Capturing discrete latent structures: choose LDs over PCs

Summary High-dimensional biological data collection across heterogeneous groups of samples has become increasingly common, creating high demand for dimensionality reduction techniques that capture underlying structure of the data. Discovering low-dimensional embeddings that describe the separation of any underlying discrete latent structure in data is an important motivation for applying these techniques since these latent classes can represent important sources of unwanted variability, such as batch effects, or interesting sources of signal such as unknown cell types. The features that define this discrete latent structure are often hard to identify in high-dimensional data. Principal component analysis (PCA) is one of the most widely used methods as an unsupervised step for dimensionality reduction. This reduction technique finds linear transformations of the data which explain total variance. When the goal is detecting discrete structure, PCA is applied with the assumption that classes will be separated in directions of maximum variance. However, PCA will fail to accurately find discrete latent structure if this assumption does not hold. Visualization techniques, such as t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP), attempt to mitigate these problems with PCA by creating a low-dimensional space where similar objects are modeled by nearby points in the low-dimensional embedding and dissimilar objects are modeled by distant points with high probability. However, since t-SNE and UMAP are computationally expensive, often a PCA reduction is done before applying them which makes it sensitive to PCAs downfalls. Also, tSNE is limited to only two or three dimensions as a visualization tool, which may not be adequate for retaining discriminatory information. The linear transformations of PCA are preferable to non-linear transformations provided by methods like t-SNE and UMAP for interpretable feature weights. Here, we propose iterative discriminant analysis (iDA), a dimensionality reduction technique designed to mitigate these limitations. iDA produces an embedding that carries discriminatory information which optimally separates latent clusters using linear transformations that permit post hoc analysis to determine features that define these latent structures.

Audio display and environmental sound analysis of diagnostic and therapeutic respiratory sounds.

The objective of this study is to provide a framework to aid physicians in identifying early respiratory ailments as well as provide a means of monitoring medication compliancy for both the patient and physicians. To aid physicians identify abnormal sounds during auscultations such as crackle, this work proposes a multimedia approach in the form of audio display (AD) to enhance crackle sounds produced in respiration. This work utilize a two step AD approach in which the crackle sound is first separated from the rest of the vesicular sound and then either sonified or audified. To aid in monitoring use of medication this work proposes an environmental sound analysis (ESA) framework to autonomously quantify adherence to medication. This work employed traditional audio features to extract meaningful discriminatory information to identify the inhaler sounds from the environment with the aid of maximum relevance and minimum redundancy algorithm and the hidden markov model.

Audio display and environmental sound analysis of diagnostic and therapeutic respiratory sounds.

The objective of this study is to provide a framework to aid physicians in identifying early respiratory ailments as well as provide a means of monitoring medication compliancy for both the patient and physicians. To aid physicians identify abnormal sounds during auscultations such as crackle, this work proposes a multimedia approach in the form of audio display (AD) to enhance crackle sounds produced in respiration. This work utilize a two step AD approach in which the crackle sound is first separated from the rest of the vesicular sound and then either sonified or audified. To aid in monitoring use of medication this work proposes an environmental sound analysis (ESA) framework to autonomously quantify adherence to medication. This work employed traditional audio features to extract meaningful discriminatory information to identify the inhaler sounds from the environment with the aid of maximum relevance and minimum redundancy algorithm and the hidden markov model.

Accurately Predicting Glutarylation Sites Using Sequential Bi-Peptide-Based Evolutionary Features

Post Translational Modification (PTM) is defined as the alteration of protein sequence upon interaction with different macromolecules after the translation process. Glutarylation is considered one of the most important PTMs, which is associated with a wide range of cellular functioning, including metabolism, translation, and specified separate subcellular localizations. During the past few years, a wide range of computational approaches has been proposed to predict Glutarylation sites. However, despite all the efforts that have been made so far, the prediction performance of the Glutarylation sites has remained limited. One of the main challenges to tackle this problem is to extract features with significant discriminatory information. To address this issue, we propose a new machine learning method called BiPepGlut using the concept of a bi-peptide-based evolutionary method for feature extraction. To build this model, we also use the Extra-Trees (ET) classifier for the classification purpose, which, to the best of our knowledge, has never been used for this task. Our results demonstrate BiPepGlut is able to significantly outperform previously proposed models to tackle this problem. BiPepGlut achieves 92.0%, 84.8%, 95.6%, 0.82, and 0.88 in accuracy, sensitivity, specificity, Matthew’s Correlation Coefficient, and F1-score, respectively. BiPepGlut is implemented as a publicly available online predictor.

PyFeat: a Python-based effective feature generation tool for DNA, RNA and protein sequences

MotivationExtracting useful feature set which contains significant discriminatory information is a critical step in effectively presenting sequence data to predict structural, functional, interaction and expression of proteins, DNAs and RNAs. Also, being able to filter features with significant information and avoid sparsity in the extracted features require the employment of efficient feature selection techniques. Here we present PyFeat as a practical and easy to use toolkit implemented in Python for extracting various features from proteins, DNAs and RNAs. To build PyFeat we mainly focused on extracting features that capture information about the interaction of neighboring residues to be able to provide more local information. We then employ AdaBoost technique to select features with maximum discriminatory information. In this way, we can significantly reduce the number of extracted features and enable PyFeat to represent the combination of effective features from large neighboring residues. As a result, PyFeat is able to extract features from 13 different techniques and represent context free combination of effective features. The source code for PyFeat standalone toolkit and employed benchmarks with a comprehensive user manual explaining its system and workflow in a step by step manner are publicly available.Resultshttps://github.com/mrzResearchArena/PyFeat/blob/master/RESULTS.md.Availability and implementationToolkit, source code and manual to use PyFeat: https://github.com/mrzResearchArena/PyFeat/Supplementary informationSupplementary data are available at Bioinformatics online.

Discriminatory Information Disclosure

A seller designs a mechanism to sell a single object to a potential buyer whose private type is his incomplete information about his valuation. The seller can disclose additional information to the buyer about his valuation without observing its realization. In both discrete-type and continuous-type settings, we show that discriminatory disclosure—releasing different amounts of additional information to different buyer types—dominates full disclosure in terms of seller revenue. An implication is that the orthogonal decomposition technique, while an important tool in dynamic mechanism design, is generally invalid when information disclosure is part of the design. (JEL D11, D82, D83)