D rug discovery requires a tremendous amount of time and cost. Computational drug - target interaction prediction, a n important part of this process, can reduce these requirements by narrowing the search space for wet lab experiments. In this survey, we provid e comprehensive details of graph machine learning - based methods in predicting drug - target interaction, as they have shown promising results in this field. These details include the overall framework, main contribution, dataset s, and their source code s . The selected papers were mainly published from 2020 to 2024 . Prior to discussing papers, we briefly introduce the datasets commonly used with these methods and measurements to assess their performance. Finally, future challenges and some crucial areas that need to be explored are discussed.

Recent advances in machine learning have demonstrated an enormous utility of deep learning approaches, particularly Graph Neural Networks (GNNs) for materials science. These methods have emerged as powerful tools for high-throughput prediction of material properties, offering a compelling enhancement and alternative to traditional first-principles calculations. While the community has predominantly focused on developing increasingly complex and universal models to enhance predictive accuracy, such approaches often lack physical interpretability and insights into materials behavior. Here, we introduce a novel computational paradigm, Self-Adaptable Graph Attention Networks integrated with Symbolic Regression (SA-GAT-SR), that synergistically combines the predictive capability of GNNs with the interpretative power of symbolic regression. Our framework employs a self-adaptable encoding algorithm that automatically identifies and adjust attention weights so as to screen critical features from an expansive 180-dimensional feature space while maintaining O(n) computational scaling. The integrated SR module subsequently distills these features into compact analytical expressions that explicitly reveal quantum-mechanically meaningful relationships, achieving 23 times acceleration compared to conventional SR implementations that heavily rely on first principle calculations-derived features as input. This work suggests a new framework in computational materials science, bridging the gap between predictive accuracy and physical interpretability, offering valuable physical insights into material behavior.

Graph neural networks (GNNs) are commonly used in semi-supervised settings. Previous research has primarily focused on finding appropriate graph filters (e.g. aggregation methods) to perform well on both homophilic and heterophilic graphs. While these methods are effective, they can still suffer from the sparsity of node features, where the initial data contain few non-zero elements. This can lead to overfitting in certain dimensions in the first projection matrix, as training samples may not cover the entire range of graph filters (hyperplanes). To address this, we propose a novel data augmentation strategy. Specifically, by flipping both the initial features and hyperplane, we create additional space for training, which leads to more precise updates of the learnable parameters and improved robustness for unseen features during inference. To the best of our knowledge, this is the first attempt to mitigate the overfitting caused by the initial features. Extensive experiments on real-world datasets show that our proposed technique increases node classification accuracy by up to 46.5% relatively.

The goal of the linear law-based feature space transformation (LLT) algorithm is to assist with the classification of univariate and multivariate time series. The presented R package, called LLT, implements this algorithm in a flexible yet user-friendly way. This package first splits the instances into training and test sets. It then utilizes time-delay embedding and spectral decomposition techniques to identify the governing patterns (called linear laws) of each input sequence (initial feature) within the training set. Finally, it applies the linear laws of the training set to transform the initial features of the test set. These steps are performed by three separate functions called trainTest, trainLaw, and testTrans. Their application requires a predefined data structure; however, for fast calculation, they use only built-in functions. The LLT R package and a sample dataset with the appropriate data structure are publicly available on GitHub.

The ability for groundwater heat pumps to meet space heating and cooling demands without relying on fossil fuels, has prompted their mass roll-out in dense urban environments. In regions with high subsurface groundwater flow rates, the thermal plume generated from a heat pump's injection well can propagate downstream, affecting surrounding users and reducing their heat pump efficiency. To reduce the probability of interference, regulators often rely on simple analytical models or high-fidelity groundwater simulations to determine the impact that a heat pump has on the subsurface aquifer and surrounding heat pumps. These are either too inaccurate or too computationally expensive for everyday use. In this work, a surrogate model was developed to provide a quick, high accuracy prediction tool of the thermal plume generated by a heat pump within heterogeneous subsurface aquifers. Three variations of a convolutional neural network were developed that accepts the known groundwater Darcy velocities as discrete 2D inputs and predicts the temperature within the subsurface aquifer around the heat pump. A data set consisting of 800 numerical simulation samples, generated from random permeability fields and pressure boundary conditions, was used to provide pseudo-randomized Darcy velocity fields as input fields and the temperature field solution for training the network. The subsurface temperature field output from the network provides a more realistic temperature field that follows the Darcy velocity streamlines, while being orders of magnitude faster than conventional high-fidelity solvers.

Multiple methods of finding the vertices belonging to a planted dense subgraph in a random dense $G(n, p)$ graph have been proposed, with an emphasis on planted cliques. Such methods can identify the planted subgraph in polynomial time, but are all limited to several subgraph structures. Here, we present PYGON, a graph neural network-based algorithm, which is insensitive to the structure of the planted subgraph. This is the first algorithm that uses advanced learning tools for recovering dense subgraphs. We show that PYGON can recover cliques of sizes $\Theta\left(\sqrt{n}\right)$, where $n$ is the size of the background graph, comparable with the state of the art. We also show that the same algorithm can recover multiple other planted subgraphs of size $\Theta\left(\sqrt{n}\right)$, in both directed and undirected graphs. We suggest a conjecture that no polynomial time PAC-learning algorithm can detect planted dense subgraphs with size smaller than $O\left(\sqrt{n}\right)$, even if in principle one could find dense subgraphs of logarithmic size.

Multiple methods of finding the vertices belonging to a planted dense subgraph in a random dense G(n, p) graph have been proposed, with an emphasis on planted cliques. Such methods can identify the planted subgraph in polynomial time, but are all limited to several subgraph structures. Here, we present PYGON, a graph neural network-based algorithm, which is insensitive to the structure of the planted subgraph. This is the first algorithm that uses learning tools for recovering dense subgraphs. We show that PYGON can recover cliques of sizes Θ (√ n), where n is the size of the background graph, comparable with the state of the art. We also show that the same algorithm can recover multiple other planted subgraphs of size Θ (√ n), in both directed and undirected graphs. We suggest a conjecture that no polynomial time PAC-learning algorithm can detect planted dense subgraphs with size smaller than O ( √ n), even if in principle one could find dense subgraphs of logarithmic size.

Since multidrug combination is widely applied, the accurate prediction of drug-drug interaction (DDI) is becoming more and more critical. In our method, we use graph to represent drug-drug interaction: nodes represent drug; edges represent drug-drug interactions. Based on our assumption, we convert the prediction of DDI to link prediction problem, utilizing known drug node characteristics and DDI types to predict unknown DDI types. This work proposes a Graph Distance Neural Network (GDNN) to predict drug-drug interactions. Firstly, GDNN generates initial features for nodes via target point method, fully including the distance information in the graph. Secondly, GDNN adopts an improved message passing framework to better generate each drug node embedded expression, comprehensively considering the nodes and edges characteristics synchronously. Thirdly, GDNN aggregates the embedded expressions, undergoing MLP processing to generate the final predicted drug interaction type.

In this paper, we address multi-modal pretraining of product data in the field of E-commerce. Current multi-modal pretraining methods proposed for image and text modalities lack robustness in the face of modality-missing and modality-noise, which are two pervasive problems of multi-modal product data in real E-commerce scenarios. To this end, we propose a novel method, K3M, which introduces knowledge modality in multi-modal pretraining to correct the noise and supplement the missing of image and text modalities. The modal-encoding layer extracts the features of each modality. The modal-interaction layer is capable of effectively modeling the interaction of multiple modalities, where an initial-interactive feature fusion model is designed to maintain the independence of image modality and text modality, and a structure aggregation module is designed to fuse the information of image, text, and knowledge modalities. We pretrain K3M with three pretraining tasks, including masked object modeling (MOM), masked language modeling (MLM), and link prediction modeling (LPM). Experimental results on a real-world E-commerce dataset and a series of product-based downstream tasks demonstrate that K3M achieves significant improvements in performances than the baseline and state-of-the-art methods when modality-noise or modality-missing exists.

The structure of a Markov network is typically learned in one of two ways. The first approach is to treat this task as a global search problem. However, these algorithms are slow as they require running the expensive operation of weight (i.e., parameter) learning many times. The second approach involves learning a set of local models and then combining them into a global model. However, it can be computationally expensive to learn the local models for datasets that contain a large number of variables and/or examples. This paper pursues a third approach that views Markov network structure learning as a feature generation problem. The algorithm combines a data-driven, specific-to-general search strategy with randomization to quickly generate a large set of candidate features that all have support in the data. It uses weight learning, with L1 regularization, to select a subset of generated features to include in the model. On a large empirical study, we find that our algorithm is equivalently accurate to other state-of-the-art methods while exhibiting a much faster run time.