arXiv research

Quantitative structure-activity relationship (QSAR) modelling is effective 'bridge' to search the reliable relationship related bioactivity to molecular structure. A QSAR classification model contains a lager number of redundant, noisy and irrelevant descriptors. To address this problem, various of methods have been pr…

Persistent homology provides a new, efficient molecular descriptor for protein dynamics.

New method uses geometric moments for accurate machine learning potentials.

A new model designs molecular latent vectors for drug discovery.

New method uses Riemannian geometry to describe molecular shapes.

Proposes a new model to predict polymer properties by integrating various data types.

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that…

A set of molecular descriptors whose length is independent of molecular size is developed for machine learning models that target thermodynamic and electronic properties of molecules. These features are evaluated by monitoring performance of kernel ridge regression models on well-studied data sets of small organic mole…

Machine learning predicts molecular crystal stability.

A framework separates chemical and structural contributions to aqueous solubility.

We introduce weighted atom-centered symmetry functions (wACSFs) as descriptors of a chemical system's geometry for use in the prediction of chemical properties such as enthalpies or potential energies via machine learning. The wACSFs are based on conventional atom-centered symmetry functions (ACSFs) but overcome the un…

In this paper, a new descriptor selection method for selecting an optimal combination of important descriptors of sulfonamide derivatives data, named self tuned reweighted sampling (STRS), is developed. descriptors are defined as the descriptors with large absolute coefficients in a multivariate linear regression model…

New method uses Riemannian geometry to quantify molecular shapes.

Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein structure hinders the direct association of the signaling activity with the molecular s…

Framework separates chemical and structural contributions to aqueous solubility.

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…

Computer-Aided Drug Discovery research has proven to be a promising direction in drug discovery. In recent years, Deep Learning approaches have been applied to problems in the domain such as Drug-Target Interaction Prediction and have shown improvements over traditional screening methods. An existing challenge is how t…

New algorithm improves model generalization in structured biomedical domains.

KANEL combines models for early hit enrichment in virtual screening.

Study compares GNNs and classical molecular featurisations for molecular property and cliff prediction.

A fundamental problem in applying machine learning techniques for chemical problems is to find suitable representations for molecular and crystal structures. While the structure representations based on atom connectivities are prevalent for molecules, two-dimensional descriptors are not suitable for describing molecula…

DECAF optimizes molecular graphs for ensemble properties, improving drug design accuracy.

Due to its high computational speed and accuracy compared to ab-initio quantum chemistry and forcefield modeling, the prediction of molecular properties using machine learning has received great attention in the fields of materials design and drug discovery. A main ingredient required for machine learning is a training…

In our study, we demonstrate the synergy effect between convolutional neural networks and the multiplicity of SMILES. The model we propose, the so-called Convolutional Neural Fingerprint (CNF) model, reaches the accuracy of traditional descriptors such as Dragon (Mauri et al. [22]), RDKit (Landrum [18]), CDK2 (Willigha…

Machine learning and deep learning have gained popularity and achieved immense success in Drug discovery in recent decades. Historically, machine learning and deep learning models were trained on either structural data or chemical properties by separated model. In this study, we proposed an architecture training simult…

AI and HPC help screen millions of molecules for SARS-CoV-2 treatments.

Tabular in-context learners perform well on biomolecular tasks, but performance depends on the representation used.

Enhances graph neural networks with random walks to improve performance.

Optimizes atomic descriptors to reduce redundancy and improve machine learning models.

This work characterizes topological descriptors of graph products and their expressive power.

One of the key requirements for incorporating machine learning into the drug discovery process is complete reproducibility and traceability of the model building and evaluation process. With this in mind, we have developed an end-to-end modular and extensible software pipeline for building and sharing machine learning …

This paper presents a novel approach to exploit the distinctive invariant features in convolutional neural network. The proposed CNN model uses Scale Invariant Feature Transform (SIFT) descriptor instead of the max-pooling layer. Max-pooling layer discards the pose, i.e., translational and rotational relationship betwe…

Informative and discriminative feature descriptors play a fundamental role in deformable shape analysis. For example, they have been successfully employed in correspondence, registration, and retrieval tasks. In the recent years, significant attention has been devoted to descriptors obtained from the spectral decomposi…

Although the recent progress in the deep neural network has led to the development of learnable local feature descriptors, there is no explicit answer for estimation of the necessary size of a neural network. Specifically, the local feature is represented in a low dimensional space, so the neural network should have mo…

For quantitative structure-property relationship (QSPR) studies in chemoinformatics, it is important to get interpretable relationship between chemical properties and chemical features. However, the predictive power and interpretability of QSPR models are usually two different objectives that are difficult to achieve s…

ALP outperforms other data descriptors in one-class classification.

Future advancement of engineering applications is dependent on design of novel materials with desired properties. Enormous size of known chemical space necessitates use of automated high throughput screening to search the desired material. The high throughput screening uses quantum chemistry calculations to predict mat…

We introduce a new learned descriptor for audio signals which is efficient for event representation. The entries of the descriptor are produced by evaluating a set of regressors on the input signal. The regressors are class-specific and trained using the random regression forests framework. Given an input signal, each …

Wittgenstein's Rule Following evolves datasets by extrapolating structural descriptors.

Support Vector Machines (SVMs) are powerful learners that have led to state-of-the-art results in various computer vision problems. SVMs suffer from various drawbacks in terms of selecting the right kernel, which depends on the image descriptors, as well as computational and memory efficiency. This paper introduces a n…

PolyGraph Discrepancy improves graph generative model evaluation.

Counting and classifying blood cells is an important diagnostic tool in medicine. Support Vector Machines are increasingly popular and efficient and could replace artificial neural network systems. Here a method to classify blood cells is proposed using SVM. A set of statistics on images are implemented in C++. The MPE…

Method separates target signal properties from noisy mixtures.

The ability to visually re-identify objects is a fundamental capability in vision systems. Oftentimes, it relies on collections of visual signatures based on descriptors, such as SIFT or SURF. However, these traditional descriptors were designed for a certain domain of surface appearances and geometries (limited relief…

Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a drug-like molecule to a given target. These models require expert-level knowled…

Combines curvature descriptors with TDA for graph model evaluation.

Paper introduces stable vectorization for multiparameter PH using signed barcodes.

The PageRank of a graph is a scalar function defined on the node set of the graph which encodes nodes centrality information of the graph. In this article, we use the PageRank function along with persistent homology to obtain a scalable graph descriptor and utilize it to compare the similarities between graphs. For a g…