The study improves compound selection in in silico screening by focusing on model's ability to predict desirable outcomes.
problem Improving compound selection in in silico screening to reduce errors and enhance generalization.
method Extending learning theory, the study analyzes the impact of selection policies on generalization and proposes a method to mitigate challenges.
result Generalization can be enhanced by considering a model's ability to predict the fraction of desired outcomes in a batch.
STMT predicts compounds in unknown areas with trend reflection.
problem Predicting properties of unknown compounds in the extrapolation area.
method Stochastic Threshold Model Trees (STMT) that reflects data trends.
result STMT improves prediction accuracy for one compound in the extrapolation area.
Bayesian learning improves reliability of molecular predictions for hit compound discovery.
problem Improving reliability of machine learning predictions for virtual screening.
method Bayesian learning algorithms applied to graph neural networks.
result Bayesian learning leads to well-calibrated predictions and higher hit compound success.
QSAR models struggle to predict activity cliffs, but graph isomorphism features improve AC-sensitivity.
problem QSAR models struggle to predict activity cliffs (ACs).
method Nine distinct QSAR models combining molecular representation methods and regression techniques.
result Graph isomorphism features improve AC-sensitivity.
Mack's estimator improves chain ladder prediction for large exposure insurance models.
problem Uncertainty quantification in compound Poisson loss models.
method Large exposure asymptotics applied to Mack's estimator.
result Chain ladder prediction uncertainty can be quantified without model assumptions.
Virtual screening (VS) is widely used during computational drug discovery to reduce costs. Chemogenomics-based virtual screening (CGBVS) can be used to predict new compound-protein interactions (CPIs) from known CPI network data using several methods, including machine learning and data mining. Although CGBVS facilitat…
In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure i…
Supervised learning models, also known as quantitative structure-activity regression (QSAR) models, are increasingly used in assisting the process of preclinical, small molecule drug discovery. The models are trained on data consisting of a finite dimensional representation of molecular structures and their correspondi…
With the rapid development of high-throughput technologies, parallel acquisition of large-scale drug-informatics data provides huge opportunities to improve pharmaceutical research and development. One significant application is the purpose prediction of small molecule compounds, aiming to specify therapeutic propertie…
DeepSIBA predicts biological effects of chemical structures using graph neural networks.
problem Predicting biological effects of chemical structures for drug discovery.
method Siamese Graph Convolutional Neural Networks for structure-biological effect mapping.
result Highly accurate predictions of biological effects for structurally dissimilar compounds.
In silico drug-target interaction (DTI) prediction is an important and challenging problem in biomedical research with a huge potential benefit to the pharmaceutical industry and patients. Most existing methods for DTI prediction including deep learning models generally have binary endpoints, which could be an oversimp…
Shear stress distribution prediction in open channels is of utmost importance in hydraulic structural engineering as it directly affects the design of stable channels. In this study, at first, a series of experimental tests were conducted to assess the shear stress distribution in prismatic compound channels. The shear…
Timely assessment of compound toxicity is one of the biggest challenges facing the pharmaceutical industry today. A significant proportion of compounds identified as potential leads are ultimately discarded due to the toxicity they induce. In this paper, we propose a novel machine learning approach for the prediction o…
ChemGrapher uses deep learning to automatically convert chemical compound images into accurate graphs.
problem Automatically converting chemical compound images into accurate graphs with correct bond multiplicity and stereochemical information.
method Developed a deep neural network model for optical compound recognition, including segmentation and classification models.
result Significant error reductions in bond multiplicity and stereochemical information compared to existing tools.
A new method reduces compounding errors in model-based reinforcement learning.
problem Compounding errors in long horizon predictions from model-based reinforcement learning.
method Maximum Entropy Model Rollouts (MEMR) with non-uniform sampling and prioritized experience replay.
result Significantly reduces computation requirements compared to other model-based methods.
With the advent of deep generative models in computational chemistry, in silico anticancer drug design has undergone an unprecedented transformation. While state-of-the-art deep learning approaches have shown potential in generating compounds with desired chemical properties, they disregard the genetic profile and prop…
The paper develops a Gaussian process model for predicting chemical efficacy.
problem Statistical methodologies for analyzing chemical databases are limited.
method Conditional Gaussian process models with Tanimoto distance and a scaling parameter.
result Predictive performance improves when accounting for chemical space correlation.
The understanding of the type of inhibitory interaction plays an important role in drug design. Therefore, researchers are interested to know whether a drug has competitive or non-competitive interaction to particular protein targets. Method: to analyze the interaction types we propose factorization method Macau which …
Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and interpretability. Results: We present a seamless integration of domain knowledges and …
Prediction of toxicity levels of chemical compounds is an important issue in Quantitative Structure-Activity Relationship (QSAR) modeling. Although toxicity prediction has achieved significant progress in recent times through deep learning, prediction accuracy levels obtained by even very recent methods are not yet ver…
Model-based reinforcement learning is an appealing framework for creating agents that learn, plan, and act in sequential environments. Model-based algorithms typically involve learning a transition model that takes a state and an action and outputs the next state---a one-step model. This model can be composed with itse…
In this paper we examine the claims reserving problem using Tweedie's compound Poisson model. We develop the maximum likelihood and Bayesian Markov chain Monte Carlo simulation approaches to fit the model and then compare the estimated models under different scenarios. The key point we demonstrate relates to the compar…
A major challenge in computational chemistry is the generation of novel molecular structures with desirable pharmacological and physiochemical properties. In this work, we investigate the potential use of autoencoder, a deep learning methodology, for de novo molecular design. Various generative autoencoders were used t…
The task of multi-step ahead prediction in language models is challenging considering the discrepancy between training and testing. At test time, a language model is required to make predictions given past predictions as input, instead of the past targets that are provided during training. This difference, known as exp…
Understanding the morphological changes of primary neuronal cells induced by chemical compounds is essential for drug discovery. Using the data from a single high-throughput imaging assay, a classification model for predicting the biological activity of candidate compounds was introduced. The image recognition model wh…
Everyday we are exposed to various chemicals via food additives, cleaning and cosmetic products and medicines -- and some of them might be toxic. However testing the toxicity of all existing compounds by biological experiments is neither financially nor logistically feasible. Therefore the government agencies NIH, EPA …
Study estimates Medallion's compounded return before fees at 31.8%.
problem Incorrectly using yearly returns for compounding leads to overestimation of fund performance.
method Used fund sizes and trading profits to estimate compounded return; used manager's wealth as proxy for Simons.
result Annualized compounded return of Medallion before fees is likely under 35%
Action chunking and data exploration improve behavior cloning in robotics.
problem Exponential errors in learning from demonstrations for continuous control tasks.
method Action chunking and exploratory data collection.
result Control-theoretic stability is key to improving imitation learning.
CRYSPNet predicts crystal structures from chemical compositions.
problem Predicting crystal structures of solids is challenging and computationally expensive.
method CRYSPNet uses a neural network to predict crystal properties from chemical composition.
result CRYSPNet outperforms alternative methods and is robustly validated.
We propose a novel computational strategy for de novo design of molecules with desired properties termed ReLeaSE (Reinforcement Learning for Structural Evolution). Based on deep and reinforcement learning approaches, ReLeaSE integrates two deep neural networks - generative and predictive - that are trained separately b…
One endeavour of modern physical chemistry is to use bottom-up approaches to design materials and drugs with desired properties. Here we introduce an atomistic structure learning algorithm (ASLA) that utilizes a convolutional neural network to build 2D compounds and layered structures atom by atom. The algorithm takes …
Characterizes measures preserving compound mixed renewal process properties.
problem Preserving compound mixed renewal process properties under different probability measures.
method Characterization of progressively equivalent probability measures.
result Any compound mixed renewal process can be converted into a compound mixed Poisson process through a change of measures.
This chapter is an attempt to present a mathematical theory of compound fractional Poisson processes. The chapter begins with the characterization of a well-known Lévy process: The compound Poisson process. The semi-Markov extension of the compound Poisson process naturally leads to the compound fractional Poisson proc…
We propose a novel transfer learning approach for orphan screening called corresponding projections. In orphan screening the learning task is to predict the binding affinities of compounds to an orphan protein, i.e., one for which no training data is available. The identification of compounds with high affinity is a ce…
Model-based collaborative filtering analyzes user-item interactions to infer latent factors that represent user preferences and item characteristics in order to predict future interactions. Most collaborative filtering algorithms assume that these latent factors are static, although it has been shown that user preferen…
Paper examines GCHP for mid-price prediction in financial data.
problem Predicting mid-price in financial data with stochastic models.
method General Compound Hawkes Process (GCHP) for mid-price prediction.
result GCHP models show potential for predicting mid-price direction and volatility.
Despite the huge success of deep neural networks (NNs), finding good mechanisms for quantifying their prediction uncertainty is still an open problem. Bayesian neural networks are one of the most popular approaches to uncertainty quantification. On the other hand, it was recently shown that ensembles of NNs, which belo…
Generates natural product-like compounds using GPT models.
problem Challenges in generating and evaluating natural product-like compounds.
method Trained GPT-based chemical language models on natural product dataset.
result Generated compounds have similar distribution to natural products.
High throughput screening of compounds (chemicals) is an essential part of drug discovery [7], involving thousands to millions of compounds, with the purpose of identifying candidate hits. Most statistical tools, including the industry standard B-score method, work on individual compound plates and do not exploit cross…
Study short-maturity VIX and European option prices with jumps.
problem Analyzing VIX and European options with jumps in short-maturity models.
method Local-stochastic volatility models with compound Poisson jumps, leading-order asymptotics in closed-form.
result Closed-form solutions for VIX and European option prices in short-maturity models.
In this paper, we introduce a new model for the risk process based on general compound Hawkes process (GCHP) for the arrival of claims. We call it risk model based on general compound Hawkes process (RMGCHP). The Law of Large Numbers (LLN) and the Functional Central Limit Theorem (FCLT) are proved. We also study the ma…
New method offsets DML's error-compounding issue and provides more stable causal parameter estimates.
problem Estimating ATE from observational data with robustness and stability.
method Robust Causal Learning (RCL) method to offset DML's deficiencies.
result RCL estimators are more stable and perform better than DML and traditional estimators.
Normalized compound random measures are flexible nonparametric priors for related distributions. We consider building general nonparametric regression models using normalized compound random measure mixture models. Posterior inference is made using a novel pseudo-marginal Metropolis-Hastings sampler for normalized comp…
Compound Finance optimizes risk metrics for V3 protocol using Chainrisk simulations.
problem Optimizing systemic risks in Compound V3 protocol.
method Millions of Chainrisk simulations to evaluate VaR and LaR, providing parameter adjustments.
result Optimization framework enhances protocol stability.
New Riemannian geometry for Compound Gaussian distributions applied to efficient change detection.
problem Change detection in multivariate image times series.
method Developed a recursive approach based on Riemannian optimization.
result Optimal performance achieved with computational efficiency.
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 paper examines data transfer methods to improve off-the-shelf Transformer models for retrosynthesis.
problem Improving prediction models for retrosynthesis using small datasets.
method Systematic examination of data transfer approaches on end-to-end generative models.
result Pre-training plus fine-tuning boosts the accuracy of a Transformer baseline, achieving state-of-the-art results.
We present a general framework, the coupled compound Poisson factorization (CCPF), to capture the missing-data mechanism in extremely sparse data sets by coupling a hierarchical Poisson factorization with an arbitrary data-generating model. We derive a stochastic variational inference algorithm for the resulting model …