Sparse Proteomics Analysis - A compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data

Background: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust against noise and outliers, while the identified feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA), based on the theory of compressed sensing that allows us to identify a minimal discriminating set of features from mass spectrometry data-sets. We show (1) how our method performs on artificial and real-world data-sets, (2) that its performance is competitive with standard (and widely used) algorithms for analyzing proteomics data, and (3) that it is robust against random and systematic noise. We further demonstrate the applicability of our algorithm to two previously published clinical data-sets

Recent Application in Biometrics

In the recent years, a number of recognition and authentication systems based on biometric measurements have been proposed. Algorithms and sensors have been developed to acquire and process many different biometric traits. Moreover, the biometric technology is being used in novel ways, with potential commercial and practical implications to our daily activities. The key objective of the book is to provide a collection of comprehensive references on some recent theoretical development as well as novel applications in biometrics. The topics covered in this book reflect well both aspects of development. They include biometric sample quality, privacy preserving and cancellable biometrics, contactless biometrics, novel and unconventional biometrics, and the technical challenges in implementing the technology in portable devices. The book consists of 15 chapters. It is divided into four sections, namely, biometric applications on mobile platforms, cancelable biometrics, biometric encryption, and other applications. The book was reviewed by editors Dr. Jucheng Yang and Dr. Norman Poh. We deeply appreciate the efforts of our guest editors: Dr. Girija Chetty, Dr. Loris Nanni, Dr. Jianjiang Feng, Dr. Dongsun Park and Dr. Sook Yoon, as well as a number of anonymous reviewers

Differential sensing with arrays of de novo designed peptide assemblies

Differential sensing attempts to mimic the mammalian senses of smell and taste to identify analytes and complex mixtures. In place of hundreds of complex, membrane-bound G-protein coupled receptors, differential sensors employ arrays of small molecules. Here we show that arrays of computationally designed de novo peptides provide alternative synthetic receptors for differential sensing. We use self-assembling α-helical barrels (αHBs) with central channels that can be altered predictably to vary their sizes, shapes and chemistries. The channels accommodate environment-sensitive dyes that fluoresce upon binding. Challenging arrays of dye-loaded barrels with analytes causes differential fluorophore displacement. The resulting fluorimetric fingerprints are used to train machine-learning models that relate the patterns to the analytes. We show that this system discriminates between a range of biomolecules, drink, and diagnostically relevant biological samples. As αHBs are robust and chemically diverse, the system has potential to sense many analytes in various settings

Vibrational spectroscopy as a powerful tool for stratifying patients using minimal amounts of blood

In the current aging society, more and more people will suffer from age-related diseases such as cardiovascular diseases or diabetes mellitus. To better diagnose and treat these diseases, individual characterisation of the patients unique condition is needed. Vibrational spectroscopy, including Raman spectroscopy and Fourier transform infrared spectroscopy (FTIR), is one of the favourite techniques being developed to enable personalized medicine. Vibrational spectroscopic techniques have the advantages of being non-destructive, rapid, and label-free, can be ultimately performed in high-throughput and provide biochemical fingerprint information on molecular level. Among the samples measured by vibrational spectroscopy, blood is a very popular and important specimen for personalized medicine

Prediction of drug-drug interaction potential using machine learning approaches

Drug discovery is a long, expensive, and complex, yet crucial process for the benefit of society. Selecting potential drug candidates requires an understanding of how well a compound will perform at its task, and more importantly, how safe the compound will act in patients. A key safety insight is understanding a molecule\u27s potential for drug-drug interactions. The metabolism of many drugs is mediated by members of the cytochrome P450 superfamily, notably, the CYP3A4 enzyme. Inhibition of these enzymes can alter the bioavailability of other drugs, potentially increasing their levels to toxic amounts. Four models were developed to predict CYP3A4 inhibition: logistic regression, random forests, support vector machine, and neural network. Two novel convolutional approaches were explored for data featurization: SMILES string auto-extraction and 2D structure auto-extraction. The logistic regression model achieved an accuracy of 83.2%, the random forests model, 83.4%, the support vector machine model, 81.9%, and the neural network model, 82.3%. Additionally, the model built with SMILE string auto-extraction had an accuracy of 82.3%, and the model with 2D structure auto-extraction, 76.4%. The advantages of the novel featurization methods are their ability to learn relevant features from compound SMILE strings, eliminating feature engineering. The developed methodologies can be extended towards predicting any structure-activity relationship and fitted for other areas of drug discovery and development

Nanomechanics of a Hydrogen Molecule Suspended between Two Equally Charged Tips

Geometric configuration and energy of a hydrogen molecule centered between two point-shaped tips of equal charge are calculated with the variational quantum Monte-Carlo (QMC) method without the restriction of the Born-Oppenheimer (BO) approximation. Ground state nuclear distribution, stability, and low vibrational excitation are investigated. Ground state results predict significant deviations from the BO treatment that is based on a potential energy surface (PES) obtained with the same QMC accuracy. The quantum mechanical distribution of molecular axis direction and bond length at a sub-nanometer level is fundamental for understanding nanomechanical dynamics with embedded hydrogen. Because of the tips' arrangement, cylindrical symmetry yields a uniform azimuthal distribution of the molecular axis vector relative to the tip-tip axis. With approaching tips towards each other, the QMC sampling shows an increasing loss of spherical symmetry with the molecular axis still uniformly distributed over the azimuthal angle but peaked at the tip-tip direction for negative tip charge while peaked at the equatorial plane for positive charge. This directional behavior can be switched between both stable configurations by changing the sign of the tip charge and by controlling the tip-tip distance. This suggests an application in the field of molecular machines.Comment: 20 pages, 10 figure

Intrinsic and post-hoc XAI approaches for fingerprint identification and response prediction in smart manufacturing processes

In quest of improving the productivity and efficiency of manufacturing processes, Artificial Intelligence (AI) is being used extensively for response prediction, model dimensionality reduction, process optimization, and monitoring. Though having superior accuracy, AI predictions are unintelligible to the end users and stakeholders due to their opaqueness. Thus, building interpretable and inclusive machine learning (ML) models is a vital part of the smart manufacturing paradigm to establish traceability and repeatability. The study addresses this fundamental limitation of AI-driven manufacturing processes by introducing a novel Explainable AI (XAI) approach to develop interpretable processes and product fingerprints. Here the explainability is implemented in two stages: by developing interpretable representations for the fingerprints, and by posthoc explanations. Also, for the first time, the concept of process fingerprints is extended to develop an interpretable probabilistic model for bottleneck events during manufacturing processes. The approach is demonstrated using two datasets: nanosecond pulsed laser ablation to produce superhydrophobic surfaces and wire EDM real-time monitoring dataset during the machining of Inconel 718. The fingerprint identification is performed using a global Lipschitz functions optimization tool (MaxLIPO) and a stacked ensemble model is used for response prediction. The proposed interpretable fingerprint approach is robust to change in processes and can responsively handle both continuous and categorical responses alike. Implementation of XAI not only provided useful insights into the process physics but also revealed the decision-making logic for local predictions

AI-assisted patent prior art searching - feasibility study

This study seeks to understand the feasibility, technical complexities and effectiveness of using artificial intelligence (AI) solutions to improve operational processes of registering IP rights. The Intellectual Property Office commissioned Cardiff University to undertake this research. The research was funded through the BEIS Regulators’ Pioneer Fund (RPF). The RPF fund was set up to help address barriers to innovation in the UK economy