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.
DOCKSTRING simplifies docking simulations for better drug design benchmarks.
Benchmark proposes to assess molecule docking efficiency.
Improved RL model for fragment-based molecule generation.
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.
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…
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…
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.
This study analyzes how weather impacts bike sharing usage in Washington D.C.
Improves drug properties using a novel LLM and reinforcement learning.
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.
New model uses pretrained biochemical language models to generate drug compounds.
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…
Learning to optimize has emerged as a powerful framework for various optimization and machine learning tasks. Current such "meta-optimizers" often learn in the space of continuous optimization algorithms that are point-based and uncertainty-unaware. To overcome the limitations, we propose a meta-optimizer that learns i…
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…
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…
Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a particular drug discovery goal. The use of deep learning technologies could augment the …
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 …
SDG uses optimal control to improve classifier guidance in low-density regions.
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.
Improves score estimation for noised targets using known clean scores.
This work improves likelihood of score-based diffusion ODEs using high-order denoising score matching.
Study compares multivariate scoring rules for distribution forecasts.
A new method improves data generation quality by correcting score mismatches.
New scoring rules improve probabilistic classification model evaluation.
Extends denoising and score estimation to energy models via Tweedie's formula.
Mixed-SCORE+ improves community detection in weak signal networks.
Examining ESG scoring method for reliability.
Classifies intrinsically linked tournaments by their score sequences.
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.
The statistical leverage scores of a complex matrix record the degree of alignment between col and the coordinate axes in . 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
New ESGM scores include a 'Missing' pillar to account for unpublished ESG data.
Forecasts of multivariate probability distributions are required for a variety of applications. Scoring rules enable the evaluation of forecast accuracy, and comparison between forecasting methods. We propose a theoretical framework for scoring rules for multivariate distributions, which encompasses the existing quadra…
The NL score optimizes speaker recognition tasks.
Regularizes attention scores in vision transformers using bootstrapping.
A framework for sensitivity measures using scoring functions.
Null-Calibrated Conformal Selection via Target-Membership Scores
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.
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…