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.
InteractionNet models noncovalent protein-ligand interactions with GNNs and explains predictions.
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…
Novel parallel GNN predicts protein-ligand interactions with high accuracy.
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…
NeuralMD accelerates protein-ligand binding simulations 1Kx faster.
Identification of high affinity drug-target interactions is a major research question in drug discovery. Proteins are generally represented by their structures or sequences. However, structures are available only for a small subset of biomolecules and sequence similarity is not always correlated with functional similar…
We present a simple, modular graph-based convolutional neural network that takes structural information from protein-ligand complexes as input to generate models for activity and binding mode prediction. Complex structures are generated by a standard docking procedure and fed into a dual-graph architecture that include…
The identification of novel drug-target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where the goal is to determine whether a DT pair interacts or not. However, protein-l…
This abstract reviews recent methods for predicting protein-ligand binding affinity.
Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning techniques can make use of the increasing amounts of structural data that are beco…
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…
New model uses pretrained biochemical language models to generate drug compounds.
The effective representation of proteins is a crucial task that directly affects the performance of many bioinformatics problems. Related proteins usually bind to similar ligands. Chemical characteristics of ligands are known to capture the functional and mechanistic properties of proteins suggesting that a ligand base…
New method for manifold topological learning avoids remeshing issues.
Unified model learns from proteins and ligands for drug design.
We present a three-dimensional graph convolutional network (3DGCN), which predicts molecular properties and biochemical activities, based on 3D molecular graph. In the 3DGCN, graph convolution is unified with learning operations on the vector to handle the spatial information from molecular topology. The 3DGCN model ex…
Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process. Currently, there is a notable shift towards machine learning (ML) methodologies to aid such procedures. Deep learning has recently gained considerable attention as it allows the model to "learn" to extra…
Molecular simulations produce very high-dimensional data-sets with millions of data points. As analysis methods are often unable to cope with so many dimensions, it is common to use dimensionality reduction and clustering methods to reach a reduced representation of the data. Yet these methods often fail to capture the…
DriftLite improves inference quality of diffusion models without retraining.
Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand Challenges. However, the intricate structural complexity and high ML dimensionality of bi…
Deep neural networks have achieved state of the art accuracy at classifying molecules with respect to whether they bind to specific protein targets. A key breakthrough would occur if these models could reveal the fragment pharmacophores that are causally involved in binding. Extracting chemical details of binding from …
GCPNet improves molecular graph learning for protein structure and binding.
Surrogate-based analysis of interactions via local effect smooths
Factorization Machine (FM) is a widely used supervised learning approach by effectively modeling of feature interactions. Despite the successful application of FM and its many deep learning variants, treating every feature interaction fairly may degrade the performance. For example, the interactions of a useless featur…
A new method detects interactions in neural networks using topological analysis.
iKF method uncovers complex variable interactions for scientific discovery.
Graph neural network predicts vehicle interactions and trajectories for autonomous driving.
A graph neural network detects beneficial feature interactions for recommender systems.
We describe and extract time-ordered multibody interactions from complex systems.
Dropout regularizes against high-order interactions by canceling interaction rates.
Understanding how features interact with each other is of paramount importance in many scientific discoveries and contemporary applications. Yet interaction identification becomes challenging even for a moderate number of covariates. In this paper, we suggest an efficient and flexible procedure, called the interaction …
Multitask Gaussian process (MTGP) is powerful for joint learning of multiple tasks with complicated correlation patterns. However, due to the assembling of additive independent latent functions, all current MTGPs including the salient linear model of coregionalization (LMC) and convolution frameworks cannot effectively…
SocialInteractionGAN generates realistic human interactions from low-dimensional data.
A new method detects interactions in machine learning models.
xDeepInt learns both vector-wise and bit-wise feature interactions.
Most existing knowledge graphs suffer from incompleteness, which can be alleviated by inferring missing links based on known facts. One popular way to accomplish this is to generate low-dimensional embeddings of entities and relations, and use these to make inferences. ConvE, a recently proposed approach, applies convo…
This study explores how feature graphs enhance GNNs' performance in modeling interactions.
Interpreting neural networks is a crucial and challenging task in machine learning. In this paper, we develop a novel framework for detecting statistical interactions captured by a feedforward multilayer neural network by directly interpreting its learned weights. Depending on the desired interactions, our method can a…
Unified framework for optimal transport on curved spaces using neural potentials.
We introduce interactive structure discovery, a generic framework that encompasses many interactive learning settings, including active learning, top-k item identification, interactive drug discovery, and others. We adapt a recently developed active learning algorithm of Tosh and Dasgupta (2017) for interactive structu…
Paper introduces IC-index to evaluate interaction prediction methods.
This paper uses Gaussian mixtures to mimic interactions in large language models.
Study reveals self-attention's role in learning and generalizing interactions.
Archipelago provides interpretable explanations of feature interactions in machine learning models.
Automated tests detect interactions in unstructured data.
We study the power of interactivity in local differential privacy. First, we focus on the difference between fully interactive and sequentially interactive protocols. Sequentially interactive protocols may query users adaptively in sequence, but they cannot return to previously queried users. The vast majority of exist…
PIN models feature interactions using a neural network that mimics decision trees.
The paper explains DNNs by quantifying interactions among input variables.