% accuracy based on 3'UTR region. For the first time ever, the relationship between the possible structural differences of coronaviruses at the sequential levels and their pathogenesis are being reported, which paves the road to deciphering the high pathogenicity of the SARS-COV-2 virus.

Machine Learning Algorithm Guiding Local Treatment Decisions to Reduce Pain for Lung Cancer Patients with Bone Metastases, a Prospective Cohort Study

INTRODUCTION

As life expectancy increases for lung cancer patients with bone metastases, the need for personalized local treatment to reduce pain is expanding.

METHODS

Patients were treated by a multidisciplinary team (MDT), and local treatment including surgery, percutaneous osteoplasty, or radiation. Visual analog scale (VAS) and quality of life (QoL) scores were analyzed. VAS at 12 weeks after treatment was the main outcome. We developed and tested machine learning models to predict which patients should receive local treatment. Model discrimination was evaluated by the area under curve (AUC), and the best model was used for prospective decision-making accuracy validation.

RESULTS

Under the direction of MDT, 161 patients in the training set, 32 patients in the test set, and 36 patients in the validation set underwent local treatment. VAS in surgery, percutaneous osteoplasty, and radiation groups decreased significantly to 4.78 ± 1.28, 4.37 ± 1.36, and 5.39 ± 1.31 at 12 weeks, respectively (p < 0.05), with no significant differences among the three datasets, and improved QoL was also observed (p < 0.05). A decision tree (DT) model that included VAS, bone metastases character, Frankel classification, Mirels score, age, driver gene, aldehyde dehydrogenase 2, and enolase 1 expression had a best AUC in predicting whether patients would receive local treatment of 0.92 (95% CI 0.89-0.94) in the training set, 0.85 (95% CI 0.77-0.94) in the test set, and 0.88 (95% CI 0.81-0.96) in the validation set.

CONCLUSION

Local treatment provided significant pain relief and improved QoL. There were no significant differences in reducing pain and improving QoL among training, test, and validation sets. The DT model was best at determining whether patients should receive local treatment. Our machine learning model can help guide clinicians to make local treatment decisions to reduce pain.

TRIAL REGISTRATION

Trial registration number ChiCRT-ROC-16009501.

Machine learning is a valid method for predicting prehospital delay after acute ischemic stroke

OBJECTIVES

This study aimed to identify the influencing factors associated with long onset-to-door time and establish predictive models that could help to assess the probability of prehospital delay in populations with a high risk for stroke.

MATERIALS AND METHODS

Patients who were diagnosed with acute ischemic stroke (AIS) and hospitalized between 1 November 2018 and 31 July 2019 were interviewed, and their medical records were extracted for data analysis. Two machine learning algorithms (support vector machine and Bayesian network) were applied in this study, and their predictive performance was compared with that of the classical logistic regression models after using several variable selection methods. Timely admission (onset-to-door time < 3 hr) and prehospital delay (onset-to-door time ≥ 3 hr) were the outcome variables. We computed the area under curve (AUC) and the difference in the mean AUC values between the models.

RESULTS

A total of 450 patients with AIS were enrolled; 57 (12.7%) with timely admission and 393 (87.3%) patients with prehospital delay. All models, both those constructed by logistic regression and those by machine learning, performed well in predicting prehospital delay (range mean AUC: 0.800-0.846). The difference in the mean AUC values between the best performing machine learning model and the best performing logistic regression model was negligible (0.014; 95% CI: 0.013-0.015).

CONCLUSIONS

Machine learning algorithms were not inferior to logistic regression models for prediction of prehospital delay after stroke. All models provided good discrimination, thereby creating valuable diagnostic programs for prehospital delay prediction.

Machine Learning Analysis of Image Data Based on Detailed MR Image Reports for Nasopharyngeal Carcinoma Prognosis

We aimed to assess the use of automatic machine learning (AutoML) algorithm based on magnetic resonance (MR) image data to assign prediction scores to patients with nasopharyngeal carcinoma (NPC). We also aimed to develop a 4-group classification system for NPC, superior to the current clinical staging system. Between January 2010 and January 2013, 792 patients with recent diagnosis of NPC, who had MR image data, were enrolled in the study. The AutoML algorithm was used and all statistical analyses were based on the 10-fold test. Primary endpoints included the probabilities of overall survival (OS), distant metastasis-free survival (DMFS), and local-region relapse-free survival (LRFS), and their sum was recorded as the final voting score, representative of progression-free survival (PFS) for each patient. The area under the receiver operating characteristic (ROC) curve generated from the MR image data-based model compared with the tumor, node, and metastasis (TNM) system-based model was 0.796 (P=0.008) for OS, 0.752 (P=0.053) for DMFS, and 0.721 (P=0.025) for LRFS. The Kaplan-Meier (KM) test values for II/I, III/II, IV/III groups in our new machine learning-based scoring system were 0.011, 0.010, and <0.001, respectively, whereas those for II/I, III/II, IV/III groups in the TNM/American Joint Committee on Cancer (AJCC) system were 0.118, 0.121, and <0.001, respectively. Significant differences were observed in the new machine learning-based scoring system analysis of each curve (P < 0.05), whereas the P values of curves obtained from the TNM/AJCC system, between II/I and III/II, were 0.118 and 0.121, respectively, without a significant difference. In conclusion, the AutoML algorithm demonstrated better prognostic performance than the TNM/AJCC system for NPC. The algorithm showed a good potential for clinical application and may aid in improving counseling and facilitate the personalized management of patients with NPC. The clinical application of our new scoring and staging system may significantly improve precision medicine.

Kernel differential subgraph reveals dynamic changes in biomolecular networks

Many major diseases, including various types of cancer, are increasingly threatening human health. However, the mechanisms of the dynamic processes underlying these diseases remain ambiguous. From the holistic perspective of systems science, complex biological networks can reveal biological phenomena. Changes among networks in different states influence the direction of living organisms. The identification of the kernel differential subgraph (KDS) that leads to drastic changes is critical. The existing studies contribute to the identification of a KDS in networks with the same nodes; however, networks in different states involve the disappearance of some nodes or the appearance of some new nodes. In this paper, we propose a new topology-based KDS (TKDS) method to explore the core module from gene regulatory networks with different nodes in this process. For the common nodes, the TKDS method considers the differential value (D-value) of the topological change. For the different nodes, TKDS identifies the most similar gene pairs and computes the D-value. Hence, TKDS discovers the essential KDS, which considers the relationships between the same nodes as well as different nodes. After applying this method to non-small cell lung cancer (NSCLC), we identified 30 genes that are most likely related to NSCLC and extracted the KDSs in both the cancer and normal states. Two significance functional modules were revealed, and gene ontology (GO) analyses and literature mining indicated that the KDSs are essential to the processes in NSCLC. In addition, compared with existing methods, TKDS provides a unique perspective in identifying particular genes and KDSs related to NSCLC. Moreover, TKDS has the potential to predict other critical disease-related genes and modules.

Exploiting machine learning for predicting skeletal-related events in cancer patients with bone metastases

The aim of the bone metastases (BM) treatment is to prevent the occurrence of skeletal-related events (SREs). In clinical, physicians could only predict the occurrence of SREs by subjective experience. Machine learning (ML) could be used as predictive models in the medical field. But there is no published research using ML to predict SREs in cancer patients with BM. The purpose of this study was to assess the associations of clinical variables with the occurrence of SREs and to subsequently develop prediction models to help identify SREs risk groups.

We analyzed 1143 cancer patients with BM. We used the statistical package of SPSS and SPSS Modeler for data analysis and the development of the prediction model. We compared the performance of logistic regression (LR), decision tree (DT) and support vector machine(SVM). The results suggested that Visual Analog Scale (VAS) scale was a key factor to SREs in LR, DT and SVM model. Modifiable factors such as Frankel classification, Mirels score, Ca, aminoterminal propeptide of type I collagen (PINP) and bone-specific alkaline phosphatase (BALP) were identified. We found that the result of applying LR, DT and SVM classification accuracy was 79.2%, 85.8% and 88.2%, with 9, 4 and 8 variables, respectively.

In conclusion, DT and SVM achieved higher accuracies with smaller number of variables than the number of variables used in LR. ML techniques can be used to build model to predict SREs in cancer patients with BM.

Evaluation of Machine Learning Algorithm Utilization for Lung Cancer Classification Based on Gene Expression Levels

BACKGROUND

Lung cancer remains one of the most common cancers in the world, both in terms of new cases (about 13% of total per year) and deaths (nearly one cancer death in five), because of the high case fatality. Errors in lung cancer type or malignant growth determination lead to degraded treatment efficacy, because anticancer strategy depends on tumor morphology.

MATERIALS AND METHODS

We have made an attempt to evaluate effectiveness of machine learning algorithms in the task of lung cancer classification based on gene expression levels. We processed four publicly available data sets. The Dana-Farber Cancer Institute data set contains 203 samples and the task was to classify four cancer types and sound tissue samples. With the University of Michigan data set of 96 samples, the task was to execute a binary classification of adenocarcinoma and non-neoplastic tissues. The University of Toronto data set contains 39 samples and the task was to detect recurrence, while with the Brigham and Women's Hospital data set of 181 samples it was to make a binary classification of malignant pleural mesothelioma and adenocarcinoma. We used the k-nearest neighbor algorithm (k=1, k=5, k=10), naive Bayes classifier with assumption of both a normal distribution of attributes and a distribution through histograms, support vector machine and C4.5 decision tree. Effectiveness of machine learning algorithms was evaluated with the Matthews correlation coefficient.

RESULTS

The support vector machine method showed best results among data sets from the Dana-Farber Cancer Institute and Brigham and Women's Hospital. All algorithms with the exception of the C4.5 decision tree showed maximum potential effectiveness in the University of Michigan data set. However, the C4.5 decision tree showed best results for the University of Toronto data set.

CONCLUSIONS

Machine learning algorithms can be used for lung cancer morphology classification and similar tasks based on gene expression level evaluation.

Lung cancer prediction from microarray data by gene expression programming

Lung cancer is a leading cause of cancer-related death worldwide. The early diagnosis of cancer has demonstrated to be greatly helpful for curing the disease effectively. Microarray technology provides a promising approach of exploiting gene profiles for cancer diagnosis. In this study, the authors propose a gene expression programming (GEP)-based model to predict lung cancer from microarray data. The authors use two gene selection methods to extract the significant lung cancer related genes, and accordingly propose different GEP-based prediction models. Prediction performance evaluations and comparisons between the authors' GEP models and three representative machine learning methods, support vector machine, multi-layer perceptron and radial basis function neural network, were conducted thoroughly on real microarray lung cancer datasets. Reliability was assessed by the cross-data set validation. The experimental results show that the GEP model using fewer feature genes outperformed other models in terms of accuracy, sensitivity, specificity and area under the receiver operating characteristic curve. It is concluded that GEP model is a better solution to lung cancer prediction problems.

A Highly Efficient Gene Expression Programming (GEP) Model for Auxiliary Diagnosis of Small Cell Lung Cancer

BACKGROUND

Lung cancer is an important and common cancer that constitutes a major public health problem, but early detection of small cell lung cancer can significantly improve the survival rate of cancer patients. A number of serum biomarkers have been used in the diagnosis of lung cancers; however, they exhibit low sensitivity and specificity.

METHODS

We used biochemical methods to measure blood levels of lactate dehydrogenase (LDH), C-reactive protein (CRP), Na+, Cl-, carcino-embryonic antigen (CEA), and neuron specific enolase (NSE) in 145 small cell lung cancer (SCLC) patients and 155 non-small cell lung cancer and 155 normal controls. A gene expression programming (GEP) model and Receiver Operating Characteristic (ROC) curves incorporating these biomarkers was developed for the auxiliary diagnosis of SCLC.

RESULTS

After appropriate modification of the parameters, the GEP model was initially set up based on a training set of 115 SCLC patients and 125 normal controls for GEP model generation. Then the GEP was applied to the remaining 60 subjects (the test set) for model validation. GEP successfully discriminated 281 out of 300 cases, showing a correct classification rate for lung cancer patients of 93.75% (225/240) and 93.33% (56/60) for the training and test sets, respectively. Another GEP model incorporating four biomarkers, including CEA, NSE, LDH, and CRP, exhibited slightly lower detection sensitivity than the GEP model, including six biomarkers. We repeat the models on artificial neural network (ANN), and our results showed that the accuracy of GEP models were higher than that in ANN. GEP model incorporating six serum biomarkers performed by NSCLC patients and normal controls showed low accuracy than SCLC patients and was enough to prove that the GEP model is suitable for the SCLC patients.

CONCLUSION

We have developed a GEP model with high sensitivity and specificity for the auxiliary diagnosis of SCLC. This GEP model has the potential for the wide use for detection of SCLC in less developed regions.

An ensemble method with hybrid features to identify extracellular matrix proteins

The extracellular matrix (ECM) is a dynamic composite of secreted proteins that play important roles in numerous biological processes such as tissue morphogenesis, differentiation and homeostasis. Furthermore, various diseases are caused by the dysfunction of ECM proteins. Therefore, identifying these important ECM proteins may assist in understanding related biological processes and drug development. In view of the serious imbalance in the training dataset, a Random Forest-based ensemble method with hybrid features is developed in this paper to identify ECM proteins. Hybrid features are employed by incorporating sequence composition, physicochemical properties, evolutionary and structural information. The Information Gain Ratio and Incremental Feature Selection (IGR-IFS) methods are adopted to select the optimal features. Finally, the resulting predictor termed IECMP (Identify ECM Proteins) achieves an balanced accuracy of 86.4% using the 10-fold cross-validation on the training dataset, which is much higher than results obtained by other methods (ECMPRED: 71.0%, ECMPP: 77.8%). Moreover, when tested on a common independent dataset, our method also achieves significantly improved performance over ECMPP and ECMPRED. These results indicate that IECMP is an effective method for ECM protein prediction, which has a more balanced prediction capability for positive and negative samples. It is anticipated that the proposed method will provide significant information to fully decipher the molecular mechanisms of ECM-related biological processes and discover candidate drug targets. For public access, we develop a user-friendly web server for ECM protein identification that is freely accessible at http://iecmp.weka.cc.

Prediction of hepatitis C virus interferon/ribavirin therapy outcome based on viral nucleotide attributes using machine learning algorithms

BACKGROUND

Hepatitis C virus (HCV) causes chronic hepatitis C in 2-3% of world population and remains one of the health threatening human viruses, worldwide. In the absence of an effective vaccine, therapeutic approach is the only option to combat hepatitis C. Interferon-alpha (IFN-alpha) and ribavirin (RBV) combination alone or in combination with recently introduced new direct-acting antivirals (DAA) is used to treat patients infected with HCV. The present study utilized feature selection methods (Gini Index, Chi Squared and machine learning algorithms) and other bioinformatics tools to identify genetic determinants of therapy outcome within the entire HCV nucleotide sequence.

RESULTS

Using combination of several algorithms, the present study performed a comprehensive bioinformatics analysis and identified several nucleotide attributes within the full-length nucleotide sequences of HCV subtypes 1a and 1b that correlated with treatment outcome. Feature selection algorithms identified several nucleotide features (e.g. count of hydrogen and CG). Combination of algorithms utilized the selected nucleotide attributes and predicted HCV subtypes 1a and 1b therapy responders from non-responders with an accuracy of 75.00% and 85.00%, respectively. In addition, therapy responders and relapsers were categorized with an accuracy of 82.50% and 84.17%, respectively. Based on the identified attributes, decision trees were induced to differentiate different therapy response groups.

CONCLUSIONS

The present study identified new genetic markers that potentially impact the outcome of hepatitis C treatment. In addition, the results suggest new viral genomic attributes that might influence the outcome of IFN-mediated immune response to HCV infection.

APPLYING MACHINE LEARNING TECHNIQUES IN DETECTING BACTERIAL VAGINOSIS

There are several diseases which arise because of changes in the microbial communities in the body. Scientists continue to conduct research in a quest to find the catalysts that provoke these changes in the naturally occurring microbiota. Bacterial Vaginosis (BV) is a disease that fits the above criteria. BV afflicts approximately 29% of women in child bearing age. Unfortunately, its causes are unknown. This paper seeks to uncover the most important features for diagnosis and in turn employ classification algorithms on those features. In order to fulfill our purpose, we conducted two experiments on the data. We isolated the clinical and medical features from the full set of raw data, we compared the accuracy, precision, recall and F-measure and time elapsed for each feature selection and classification grouping. We noticed that classification results were as good or better after performing feature selection although there was a wide range in the number of features produced from the feature selection process. After comparing the experiments, the algorithms performed best on the medical dataset.

Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology

Due to the central roles of lipid binding proteins (LBPs) in many biological processes, sequence based identification of LBPs is of great interest. The major challenge is that LBPs are diverse in sequence, structure, and function which results in low accuracy of sequence homology based methods. Therefore, there is a need for developing alternative functional prediction methods irrespective of sequence similarity. To identify LBPs from non-LBPs, the performances of support vector machine (SVM) and neural network were compared in this study. Comprehensive protein features and various techniques were employed to create datasets. Five-fold cross-validation (CV) and independent evaluation (IE) tests were used to assess the validity of the two methods. The results indicated that SVM outperforms neural network. SVM achieved 89.28% (CV) and 89.55% (IE) overall accuracy in identification of LBPs from non-LBPs and 92.06% (CV) and 92.90% (IE) (in average) for classification of different LBPs classes. Increasing the number and the range of extracted protein features as well as optimization of the SVM parameters significantly increased the efficiency of LBPs class prediction in comparison to the only previous report in this field. Altogether, the results showed that the SVM algorithm can be run on broad, computationally calculated protein features and offers a promising tool in detection of LBPs classes. The proposed approach has the potential to integrate and improve the common sequence alignment based methods.

Understanding the undelaying mechanism of HA-subtyping in the level of physic-chemical characteristics of protein

The evolution of the influenza A virus to increase its host range is a major concern worldwide. Molecular mechanisms of increasing host range are largely unknown. Influenza surface proteins play determining roles in reorganization of host-sialic acid receptors and host range. In an attempt to uncover the physic-chemical attributes which govern HA subtyping, we performed a large scale functional analysis of over 7000 sequences of 16 different HA subtypes. Large number (896) of physic-chemical protein characteristics were calculated for each HA sequence. Then, 10 different attribute weighting algorithms were used to find the key characteristics distinguishing HA subtypes. Furthermore, to discover machine leaning models which can predict HA subtypes, various Decision Tree, Support Vector Machine, Naïve Bayes, and Neural Network models were trained on calculated protein characteristics dataset as well as 10 trimmed datasets generated by attribute weighting algorithms. The prediction accuracies of the machine learning methods were evaluated by 10-fold cross validation. The results highlighted the frequency of Gln (selected by 80% of attribute weighting algorithms), percentage/frequency of Tyr, percentage of Cys, and frequencies of Try and Glu (selected by 70% of attribute weighting algorithms) as the key features that are associated with HA subtyping. Random Forest tree induction algorithm and RBF kernel function of SVM (scaled by grid search) showed high accuracy of 98% in clustering and predicting HA subtypes based on protein attributes. Decision tree models were successful in monitoring the short mutation/reassortment paths by which influenza virus can gain the key protein structure of another HA subtype and increase its host range in a short period of time with less energy consumption. Extracting and mining a large number of amino acid attributes of HA subtypes of influenza A virus through supervised algorithms represent a new avenue for understanding and predicting possible future structure of influenza pandemics.