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Register a new userMachine learning applications to DNA subsequence and restriction site analysis
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Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.
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Submodularity is a discrete domain functional property that can be interpreted as mimicking the role of the well-known convexity/concavity properties in the continuous domain. Submodular functions exhibit strong structure that lead to efficient optimization algorithms with provable near-optimality guarantees. These characteristics, namely, efficiency and provable performance bounds, are of particular interest for signal processing (SP) and machine learning (ML) practitioners as a variety of discrete optimization problems are encountered in a wide range of applications. Conventionally, two general approaches exist to solve discrete problems: $(i)$ relaxation into the continuous domain to obtain an approximate solution, or $(ii)$ development of a tailored algorithm that applies directly in the discrete domain. In both approaches, worst-case performance guarantees are often hard to establish. Furthermore, they are often complex, thus not practical for large-scale problems. In this paper, we show how certain scenarios lend themselves to exploiting submodularity so as to construct scalable solutions with provable worst-case performance guarantees. We introduce a variety of submodular-friendly applications, and elucidate the relation of submodularity to convexity and concavity which enables efficient optimization. With a mixture of theory and practice, we present different flavors of submodularity accompanying illustrative real-world case studies from modern SP and ML. In all cases, optimization algorithms are presented, along with hints on how optimality guarantees can be established.
With the development and widespread use of wireless devices in recent years (mobile phones, Internet of Things, Wi-Fi), the electromagnetic spectrum has become extremely crowded. In order to counter security threats posed by rogue or unknown transmitters, it is important to identify RF transmitters not by the data content of the transmissions but based on the intrinsic physical characteristics of the transmitters. RF waveforms represent a particular challenge because of the extremely high data rates involved and the potentially large number of transmitters present in a given location. These factors outline the need for rapid fingerprinting and identification methods that go beyond the traditional hand-engineered approaches. In this study, we investigate the use of machine learning (ML) strategies to the classification and identification problems, and the use of wavelets to reduce the amount of data required. Four different ML strategies are evaluated: deep neural nets (DNN), convolutional neural nets (CNN), support vector machines (SVM), and multi-stage training (MST) using accelerated Levenberg-Marquardt (A-LM) updates. The A-LM MST method preconditioned by wavelets was by far the most accurate, achieving 100% classification accuracy of transmitters, as tested using data originating from 12 different transmitters. We discuss strategies for extension of MST to a much larger number of transmitters.
Radiomic models have been shown to outperform clinical data for outcome prediction in glioblastoma (GBM). However, clinical implementation is limited by lack of parameters standardization. We aimed to compare nine machine learning classifiers, with different optimization parameters, to predict overall survival (OS), isocitrate dehydrogenase (IDH) mutation, O-6-methylguanine-DNA-methyltransferase (MGMT) promoter methylation, epidermal growth factor receptor (EGFR) VII amplification and Ki-67 expression in GBM patients, based on radiomic features from conventional and advanced MR. 156 adult patients with pathologic diagnosis of GBM were included. Three tumoral regions were analyzed: contrast-enhancing tumor, necrosis and non-enhancing tumor, selected by manual segmentation. Radiomic features were extracted with a custom version of Pyradiomics, and selected through Boruta algorithm. A Grid Search algorithm was applied when computing 4 times K-fold cross validation (K=10) to get the highest mean and lowest spread of accuracy. Once optimal parameters were identified, model performances were assessed in terms of Area Under The Curve-Receiver Operating Characteristics (AUC-ROC). Metaheuristic and ensemble classifiers showed the best performance across tasks. xGB obtained maximum accuracy for OS (74.5%), AB for IDH mutation (88%), MGMT methylation (71,7%), Ki-67 expression (86,6%), and EGFR amplification (81,6%). Best performing features shed light on possible correlations between MR and tumor histology.
Classical and exceptional Lie algebras and their representations are among the most important tools in the analysis of symmetry in physical systems. In this letter we show how the computation of tensor products and branching rules of irreducible representations are machine-learnable, and can achieve relative speed-ups of orders of magnitude in comparison to the non-ML algorithms.
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one run for each symbol (a run is a maximum substring of consecutive identical symbols). The problem has been shown to be NP-hard and to be fixed-parameter tractable when the parameter is the size of the alphabet on which the input string is defined. In this paper we further investigate the complexity of the problem and we show that it is fixed-parameter tractable when it is parameterized by the number of runs in a solution, a smaller parameter. Moreover, we investigate the kernelization complexity of Longest Run Subsequence and we prove that it does not admit a polynomial kernel when parameterized by the size of the alphabet or by the number of runs. Finally, we consider the restriction of Longest Run Subsequence when each symbol has at most two occurrences in the input string and we show that it is APX-hard.
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