Modelling and classification of respiratory volume wavefourms

A technique is proposed for classifying respiratory volume waveforms(RVW) into normal and abnormal categories of respiratory pathways. The proposed method transforms the temporal sequence into frequency domain by using an orthogonal transform, namely discrete cosine transform (DCT) and the transformed signal is pole-zero modelled. A Bayes classifier using model pole angles as the feature vector performed satisfactorily when a limited number of RVWs recorded under deep and rapid (DR) manoeuvre are classified.

Classification of road damage due to earthquakes

Earthquakes cause massive road damage which in turn causes adverse effects on the society. Previous studies have quantified the damage caused to residential and commercial buildings; however, not many studies have been conducted to quantify road damage caused by earthquakes. In this study, an attempt has been made to propose a new scale to classify and quantify the road damage due to earthquakes based on the data collected from major earthquakes in the past. The proposed classification for road damage due to earthquake is called as road damage scale (RDS). Earthquake details such as magnitude, distance of road damage from the epicenter, focal depth, and photographs of damaged roads have been collected from various sources with reported modified Mercalli intensity (MMI). The widely used MMI scale is found to be inadequate to clearly define the road damage. The proposed RDS is applied to various reported road damage and reclassified as per RDS. The correlation between RDS and earthquake parameters of magnitude, epicenter distance, hypocenter distance, and combination of magnitude with epicenter and hypocenter distance has been studied using available data. It is observed that the proposed RDS correlates well with the available earthquake data when compared with the MMI scale. Among several correlations, correlation between RDS and combination of magnitude and epicenter distance is appropriate. Summary of these correlations, their limitations, and the applicability of the proposed scale to forecast road damages and to carry out vulnerability analysis in urban areas is presented in the paper.

Classification of Vehicles using Magnetic Dipole Model

This paper presents an efficient approach to the modeling and classification of vehicles using the magnetic signature of the vehicle. A database was created using the magnetic signature collected over a wide range of vehicles(cars). A vehicle is modeled as an array of magnetic dipoles. The strength of the magnetic dipole and the separation between the magnetic dipoles varies for different vehicles and is dependent on the metallic composition and configuration of the vehicle. Based on the magnetic dipole data model, we present a novel method to extract a feature vector from the magnetic signature. In the classification of vehicles, a linear support vector machine configuration is used to classify the vehicles based on the obtained feature vectors.

Crop stage classification of hyperspectral data using unsupervised techniques

The presence of a large number of spectral bands in the hyperspectral images increases the capability to distinguish between various physical structures. However, they suffer from the high dimensionality of the data. Hence, the processing of hyperspectral images is applied in two stages: dimensionality reduction and unsupervised classification techniques. The high dimensionality of the data has been reduced with the help of Principal Component Analysis (PCA). The selected dimensions are classified using Niche Hierarchical Artificial Immune System (NHAIS). The NHAIS combines the splitting method to search for the optimal cluster centers using niching procedure and the merging method is used to group the data points based on majority voting. Results are presented for two hyperspectral images namely EO-1 Hyperion image and Indian pines image. A performance comparison of this proposed hierarchical clustering algorithm with the earlier three unsupervised algorithms is presented. From the results obtained, we deduce that the NHAIS is efficient.

Classification of Vehicles Using Magnetic Field Angle Model

This paper presents an efficient approach to the modeling and classification of vehicles using the magnetic signature of the vehicle. A database was created using the magnetic signature collected over a wide range of vehicles(cars). A sensor dependent approach called as Magnetic Field Angle Model is proposed for modeling the obtained magnetic signature. Based on the data model, we present a novel method to extract the feature vector from the magnetic signature. In the classification of vehicles, a linear support vector machine configuration is used to classify the vehicles based on the obtained feature vectors.

Classification of Myopathies on Molecular basis in Drosophila using Raman spectroscopy

Myopathies are muscular diseases in which muscle fibers degenerate due to many factors such as nutrient deficiency, infection and mutations in myofibrillar etc. The objective of this study is to identify the bio-markers to distinguish various muscle mutants in Drosophila (fruit fly) using Raman Spectroscopy. Principal Components based Linear Discriminant Analysis (PC-LDA) classification model yielding >95% accuracy was developed to classify such different mutants representing various myopathies according to their physiopathology.

Classification of Myopathies on Molecular basis in Drosophila using Raman spectroscopy

Myopathies are muscular diseases in which muscle fibers degenerate due to many factors such as nutrient deficiency, infection and mutations in myofibrillar etc. The objective of this study is to identify the bio-markers to distinguish various muscle mutants in Drosophila (fruit fly) using Raman Spectroscopy. Principal Components based Linear Discriminant Analysis (PC-LDA) classification model yielding >95% accuracy was developed to classify such different mutants representing various myopathies according to their physiopathology.

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

Two new atom centered fragment descriptors and scoring function enhance classification of antibacterial activity

Classification of pharmacologic activity of a chemical compound is an essential step in any drug discovery process. We develop two new atom-centered fragment descriptors (vertex indices) - one based solely on topological considerations without discriminating atomor bond types, and another based on topological and electronic features. We also assess their usefulness by devising a method to rank and classify molecules with regard to their antibacterial activity. Classification performances of our method are found to be superior compared to two previous studies on large heterogeneous data sets for hit finding and hit-to-lead studies even though we use much fewer parameters. It is found that for hit finding studies topological features (simple graph) alone provide significant discriminating power, and for hit-to-lead process small but consistent improvement can be made by additionally including electronic features (colored graph). Our approach is simple, interpretable, and suitable for design of molecules as we do not use any physicochemical properties. The singular use of vertex index as descriptor, novel range based feature extraction, and rigorous statistical validation are the key elements of this study.

Multi Label Classification of Discrete Data

The paper describes an algorithm for multi-label classification. Since a pattern can belong to more than one class, the task of classifying a test pattern is a challenging one. We propose a new algorithm to carry out multi-label classification which works for discrete data. We have implemented the algorithm and presented the results for different multi-label data sets. The results have been compared with the algorithm multi-label KNN or ML-KNN and found to give good results.

Fuzzy Classification of Time Series Data

The problem of classification of time series data is an interesting problem in the field of data mining. Even though several algorithms have been proposed for the problem of time series classification we have developed an innovative algorithm which is computationally fast and accurate in several cases when compared with 1NN classifier. In our method we are calculating the fuzzy membership of each test pattern to be classified to each class. We have experimented with 6 benchmark datasets and compared our method with 1NN classifier.

A radial differential mobility analyzer for the size-classification of gas-phase synthesized nanoparticles at low pressures

Differential mobility analyzers (DMAs) are commonly used to generate monodisperse nanoparticle aerosols. Commercial DMAs operate at quasi-atmospheric pressures and are therefore not designed to be vacuum-tight. In certain particle synthesis methods, the use of a vacuum-compatible DMA is a requirement as a process step for producing high-purity metallic particles. A vacuum-tight radial DMA (RDMA) has been developed and tested at low pressures. Its performance has been evaluated by using a commercial NANO-DMA as the reference. The performance of this low-pressure RDMA (LP-RDMA) in terms of the width of its transfer function is found to be comparable with that of other NANO-DMAs at atmospheric pressure and is almost independent of the pressure down to 30 mbar. It is shown that LP-RDMA can be used for the classification of nanometer-sized particles (5-20 nm) under low pressure condition (30 mbar) and has been successfully applied to nanoparticles produced by ablating FeNi at low pressures.

Phylogenetic relationships and classification of thiolases and thiolase-like proteins of Mycobacterium tuberculosis and Mycobacterium smegmatis

Thiolases are enzymes involved in lipid metabolism. Thiolases remove the acetyl-CoA moiety from 3-ketoacyl-CoAs in the degradative reaction. They can also catalyze the reverse Claisen condensation reaction, which is the first step of biosynthetic processes such as the biosynthesis of sterols and ketone bodies. In human, six distinct thiolases have been identified. Each of these thiolases is different from the other with respect to sequence, oligomeric state, substrate specificity and subcellular localization. Four sequence fingerprints, identifying catalytic loops of thiolases, have been described. In this study genome searches of two mycobacterial species (Mycobacterium tuberculosis and Mycobacterium smegmatis), were carried out, using the six human thiolase sequences as queries. Eight and thirteen different thiolase sequences were identified in M. tuberculosis and M. smegmatis, respectively. In addition, thiolase-like proteins (one encoded in the Mtb and two in the Msm genome) were found. The purpose of this study is to classify these mostly uncharacterized thiolases and thiolase-like proteins. Several other sequences obtained by searches of genome databases of bacteria, mammals and the parasitic protist family of the Trypanosomatidae were included in the analysis. Thiolase-like proteins were also found in the trypanosomatid genomes, but not in those of mammals. In order to study the phylogenetic relationships at a high confidence level, additional thiolase sequences were included such that a total of 130 thiolases and thiolase-like protein sequences were used for the multiple sequence alignment. The resulting phylogenetic tree identifies 12 classes of sequences, each possessing a characteristic set of sequence fingerprints for the catalytic loops. From this analysis it is now possible to assign the mycobacterial thiolases to corresponding homologues in other kingdoms of life. The results of this bioinformatics analysis also show interesting differences between the distributions of M. tuberculosis and M. smegmatis thiolases over the 12 different classes. (C) 2014 Elsevier Ltd. All rights reserved.

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better. Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions. Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family. Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.