A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
A new method for virtual drug screening detects top treatments.
Efficiently allocate budgets for LLM-assisted virtual screening to reduce costs.
KANEL combines models for early hit enrichment in virtual screening.
Study improves reliability of neural models for virtual screening.
Rapid overlay of chemical structures (ROCS) is a standard tool for the calculation of 3D shape and chemical ("color") similarity. ROCS uses unweighted sums to combine many aspects of similarity, yielding parameter-free models for virtual screening. In this report, we decompose the ROCS color force field into "color com…
We introduce a deep learning architecture for structure-based virtual screening that generates fixed-sized fingerprints of proteins and small molecules by applying learnable atom convolution and softmax operations to each compound separately. These fingerprints are further transformed non-linearly, their inner-product …
Deep neural network identifies potential SARS-CoV-2 inhibitors.
Bayesian learning improves reliability of molecular predictions for hit compound discovery.
Deep learning uses ROC cost functions to improve virtual screening accuracy.
FlowMO uses Gaussian Processes for molecular property prediction with uncertainty.
Excellent ranking power along with well calibrated probability estimates are needed in many classification tasks. In this paper, we introduce a technique, Calibrated Boosting-Forest that captures both. This novel technique is an ensemble of gradient boosting machines that can support both continuous and binary labels. …
New method uses Riemannian geometry to describe molecular shapes.
Virtual screening (VS) is widely used during computational drug discovery to reduce costs. Chemogenomics-based virtual screening (CGBVS) can be used to predict new compound-protein interactions (CPIs) from known CPI network data using several methods, including machine learning and data mining. Although CGBVS facilitat…
Unified model learns from proteins and ligands for drug design.
Computational chemists typically assay drug candidates by virtually screening compounds against crystal structures of a protein despite the fact that some targets, like the Opioid Receptor and other members of the GPCR family, traverse many non-crystallographic states. We discover new conformational states of …
Computational approaches to drug discovery can reduce the time and cost associated with experimental assays and enable the screening of novel chemotypes. Structure-based drug design methods rely on scoring functions to rank and predict binding affinities and poses. The ever-expanding amount of protein-ligand binding an…
Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based neural network architectures have emerged in recent years as the most successful …
Accurate prediction of drug-target interaction (DTI) is essential for in silico drug design. For the purpose, we propose a novel approach for predicting DTI using a GNN that directly incorporates the 3D structure of a protein-ligand complex. We also apply a distance-aware graph attention algorithm with gate augmentatio…
Chemical space is so large that brute force searches for new interesting molecules are infeasible. High-throughput virtual screening via computer cluster simulations can speed up the discovery process by collecting very large amounts of data in parallel, e.g., up to hundreds or thousands of parallel measurements. Bayes…
Undetected overfitting can occur when there are significant redundancies between training and validation data. We describe AVE, a new measure of training-validation redundancy for ligand-based classification problems that accounts for the similarity amongst inactive molecules as well as active. We investigated seven wi…
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-d…
RaSE screens variables via random subspaces, identifying joint effects.
Deep learning methods such as multitask neural networks have recently been applied to ligand-based virtual screening and other drug discovery applications. Using a set of industrial ADMET datasets, we compare neural networks to standard baseline models and analyze multitask learning effects with both random cross-valid…
Timely assessment of compound toxicity is one of the biggest challenges facing the pharmaceutical industry today. A significant proportion of compounds identified as potential leads are ultimately discarded due to the toxicity they induce. In this paper, we propose a novel machine learning approach for the prediction o…
The problem of learning a sparse model is conceptually interpreted as the process of identifying active features/samples and then optimizing the model over them. Recently introduced safe screening allows us to identify a part of non-active features/samples. So far, safe screening has been individually studied either fo…
New Bayesian optimization models for efficient material screening.
This paper treats the problem of screening for variables with high correlations in high dimensional data in which there can be many fewer samples than variables. We focus on threshold-based correlation screening methods for three related applications: screening for variables with large correlations within a single trea…
Statistical inference can be computationally prohibitive in ultrahigh-dimensional linear models. Correlation-based variable screening, in which one leverages marginal correlations for removal of irrelevant variables from the model prior to statistical inference, can be used to overcome this challenge. Prior works on co…
New screening rules improve lasso model fitting efficiency.
A new screening rule 'dynamic Sasvi' improves sparse optimization speed.
In the present paper, we introduce screen transversal lightlike submanifolds of metallic semi-Riemannian manifolds with its subclasses, namely screen transversal anti-invariant, radical screen transversal and isotropic screen transversal lightlike submanifolds, and give an example. We show that there do not exist co-is…
New AI platform screens portfolios for desirable firms and news.
A variable screening procedure via correlation learning was proposed Fan and Lv (2008) to reduce dimensionality in sparse ultra-high dimensional models. Even when the true model is linear, the marginal regression can be highly nonlinear. To address this issue, we further extend the correlation learning to marginal nonp…
Recent computational strategies based on screening tests have been proposed to accelerate algorithms addressing penalized sparse regression problems such as the Lasso. Such approaches build upon the idea that it is worth dedicating some small computational effort to locate inactive atoms and remove them from the dictio…
A new screening method for high-dimensional data reduces computational cost.
We study safe screening for metric learning. Distance metric learning can optimize a metric over a set of triplets, each one of which is defined by a pair of same class instances and an instance in a different class. However, the number of possible triplets is quite huge even for a small dataset. Our safe triplet scree…
In this paper we develop the notion of screen isoparametric hypersurface for null hypersurfaces of Robertson-Walker spacetimes. Using this formalism we derive Cartan identities for the screen principal curvatures of null screen hypersurfaces in Lorentzian space forms and provide a local characterization of such hypersu…
A new screening rule improves lasso solving speed.
Recently, to solve large-scale lasso and group lasso problems, screening rules have been developed, the goal of which is to reduce the problem size by efficiently discarding zero coefficients using simple rules independently of the others. However, screening for overlapping group lasso remains an open challenge because…
The main purpose of the present paper is to study the geometry of screen transversal lightlike submanifolds and radical screen transversal lightlike submanifolds and screen transversal anti-invariant lightlike submanifolds of Golden Semi-Riemannian manifolds. We investigate the geometry of distributions and obtain nece…
In data sets with many more features than observations, independent screening based on all univariate regression models leads to a computationally convenient variable selection method. Recent efforts have shown that in the case of generalized linear models, independent screening may suffice to capture all relevant feat…
Deep learning predicts breast cancer with high accuracy from patient data.
New rules reduce SLOPE model fitting time by screening out irrelevant variables.
A new method reduces feature screening cost from to .
To find efficient screening methods for high dimensional linear regression models, this paper studies the relationship between model fitting and screening performance. Under a sparsity assumption, we show that a subset that includes the true submodel always yields smaller residual sum of squares (i.e., has better model…
Variable screening is a fast dimension reduction technique for assisting high dimensional feature selection. As a preselection method, it selects a moderate size subset of candidate variables for further refining via feature selection to produce the final model. The performance of variable screening depends on both com…
This paper introduces LR-FFS for robust feature screening in federated learning under label shift.
Robust support vector machine (RSVM) has been shown to perform remarkably well to improve the generalization performance of support vector machine under the noisy environment. Unfortunately, in order to handle the non-convexity induced by ramp loss in RSVM, existing RSVM solvers often adopt the DC programming framework…