FastSK: fast sequence analysis with gapped string kernels

Krein support vector machine classification of antimicrobial peptides

Antimicrobial peptides (AMPs) represent a potential solution to the growing problem of antimicrobial resistance, yet their identification through wet-lab experiments is a costly and time-consuming process. Accurate computational predictions would allow rapid in silico screening of candidate AMPs, thereby accelerating the discovery process. Kernel methods are a class of machine learning algorithms that utilise a kernel function to transform input data into a new representation. When appropriately normalised, the kernel function can be regarded as a notion of similarity between instances. However, many expressive notions of similarity are not valid kernel functions, meaning they cannot be used with standard kernel methods such as the support-vector machine (SVM). The Kreĭn-SVM represents generalisation of the standard SVM that admits a much larger class of similarity functions. In this study, we propose and develop Kreĭn-SVM models for AMP classification and prediction by employing the Levenshtein distance and local alignment score as sequence similarity functions. Utilising two datasets from the literature, each containing more than 3000 peptides, we train models to predict general antimicrobial activity. Our best models achieve an AUC of 0.967 and 0.863 on the test sets of each respective dataset, outperforming the in-house and literature baselines in both cases. We also curate a dataset of experimentally validated peptides, measured against Staphylococcus aureus and Pseudomonas aeruginosa, in order to evaluate the applicability of our methodology in predicting microbe-specific activity. In this case, our best models achieve an AUC of 0.982 and 0.891, respectively. Models to predict both general and microbe-specific activities are made available as web applications.

Gnocis: An integrated system for interactive and reproducible analysis and modelling of cis-regulatory elements in Python 3

Gene expression is regulated through cis-regulatory elements (CREs), among which are promoters, enhancers, Polycomb/Trithorax Response Elements (PREs), silencers and insulators. Computational prediction of CREs can be achieved using a variety of statistical and machine learning methods combined with different feature space formulations. Although Python packages for DNA sequence feature sets and for machine learning are available, no existing package facilitates the combination of DNA sequence feature sets with machine learning methods for the genome-wide prediction of candidate CREs. We here present Gnocis, a Python package that streamlines the analysis and the modelling of CRE sequences by providing extensible APIs and implementing the glue required for combining feature sets and models for genome-wide prediction. Gnocis implements a variety of base feature sets, including motif pair occurrence frequencies and the k-spectrum mismatch kernel. It integrates with Scikit-learn and TensorFlow for state-of-the-art machine learning. Gnocis additionally implements a broad suite of tools for the handling and preparation of sequence, region and curve data, which can be useful for general DNA bioinformatics in Python. We also present Deep-MOCCA, a neural network architecture inspired by SVM-MOCCA that achieves moderate to high generalization without prior motif knowledge. To demonstrate the use of Gnocis, we applied multiple machine learning methods to the modelling of D. melanogaster PREs, including a Convolutional Neural Network (CNN), making this the first study to model PREs with CNNs. The models are readily adapted to new CRE modelling problems and to other organisms. In order to produce a high-performance, compiled package for Python 3, we implemented Gnocis in Cython. Gnocis can be installed using the PyPI package manager by running ‘pip install gnocis’. The source code is available on GitHub, at https://github.com/bjornbredesen/gnocis.

Corpus Statistics Empowered Document Classification

In natural language processing (NLP), document classification is an important task that relies on the proper thematic representation of the documents. Gaussian mixture-based clustering is widespread for capturing rich thematic semantics but ignores emphasizing potential terms in the corpus. Moreover, the soft clustering approach causes long-tail noise by putting every word into every cluster, which affects the natural thematic representation of documents and their proper classification. It is more challenging to capture semantic insights when dealing with short-length documents where word co-occurrence information is limited. In this context, for long texts, we proposed Weighted Sparse Document Vector (WSDV), which performs clustering on the weighted data that emphasizes vital terms and moderates the soft clustering by removing outliers from the converged clusters. Besides the removal of outliers, WSDV utilizes corpus statistics in different steps for the vectorial representation of the document. For short texts, we proposed Weighted Compact Document Vector (WCDV), which captures better semantic insights in building document vectors by emphasizing potential terms and capturing uncertainty information while measuring the affinity between distributions of words. Using available corpus statistics, WCDV sufficiently handles the data sparsity of short texts without depending on external knowledge sources. To evaluate the proposed models, we performed a multiclass document classification using standard performance measures (precision, recall, f1-score, and accuracy) on three long- and two short-text benchmark datasets that outperform some state-of-the-art models. The experimental results demonstrate that in the long-text classification, WSDV reached 97.83% accuracy on the AgNews dataset, 86.05% accuracy on the 20Newsgroup dataset, and 98.67% accuracy on the R8 dataset. In the short-text classification, WCDV reached 72.7% accuracy on the SearchSnippets dataset and 89.4% accuracy on the Twitter dataset.