Related papers: Exploiting Pre-trained Models for Drug Target Affi…
Identifying novel drug-target interactions (DTI) is a critical and rate limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, we show that state-of-the-art models fail to…
Despite a large amount of attention on adversarial examples, very few works have demonstrated an effective defense against this threat. We examine Deep k-Nearest Neighbor (DkNN), a proposed defense that combines k-Nearest Neighbor (kNN) and…
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…
Nearest neighbor (kNN) methods have been gaining popularity in recent years in light of advances in hardware and efficiency of algorithms. There is a plethora of methods to choose from today, each with their own advantages and…
Nearest neighbor-based methods are commonly used for classification tasks and as subroutines of other data-analysis methods. An attacker with the capability of inserting their own data points into the training set can manipulate the…
Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the…
The $k$-nearest neighbor ($k$-NN) algorithm is one of the most popular methods for nonparametric classification. However, a relevant limitation concerns the definition of the number of neighbors $k$. This parameter exerts a direct impact on…
Deep neural networks are known to be vulnerable to unseen data: they may wrongly assign high confidence stcores to out-distribuion samples. Recent works try to solve the problem using representation learning methods and specific metrics. In…
$k$ Nearest Neighbors ($k$NN) is one of the most widely used supervised learning algorithms to classify Gaussian distributed data, but it does not achieve good results when it is applied to nonlinear manifold distributed data, especially…
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…
The traditional k nearest neighbor (kNN) approach uses a distance formula within a spherical region to determine the k closest training observations to a test sample point. However, this approach may not work well when test point is located…
Traditional deep learning models implicity encode knowledge limiting their transparency and ability to adapt to data changes. Yet, this adaptability is vital for addressing user data privacy concerns. We address this limitation by storing…
While high-dimensional embedding vectors are being increasingly employed in various tasks like Retrieval-Augmented Generation and Recommendation Systems, popular dimensionality reduction (DR) methods such as PCA and UMAP have rarely been…
We introduce $k$-nearest-neighbor machine translation ($k$NN-MT), which predicts tokens with a nearest neighbor classifier over a large datastore of cached examples, using representations from a neural translation model for similarity…
Linear regression analysis focuses on predicting a numeric regressand value based on certain regressor values. In this context, k-Nearest Neighbors (k-NN) is a common non-parametric regression algorithm, which achieves efficient performance…
Various kinds of k-nearest neighbor (KNN) based classification methods are the bases of many well-established and high-performance pattern-recognition techniques, but both of them are vulnerable to their parameter choice. Essentially, the…
Nearest neighbor search is known as a challenging issue that has been studied for several decades. Recently, this issue becomes more and more imminent in viewing that the big data problem arises from various fields. In this paper, a…
Approximate k-Nearest Neighbor (AKNN) search is widely used in vector databases. When vectors carry additional attributes (e.g., labels or numerical values), filtered AKNN search retrieves the nearest vectors to a query vector under…
In the classic setting of unsupervised domain adaptation (UDA), the labeled source data are available in the training phase. However, in many real-world scenarios, owing to some reasons such as privacy protection and information security,…
Latent Dirichlet Allocation (LDA) is a three-level hierarchical Bayesian model for topic inference. In spite of its great success, inferring the latent topic distribution with LDA is time-consuming. Motivated by the transfer learning…