DOCKSTRING simplifies docking simulations for better drug design benchmarks.
problem Lack of meaningful benchmarks for ligand design.
method Open-source Python package for docking scores, extensive dataset, and pharmaceutically-relevant tasks.
result Docking scores are more appropriate benchmarks than simple physicochemical properties.
Benchmark proposes to assess molecule docking efficiency.
problem Lack of realistic benchmarks for measuring progress in drug design.
method Proposes a docking-based benchmark using SMINA software.
result Graph-based generative models fail to generate high-scoring molecules.
Improved RL model for fragment-based molecule generation.
problem Generating molecules with high docking scores.
method Thorough reproduction, scrutiny, and improvement of the FREED model.
result The improved model produces molecules with superior docking scores.
Docking is an important tool in computational drug discovery that aims to predict the binding pose of a ligand to a target protein through a combination of pose scoring and optimization. A scoring function that is differentiable with respect to atom positions can be used for both scoring and gradient-based optimization…
CNP improves few-shot learning for docking scores in molecular datasets.
problem Few observations of many related functions in chemical datasets.
method Conditional Neural Processes (CNP) applied to docking scores.
result CNP shows competitive performance in few-shot learning tasks.
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.
Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous uncertainty quantification (UQ) of its solution quality (e.g. interface RMSD or iR…
Motivation: Prediction of ligands for proteins of known 3D structure is important to understand structure-function relationship, predict molecular function, or design new drugs. Results: We explore a new approach for ligand prediction in which binding pockets are represented by atom clouds. Each target pocket is compar…
In recent years, dock-less shared bikes have been widely spread across many cities in China and facilitate people's lives. However, at the same time, it also raises many problems about dock-less shared bike management due to the mismatching between demands and real distribution of bikes. Before deploying dock-less shar…
CogMol designs novel drug-like molecules for SARS-CoV-2 targets.
problem Designing efficient drugs for novel viral proteins.
method End-to-end framework combining VAE, controlled sampling, and predictors.
result Highly selective and affinity molecules for SARS-CoV-2 targets.
This study analyzes how weather impacts bike sharing usage in Washington D.C.
problem Understanding how weather affects bike sharing usage patterns.
method Gathered bike usage and weather data, used k-means clustering algorithm to identify clusters.
result Weather significantly impacts bike usage, with temperature and precipitation being the most influential factors.
Improves drug properties using a novel LLM and reinforcement learning.
problem Optimizing drug properties while retaining chemical stability.
method Structured Policy Optimization (SPO) for fine-tuning a large language model.
result Enhanced drug properties across multiple target objectives.
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…
This tutorial reviews RL-based methods for optimizing diffusion models to maximize specific metrics.
problem Optimizing diffusion models to generate samples that maximize specific metrics in practical applications.
method Various RL algorithms including PPO, differentiable optimization, reward-weighted MLE, value-weighted sampling, and path consistency learning.
result Exploration of strengths and limitations of RL-based fine-tuning algorithms and their benefits compared to non-RL-based approaches.
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.
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…
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…
New meta-optimizer learns from both point-based and population-based algorithms.
problem Current meta-optimizers are limited in space and unaware of uncertainty.
method Proposes a new meta-optimizer that learns in the space of both point-based and population-based algorithms, targeting a meta-loss function of cumulative regret and entropy.
result Empirical results show superior performance over existing competitors.
A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design. Current widely-adopted methods use physics-based energy functions to evaluate s…
Like many numerical methods, solvers for initial value problems (IVPs) on ordinary differential equations estimate an analytically intractable quantity, using the results of tractable computations as inputs. This structure is closely connected to the notion of inference on latent variables in statistics. We describe a …
Deep convolutional neural networks comprise a subclass of deep neural networks (DNN) with a constrained architecture that leverages the spatial and temporal structure of the domain they model. Convolutional networks achieve the best predictive performance in areas such as speech and image recognition by hierarchically …
DESMILES uses deep learning to improve drug discovery by optimizing molecule properties.
problem Improving the efficiency and accuracy of drug discovery through better molecular design.
method DESMILES is a deep neural network model that optimizes molecular properties for drug discovery.
result DESMILES achieved a 77% lower failure rate in modifying molecules to inhibit the dopamine receptor D2 compared to state-of-the-art models.
SDG uses optimal control to improve classifier guidance in low-density regions.
problem Inefficient guidance in low-density regions of posterior distributions.
method Integrates stochastic optimal control with Stein variational inference to compute the steepest descent direction.
result SDG improves guidance in low-density regions, outperforming standard methods.
In urban environments, supply resources have to be constantly matched to the "right" locations (where customer demand is present) so as to improve quality of life. For instance, ambulances have to be matched to base stations regularly so as to reduce response time for emergency incidents in EMS (Emergency Management Sy…
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.
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.
Score matching is a popular method for estimating unnormalized statistical models. However, it has been so far limited to simple, shallow models or low-dimensional data, due to the difficulty of computing the Hessian of log-density functions. We show this difficulty can be mitigated by projecting the scores onto random…
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.
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.
This paper proposes a two-stage scoring approach to help lenders decide their fund allocations in the peer-to-peer (P2P) lending market. The existing scoring approaches focus on only either probability of default (PD) prediction, known as credit scoring, or profitability prediction, known as profit scoring, to identify…
In political redistricting, the compactness of a district is used as a quantitative proxy for its fairness. Several well-established, yet competing, notions of geographic compactness are commonly used to evaluate the shapes of regions, including the Polsby-Popper score, the convex hull score, and the Reock score, and t…