Visualizes 3D CNNs for protein-ligand scoring.
problem Interpreting complex neural network decisions for protein-ligand scoring.
method Three visualization methods for 3D CNNs, including filters and weights.
result Visualizations aid in tuning and designing neural networks.
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…
Deep learning predicts protein-ligand binding affinity with high accuracy.
problem Predicting protein-ligand binding affinity for drug discovery.
method 3D convolutional neural network trained on CASF and Astex Diverse Set benchmarks.
result Deep learning model outperformed classical scoring functions.
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…
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.
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.
ChemBoost predicts protein-ligand binding affinity using SMILES syntax.
problem Predicting high affinity drug-target interactions from sequence similarity alone.
method ChemBoost uses SMILES syntax to represent ligands as documents and proteins as sequences or ligand-centric features. It learns chemical word embeddings and predicts affinities using eXtreme Gradient Boosting.
result ChemBoost outperforms state-of-the-art systems in predicting protein-ligand affinities.
Novel GNN predicts drug-target interactions using protein-ligand 3D structures.
problem Accurate prediction of drug-target interactions for in silico drug design.
method 3D structure-embedded graph representations and distance-aware graph attention algorithm with gate augmentation.
result Our model outperforms docking and other deep learning methods in virtual screening and pose prediction.
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.
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.
Dimensionality reduction helps analyze molecular simulations data.
problem High-dimensional molecular simulation data is hard to analyze.
method Various dimensionality reduction methods (k-means, autoencoder, PCA, tICA) applied to molecular simulation data.
result Methods learned different conformations of molecular processes.
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.
DeepDTA predicts drug-target binding affinities using deep learning.
problem Predicting the continuum of binding strength values between drugs and targets.
method Uses deep learning, specifically CNNs, to model 1D representations of drug and target sequences.
result Deep learning model outperforms state-of-the-art methods in predicting DT binding affinities.
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.
3DGCN predicts molecular properties and biochemical activities using 3D molecular graph.
problem Predicting molecular properties and biochemical activities from 3D molecular graphs.
method Unified graph convolution with learning operations to handle spatial information, distinguishing 3D rotations.
result Significantly higher performance on various molecular tasks compared to other deep-learning models.
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.
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.
Novel ligand-based method improves protein representation performance.
problem Improving protein representation for bioinformatics tasks.
method Proposes SMILESVec method to represent ligands and compute protein similarity.
result Ligand-based protein representation performs as well as sequence-based methods.
Generative models' evaluation scores can be misleading, leading to inflated grades.
problem Misleading evaluation scores for generative models.
method Analyzed and compared various scores for evaluating synthetic vs. ground-truth data.
result The Eden score avoids grade inflation and better aligns with human perception.
Deep models learn biases from datasets, hindering understanding of binding mechanisms.
problem Dataset biases prevent deep models from revealing fragment logic of protein-ligand binding.
method Attribution method to identify and exploit dataset biases in neural networks.
result Deep models can be fooled into learning spurious correlations from biased datasets.
Improves score estimation for noised targets using known clean scores.
problem Poor score estimation at low noise levels in Denoising Score Matching.
method Introduces Target Score Identity and Target Score Matching loss.
result Score estimates are more accurate at low noise levels.
This work improves likelihood of score-based diffusion ODEs using high-order denoising score matching.
problem The gap between maximum likelihood and score matching objectives for score-based diffusion ODEs.
method High-order denoising score matching to maximize likelihood.
result Score-based diffusion ODEs achieve better likelihood on synthetic and CIFAR-10 data.
Study compares multivariate scoring rules for distribution forecasts.
problem Evaluating the discrimination ability of multivariate scoring rules.
method Simulation study comparing energy and variogram scores using historical data.
result Variogram score with p=0.5 outperforms other scores.
A new method improves data generation quality by correcting score mismatches.
problem Score mismatch issue in conditional score-based data generation methods.
method Denoising Likelihood Score Matching (DLSM) loss for classifier training.
result The proposed method outperforms previous methods on Cifar-10 and Cifar-100 benchmarks.
New scoring rules improve probabilistic classification model evaluation.
problem Traditional scoring rules misalign with the preference for correct classifications.
method Introduces Penalized Brier Score (PBS) and Penalized Logarithmic Loss (PLL) to modify proper scoring rules.
result PBS and PLL better identify optimal checkpoints and early stopping points, leading to superior F1 scores.
Extends denoising and score estimation to energy models via Tweedie's formula.
problem Linking denoising and score estimation for a wider range of distributions.
method Derives a fundamental identity connecting energy score derivatives and scores.
result Establishes a new identity for energy scores analogous to Tweedie's formula.
Mixed-SCORE+ improves community detection in weak signal networks.
problem Detecting communities in weak signal networks.
method Proposes Mixed-SCORE+ combining properties of Mixed-SCORE and SCORE+.
result Significantly improves detection error rates on Polblogs and weak signal networks.
Examining ESG scoring method for reliability.
problem Reliability of ESG scoring methodology.
method Analyzing Refinitiv's ESG scoring process.
result Methodology needs improvement for trustworthiness.
New scoring rules for multivariate distributions and level sets.
problem Evaluating forecast accuracy for multivariate distributions and level sets.
method Theoretical framework for scoring rules, decomposition of multivariate scoring functions, numerical algorithm for computation.
result New scoring functions for multivariate distributions and level sets, including density and cumulative distribution level sets.
Classifies intrinsically linked tournaments by their score sequences.
problem Classifying intrinsically linked tournaments using their score sequences.
method Examining the score sequences of tournaments and identifying linkless sequences.
result The vast majority of score sequences for 8-vertex tournaments are linkless.
A new method for estimating complex models and high-dimensional data.
problem Difficulty in computing Hessian of log-density functions for complex models and high-dimensional data.
method Sliced score matching, which projects scores onto random vectors before comparison.
result Sliced score matching can learn deep energy-based models and produce accurate score estimates.
Improved score matching methods for estimating score functions and Hessians without high dimensionality.
problem Estimating score functions and Hessians efficiently in high-dimensional data.
method Implicit score matching and denoising score matching, leveraging Gagliardo-Nirenberg inequalities.
result Achieves convergence rates similar to denoising score matching and estimates Hessians without dimensionality issues.
Map projections can reverse district compactness scores, affecting fairness evaluations.
problem District compactness scores can be reordered by map projections, impacting fairness evaluations.
method Mathematical proof and empirical demonstration of map projection effects on compactness scores.
result Map projections can reverse the order of compactness scores, altering fairness evaluations.
Two-stage scoring approach for P2P lending improves loan profitability prediction.
problem Class imbalance and lack of profitability prediction in existing scoring methods.
method Integrates credit scoring and profit scoring using wide and deep learning.
result Two-stage scoring approach outperforms existing methods in loan profitability prediction.
The statistical leverage scores of a complex matrix A∈Cn×d record the degree of alignment between col(A) and the coordinate axes in Cn. These score are used in random sampling algorithms for solving certain numerical linear algebra problems. In this paper we present a max-plus algebr…
Optimal score function estimation via empirical risk minimization
problem Estimating the score function of a probability measure on the flat torus from a sample
method Constraining the hypothesis space to a Sobolev ball
result Minimax estimation rates are achieved
New ESGM scores include a 'Missing' pillar to account for unpublished ESG data.
problem Unpublished ESG data affects the reliability of ESG scores.
method Formulated a new 'Missing' pillar and introduced ESGM scores.
result ESGM scores improve risk assessment and avoid exclusion of assets.
The NL score optimizes speaker recognition tasks.
problem Improving speaker recognition accuracy.
method Established the theory of optimal scores based on normalized likelihood.
result NL score is equivalent to PLDA likelihood ratio under certain conditions.
Regularizes attention scores in vision transformers using bootstrapping.
problem Noisy and diffused attention maps in ViT limit interpretability.
method Statistical learning techniques, bootstrapping of attention scores.
result Improves shrinkage and sparsity of attention scores.
Null-Calibrated Conformal Selection via Target-Membership Scores
problem Identifying test candidates whose unknown responses fall in a target region while controlling the false discovery rate
method Membership-score-based conformal selection
result Finite-sample valid null p-values
A framework for sensitivity measures using scoring functions.
problem Constructing sensitivity measures for any elicitable functional.
method Score-based sensitivities constructed via consistent scoring functions.
result Demonstrated intuitive and desirable properties of score-based sensitivities.
Score matching is a recently developed parameter learning method that is particularly effective to complicated high dimensional density models with intractable partition functions. In this paper, we study two issues that have not been completely resolved for score matching. First, we provide a formal link between maxim…
The paper establishes bounds for score-matching in causal discovery and generative modeling.
problem Estimating causal relationships from data.
method Training a deep neural network to estimate the score function and applying it to causal discovery.
result Bounds on the error rate of causal discovery methods using score-matching.
SCORE improves community detection for networks with weak signals.
problem Detecting communities in networks with weak signals and severe degree heterogeneity.
method SCORE+ incorporates new features to improve SCORE's performance.
result SCORE+ achieves lower clustering errors for networks with weak signals.
Paper bridges score estimation to parameter and density estimation in DDPMs.
problem Efficiently estimating scores for generative models.
method Introduces a framework linking score estimation to parameter and density estimation.
result Denoising score-matching in DDPMs is asymptotically efficient for parameter estimation.