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.
Proposes a self-attention-based method for drug-target interaction prediction.
The task of drug-target interaction prediction holds significant importance in pharmacology and therapeutic drug design. In this paper, we present FRnet-DTI, an auto encoder and a convolutional classifier for feature manipulation and drug target interaction prediction. Two convolutional neural neworks are proposed wher…
ISAAC audits deep models for drug-target interactions, revealing structural differences.
DeepPurpose simplifies DL for DTI prediction.
GEFA predicts drug-target affinity using graph neural networks.
Predicting drug-target interactions (DTI) is an essential part of the drug discovery process, which is an expensive process in terms of time and cost. Therefore, reducing DTI cost could lead to reduced healthcare costs for a patient. In addition, a precisely learned molecule representation in a DTI model could contribu…
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…
Paper introduces IC-index to evaluate interaction prediction methods.
HiGraphDTI learns drug and target representations from molecular graphs to predict DTIs.
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…
Computer-Aided Drug Discovery research has proven to be a promising direction in drug discovery. In recent years, Deep Learning approaches have been applied to problems in the domain such as Drug-Target Interaction Prediction and have shown improvements over traditional screening methods. An existing challenge is how t…
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…
A fast algorithm speeds up training of pairwise kernels.
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…
Motivation: Prediction of the interaction affinity between proteins and compounds is a major challenge in the drug discovery process. WideDTA is a deep-learning based prediction model that employs chemical and biological textual sequence information to predict binding affinity. Results: WideDTA uses four text-based inf…
Active learning has shown to reduce the number of experiments needed to obtain high-confidence drug-target predictions. However, in order to actually save experiments using active learning, it is crucial to have a method to evaluate the quality of the current prediction and decide when to stop the experimentation proce…
Co-Diffusion predicts drug-target affinity by learning latent manifolds and diffusion, improving generalization.
Deep generative model discovers inhibitors for unknown targets.
This Perspective provides examples of current and future applications of deep learning in pharmacogenomics, including: (1) identification of novel regulatory variants located in noncoding domains and their function as applied to pharmacoepigenomics; (2) patient stratification from medical records; and (3) prediction of…
We present the Network-based Biased Tree Ensembles (NetBiTE) method for drug sensitivity prediction and drug sensitivity biomarker identification in cancer using a combination of prior knowledge and gene expression data. Our devised method consists of a biased tree ensemble that is built according to a probabilistic bi…
Deep Matrix Factorization (DMF) is an emerging approach to the problem of matrix completion. Recent works have established that gradient descent applied to a DMF model induces an implicit regularization on the rank of the recovered matrix. In this work we interpret the DMF model through the lens of spectral geometry. T…
Background: Predictive, stable and interpretable gene signatures are generally seen as an important step towards a better personalized medicine. During the last decade various methods have been proposed for that purpose. However, one important obstacle for making gene signatures a standard tool in clinics is the typica…
Synthetic lethality (SL) is a promising concept for novel discovery of anti-cancer drug targets. However, wet-lab experiments for detecting SLs are faced with various challenges, such as high cost, low consistency across platforms or cell lines. Therefore, computational prediction methods are needed to address these is…
CardiGraphormer uses SSL and GNNs to improve drug discovery.
A neural network predicts drug interactions using attention mechanisms.
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 …
Kronecker product kernel provides the standard approach in the kernel methods literature for learning from graph data, where edges are labeled and both start and end vertices have their own feature representations. The methods allow generalization to such new edges, whose start and end vertices do not appear in the tra…
Novel method identifies proteomic risk markers for Alzheimer disease.
Study improves neural network calibration for drug discovery.
GG-SAGE predicts links in directed graphs with attributes, outperforming existing methods.
Motivation : Molecular signatures for diagnosis or prognosis estimated from large-scale gene expression data often lack robustness and stability, rendering their biological interpretation challenging. Increasing the signature's interpretability and stability across perturbations of a given dataset and, if possible, acr…
DRFLM improves federated learning by handling data heterogeneity and noise.
Inferring the structure of gene regulatory networks (GRN) from gene expression data has many applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously difficult problem, for which the many existing methods reach limited accuracy. In t…
Enhances ENet's prediction accuracy while maintaining uncertainty estimation.
Deep learning uses ROC cost functions to improve virtual screening accuracy.
Surrogate-based analysis of interactions via local effect smooths
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.
iKF method uncovers complex variable interactions for scientific discovery.
A graph neural network detects beneficial feature interactions for recommender systems.
We describe and extract time-ordered multibody interactions from complex systems.
Dropout regularizes against high-order interactions by canceling interaction rates.
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.
A new method detects interactions in machine learning models.
xDeepInt learns both vector-wise and bit-wise feature interactions.
In this work, we aim to predict the future motion of vehicles in a traffic scene by explicitly modeling their pairwise interactions. Specifically, we propose a graph neural network that jointly predicts the discrete interaction modes and 5-second future trajectories for all agents in the scene. Our model infers an inte…