Separation of pulsar signals from noise with supervised machine learning algorithms

We evaluate the performance of four different machine learning (ML) algorithms: an Artificial Neural Network Multi-Layer Perceptron (ANN MLP ), Adaboost, Gradient Boosting Classifier (GBC), XGBoost, for the separation of pulsars from radio frequency interference (RFI) and other sources of noise, using a dataset obtained from the post-processing of a pulsar search pi peline. This dataset was previously used for cross-validation of the SPINN-based machine learning engine, used for the reprocessing of HTRU-S survey data arXiv:1406.3627. We have used Synthetic Minority Over-sampling Technique (SMOTE) to deal with high class imbalance in the dataset. We report a variety of quality scores from all four of these algorithms on both the non-SMOTE and SMOTE datasets. For all the above ML methods, we report high accuracy and G-mean in both the non-SMOTE and SMOTE cases. We study the feature importances using Adaboost, GBC, and XGBoost and also from the minimum Redundancy Maximum Relevance approach to report algorithm-agnostic feature ranking. From these methods, we find that the signal to noise of the folded profile to be the best feature. We find that all the ML algorithms report FPRs about an order of magnitude lower than the corresponding FPRs obtained in arXiv:1406.3627, for the same recall value.Comment: 14 pages, 2 figures. Accepted for publication in Astronomy and Computin

Random Forest as a tumour genetic marker extractor

Identifying tumour genetic markers is an essential task for biomedicine. In this thesis, we analyse a dataset of chromosomal rearrangements of cancer samples and present a methodology for extracting genetic markers from this dataset by using a Random Forest as a feature selection tool

VarSight: prioritizing clinically reported variants with binary classification algorithms.

BackgroundWhen applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient's phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance.MethodsWe tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network.ResultsWe treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20.ConclusionsWe demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets

Learning to Estimate Driver Drowsiness from Car Acceleration Sensors using Weakly Labeled Data

This paper addresses the learning task of estimating driver drowsiness from the signals of car acceleration sensors. Since even drivers themselves cannot perceive their own drowsiness in a timely manner unless they use burdensome invasive sensors, obtaining labeled training data for each timestamp is not a realistic goal. To deal with this difficulty, we formulate the task as a weakly supervised learning. We only need to add labels for each complete trip, not for every timestamp independently. By assuming that some aspects of driver drowsiness increase over time due to tiredness, we formulate an algorithm that can learn from such weakly labeled data. We derive a scalable stochastic optimization method as a way of implementing the algorithm. Numerical experiments on real driving datasets demonstrate the advantages of our algorithm against baseline methods.Comment: Accepted by ICASSP202

Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.

Deciphering the potential of noncoding loci to influence gene regulation has been the subject of intense research, with important implications in understanding genetic underpinnings of human diseases. Massively parallel reporter assays (MPRAs) can measure regulatory activity of thousands of DNA sequences and their variants in a single experiment. With increasing number of publically available MPRA data sets, one can now develop data-driven models which, given a DNA sequence, predict its regulatory activity. Here, we performed a comprehensive meta-analysis of several MPRA data sets in a variety of cellular contexts. We first applied an ensemble of methods to predict MPRA output in each context and observed that the most predictive features are consistent across data sets. We then demonstrate that predictive models trained in one cellular context can be used to predict MPRA output in another, with loss of accuracy attributed to cell-type-specific features. Finally, we show that our approach achieves top performance in the Fifth Critical Assessment of Genome Interpretation "Regulation Saturation" Challenge for predicting effects of single-nucleotide variants. Overall, our analysis provides insights into how MPRA data can be leveraged to highlight functional regulatory regions throughout the genome and can guide effective design of future experiments by better prioritizing regions of interest

A Framework for Evaluating Land Use and Land Cover Classification Using Convolutional Neural Networks

Analyzing land use and land cover (LULC) using remote sensing (RS) imagery is essential for many environmental and social applications. The increase in availability of RS data has led to the development of new techniques for digital pattern classification. Very recently, deep learning (DL) models have emerged as a powerful solution to approach many machine learning (ML) problems. In particular, convolutional neural networks (CNNs) are currently the state of the art for many image classification tasks. While there exist several promising proposals on the application of CNNs to LULC classification, the validation framework proposed for the comparison of different methods could be improved with the use of a standard validation procedure for ML based on cross-validation and its subsequent statistical analysis. In this paper, we propose a general CNN, with a fixed architecture and parametrization, to achieve high accuracy on LULC classification over RS data from different sources such as radar and hyperspectral. We also present a methodology to perform a rigorous experimental comparison between our proposed DL method and other ML algorithms such as support vector machines, random forests, and k-nearest-neighbors. The analysis carried out demonstrates that the CNN outperforms the rest of techniques, achieving a high level of performance for all the datasets studied, regardless of their different characteristics.Ministerio de Economía y Competitividad TIN2014-55894-C2-1-RMinisterio de Economía y Competitividad TIN2017-88209-C2-2-