InteractionNet models noncovalent protein-ligand interactions with GNNs and explains predictions.
problem Modeling noncovalent protein-ligand interactions with graph neural networks.
method InteractionNet uses a GNN architecture with separated covalent and noncovalent convolution layers and layer-wise relevance propagation for explainability.
result InteractionNet successfully predicts noncovalent protein-ligand interactions with chemical relevance.
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.
problem Accurate prediction of protein-ligand interactions for drug design.
method Parallel Graph Neural Networks (GNN) integrating 3D structural data.
result GNN achieves high accuracy in predicting binary interactions and activity.
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.
problem Accurate and efficient simulation of protein-ligand binding dynamics.
method Physics-informed multi-grained group symmetric framework with BindingNet and augmented neural differential equation solver.
result Achieves over 1Kx speedup and up to 15x reduction in reconstruction error compared to standard methods.
Deep learning model predicts protein-ligand binding modes from docking data.
problem Improving protein-ligand binding mode prediction accuracy.
method Dual-graph architecture with separate sub-networks for ligand topology and protein-ligand interactions.
result Deep learning model outperforms docking programs in binding mode prediction.
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…
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.
problem Predicting protein-ligand binding affinity for various applications in life sciences.
method Traditional and deep learning models for binding affinity prediction.
result Improved predictive performance of AI-driven models.
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.
problem Developing novel compounds targeting specific proteins.
method Exploits pretrained language models to initialize and fine-tune targeted molecule generation models.
result Warm-started models outperform baseline models, with one-stage strategy showing better generalization.
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.
problem Persistent homology on manifolds is numerically inconsistent.
method Persistent de Rham-Hodge Laplacians in Eulerian representation.
result Avoids numerical inconsistency over multiscale manifolds.
Unified model learns from proteins and ligands for drug design.
problem Disjoint data sources and modeling assumptions limit joint use of structure- and ligand-based drug design.
method Contrastive Geometric Learning for Unified Computational Drug Design (ConGLUDe)
result Unified model achieves competitive zero-shot virtual screening performance and state-of-the-art ligand-conditioned pocket selection.
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.
problem Adapting pre-trained diffusion models to new target distributions without retraining.
method Lightweight, training-free particle-based approach that steers inference dynamics with optimal stability control.
result Consistently reduces variance and improves sample quality over existing methods.
Review of mathematical representations for biomolecular data.
problem Complexity and high dimensionality of biomolecular datasets hinder ML applications.
method Developed low-dimensional and scalable mathematical representations using algebraic topology, differential geometry, and graph theory.
result Mathematical representations improve protein-ligand binding predictions and other biomolecular applications.
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.
problem Learning from 3D molecular graphs for protein structure and binding.
method SE(3)-equivariant graph neural network for 3D molecular graphs.
result GCPNet achieves state-of-the-art performance in multiple molecular tasks.
Surrogate-based analysis of interactions via local effect smooths
problem Detecting and characterizing feature interactions in machine learning models
method Surrogate-based analysis using generalized additive models
result Empirical validation of effectiveness for pairwise interactions
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.
problem Detecting interactions between input features in neural networks.
method Topological analysis of neural network connectivity to quantify interaction strength.
result The PID algorithm outperforms state-of-the-art baselines in interaction detection tasks.
InteractE improves link prediction in KGs by increasing feature interactions.
problem Improving link prediction in knowledge graphs by inferring missing links.
method Feature permutation, novel feature reshaping, circular convolution.
result InteractE outperforms ConvE on multiple KG datasets.
iKF method uncovers complex variable interactions for scientific discovery.
problem Limited interpretability of existing models in decision-making applications.
method Iterative Kings' Forests (iKF) method to uncover multi-order interactions.
result iKF provides strong interpretive power for explainable modeling.
Graph neural network predicts vehicle interactions and trajectories for autonomous driving.
problem Predicting future motion of vehicles in traffic scenes.
method Graph neural network that jointly predicts interaction modes and 5-second future trajectories.
result Jointly predicting trajectories and interaction modes leads to lower trajectory error.
A graph neural network detects beneficial feature interactions for recommender systems.
problem Feature interactions are crucial but not all are beneficial for recommendation accuracy.
method Graph neural network with L0 activation regularization for edge prediction.
result The model outperforms baselines and automatically identifies beneficial feature interactions.
We describe and extract time-ordered multibody interactions from complex systems.
problem Complex systems with temporal and multibody dependencies.
method Decompose multivariate Markov chains into time-ordered multibody interactions. Algorithm to extract interactions from data. Measure complexity of interaction ensembles.
result Robust and efficient algorithm to infer time-ordered multibody interactions from data.
Dropout regularizes against high-order interactions by canceling interaction rates.
problem Overfitting to high-order interactions in neural networks.
method Analyzes Dropout through the lens of interaction effects, showing how it effectively cancels out the probability of surviving interactions of different orders.
result Dropout regularizes against high-order interactions by effectively canceling out the probability of surviving interactions of different orders.
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.
problem Generating realistic human interactions from limited data.
method Adversarial architecture with a recurrent encoder-decoder generator and dual-stream discriminator.
result SocialInteractionGAN produces high-quality action sequences of interacting people.
A new method detects interactions in machine learning models.
problem Interpreting non-linear and interaction effects in machine learning models.
method Regional effect plots with implicit interaction detection.
result The method quantifies and interprets feature effects reliably, less confounded by interactions.
Robot learns to imitate human interactions through deep learning.
problem Teaching robots to coordinate actions with human partners.
method Deep learning framework for motion embedding, prediction, and trajectory generation.
result Importance of predictive and adaptive components for successful imitation.
xDeepInt learns both vector-wise and bit-wise feature interactions.
problem Learning feature interactions for CTR prediction and recommendation.
method Polynomial Interaction Network (PIN) architecture with subspace-crossing mechanism.
result xDeepInt outperforms state-of-the-art models in CTR prediction and recommendation.
Unified framework for optimal transport on curved spaces using neural potentials.
problem Optimal transport on curved Riemannian manifolds.
method Entropic RNOT combines entropic regularization with neural pullback parameterization.
result Unified framework recovers entropic optimal coupling in strong probabilistic metrics.
This study explores how feature graphs enhance GNNs' performance in modeling interactions.
problem Improving GNNs' ability to model feature interactions effectively.
method Investigates feature graphs and their importance in GNNs, using experiments and theoretical support.
result Edges between interacting features are crucial for GNNs, while non-interaction edges can degrade performance.
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…
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.
problem Evaluate interaction prediction methods using IC-index.
method IC-index measures interaction direction prediction performance.
result IC-index complements existing prediction performance estimators.
This paper uses Gaussian mixtures to mimic interactions in large language models.
problem Simulating interactions in large language models (LLMs) is computationally expensive.
method Developed an interacting Gaussian mixture model (GMM) system to mimic LLM interactions.
result The interacting Gaussian mixture model system can generate, exchange, and update data and parameters efficiently.
Study reveals self-attention's role in learning and generalizing interactions.
problem Understanding self-attention's theoretical role in neural architectures.
method Interacting entities analysis, including multi-agent RL and genetic sequences.
result Self-attention efficiently represents, learns, and generalizes pairwise interactions.
Automated tests detect interactions in unstructured data.
problem Detecting interactions between latent variables in low-dimensional systems.
method Derive two interaction tests based on pairwise interventions and integrate them into an active learning pipeline.
result Tests can identify more known biological interactions than random search and standard active learning baselines.
Archipelago provides interpretable explanations of feature interactions in machine learning models.
problem Interpreting the impact of feature interactions on predictions in machine learning models.
method Archipelago is a novel framework for extracting and attributing feature interactions in a scalable and interpretable manner.
result Archipelago provides significantly more interpretable explanations of feature interactions than comparable methods.
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.
problem Modeling feature interactions in tabular data for predictive modeling.
method Tree-like Pairwise Interaction Network (PIN) architecture that captures pairwise feature interactions through a shared feed-forward neural network.
result PIN outperforms traditional and modern neural networks benchmarks in predictive accuracy.