Related papers: Persistent spectral based machine learning (PerSpe…

This work proposes a new image analysis tool called Label Consistent Transform Learning (LCTL). Transform learning is a recent unsupervised representation learning approach; we add supervision by incorporating a label consistency…

We consider deep multivariate models for heterogeneous collections of random variables. In the context of computer vision, such collections may e.g. consist of images, segmentations, image attributes, and latent variables. When developing…

Machine learning (ML) has been playing important roles in drug discovery in the past years by providing (pre-)screening tools for prioritising chemical compounds to pass through wet lab experiments. One of the main ML tasks in drug…

Deep learning (DL) is one of the fastest growing topics in materials data science, with rapidly emerging applications spanning atomistic, image-based, spectral, and textual data modalities. DL allows analysis of unstructured data and…

The study of machine learning (ML) techniques for the autonomous classification of astrophysical sources is of great interest, and we explore its applications in the context of a multifrequency data-frame. We test the use of supervised ML…

Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…

This work introduces a number of algebraic topology approaches, such as multicomponent persistent homology, multi-level persistent homology and electrostatic persistence for the representation, characterization, and description of small…

Hyperparameters in machine learning (ML) have received a fair amount of attention, and hyperparameter tuning has come to be regarded as an important step in the ML pipeline. But just how useful is said tuning? While smaller-scale…

We explore the recently introduced persistent reachability homology (PRH) of digraph data, i.e. data in the form of directed graphs. In particular, we study the effectiveness of PRH in network classification task in a key neuroscience…

Cardiac resynchronization therapy (CRT) has been established as an important therapy for heart failure. Mechanical dyssynchrony has the potential to predict responders to CRT. The aim of this study was to report the development and the…

The theory of multidimensional persistent homology was initially developed in the discrete setting, and involved the study of simplicial complexes filtered through an ordering of the simplices. Later, stability properties of…

We present a novel spectral machine learning (SML) method in screening for pancreatic mass using CT imaging. Our algorithm is trained with approximately 30,000 images from 250 patients (50 patients with normal pancreas and 200 patients with…

Peptide therapeutics are widely regarded as the "third generation" of drugs, yet progress in peptide Machine Learning (ML) are hindered by the absence of standardized benchmarks. Here we present PepBenchmark, which unifies datasets,…

Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be…

In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions with persistent homology analysis, so as to construct a series of…

Recently, persistent homology has had tremendous success in biomolecular data analysis. It works by examining the topological relationship or connectivity of a group of atoms in a molecule at a variety of scales, then rendering a family of…

Modern drug discovery is often time-consuming, complex and cost-ineffective due to the large volume of molecular data and complicated molecular properties. Recently, machine learning algorithms have shown promising results in virtual…

3-D shape is important to chemistry, but how important? Machine learning works best when the inputs are simple and match the problem well. Chemistry datasets tend to be very small compared to those generally used in machine learning so we…

Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…

This paper introduces the Mixed Aggregate Preference Logit (MAPL, pronounced "maple'') model, a novel class of discrete choice models that leverages machine learning to model unobserved heterogeneity in discrete choice analysis. The…