The Normalised Compression Distance as a file fragment classifier

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.

Hierarchy-Based File Fragment Classification

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.

A Survey on Using Kolmogorov Complexity in Cybersecurity

Security and privacy concerns are challenging the way users interact with devices. The number of devices connected to a home or enterprise network increases every day. Nowadays, the security of information systems is relevant as user information is constantly being shared and moving in the cloud; however, there are still many problems such as, unsecured web interfaces, weak authentication, insecure networks, lack of encryption, among others, that make services insecure. The software implementations that are currently deployed in companies should have updates and control, as cybersecurity threats increasingly appearing over time. There is already some research towards solutions and methods to predict new attacks or classify variants of previous known attacks, such as (algorithmic) information theory. This survey combines all relevant applications of this topic (also known as Kolmogorov Complexity) in the security and privacy domains. The use of Kolmogorov-based approaches is resource-focused without the need for specific knowledge of the topic under analysis. We have defined a taxonomy with already existing work to classify their different application areas and open up new research questions.