Identifying and discovering drug-target interactions(DTIs) are vital steps in drug discovery and development. They play a crucial role in assisting scientists in finding new drugs and accelerating the drug development process. Recently, knowledge graph and knowledge graph embedding (KGE) models have made rapid advancements and demonstrated impressive performance in drug discovery. However, such models lack authenticity and accuracy in drug target identification, leading to an increased misjudgment rate and reduced drug development efficiency. To address these issues, we focus on the problem of drug-target interactions, with knowledge mapping as the core technology. Specifically, a causal intervention-based confidence measure is employed to assess the triplet score to improve the accuracy of the drug-target interaction prediction model. Experimental results demonstrate that the developed confidence measurement method based on causal intervention can significantly enhance the accuracy of DTI link prediction, particularly for high-precision models. The predicted results are more valuable in guiding the design and development of subsequent drug development experiments, thereby significantly improving the efficiency of drug development.

Identifying meaningful concepts in large data sets can provide valuable insights into engineering design problems. Concept identification aims at identifying non-overlapping groups of design instances that are similar in a joint space of all features, but which are also similar when considering only subsets of features. These subsets usually comprise features that characterize a design with respect to one specific context, for example, constructive design parameters, performance values, or operation modes. It is desirable to evaluate the quality of design concepts by considering several of these feature subsets in isolation. In particular, meaningful concepts should not only identify dense, well separated groups of data instances, but also provide non-overlapping groups of data that persist when considering pre-defined feature subsets separately. In this work, we propose to view concept identification as a special form of clustering algorithm with a broad range of potential applications beyond engineering design. To illustrate the differences between concept identification and classical clustering algorithms, we apply a recently proposed concept identification algorithm to two synthetic data sets and show the differences in identified solutions. In addition, we introduce the mutual information measure as a metric to evaluate whether solutions return consistent clusters across relevant subsets. To support the novel understanding of concept identification, we consider a simulated data set from a decision-making problem in the energy management domain and show that the identified clusters are more interpretable with respect to relevant feature subsets than clusters found by common clustering algorithms and are thus more suitable to support a decision maker.

In this paper, we improve the kernel alignment regret bound for online kernel learning in the regime of the Hinge loss function. Previous algorithm achieves a regret of $O((\mathcal{A}_TT\ln{T})^{\frac{1}{4}})$ at a computational complexity (space and per-round time) of $O(\sqrt{\mathcal{A}_TT\ln{T}})$, where $\mathcal{A}_T$ is called \textit{kernel alignment}. We propose an algorithm whose regret bound and computational complexity are better than previous results. Our results depend on the decay rate of eigenvalues of the kernel matrix. If the eigenvalues of the kernel matrix decay exponentially, then our algorithm enjoys a regret of $O(\sqrt{\mathcal{A}_T})$ at a computational complexity of $O(\ln^2{T})$. Otherwise, our algorithm enjoys a regret of $O((\mathcal{A}_TT)^{\frac{1}{4}})$ at a computational complexity of $O(\sqrt{\mathcal{A}_TT})$. We extend our algorithm to batch learning and obtain a $O(\frac{1}{T}\sqrt{\mathbb{E}[\mathcal{A}_T]})$ excess risk bound which improves the previous $O(1/\sqrt{T})$ bound.

Existing graph clustering networks heavily rely on a predefined yet fixed graph, which can lead to failures when the initial graph fails to accurately capture the data topology structure of the embedding space. In order to address this issue, we propose a novel clustering network called Embedding-Induced Graph Refinement Clustering Network (EGRC-Net), which effectively utilizes the learned embedding to adaptively refine the initial graph and enhance the clustering performance. To begin, we leverage both semantic and topological information by employing a vanilla auto-encoder and a graph convolution network, respectively, to learn a latent feature representation. Subsequently, we utilize the local geometric structure within the feature embedding space to construct an adjacency matrix for the graph. This adjacency matrix is dynamically fused with the initial one using our proposed fusion architecture. To train the network in an unsupervised manner, we minimize the Jeffreys divergence between multiple derived distributions. Additionally, we introduce an improved approximate personalized propagation of neural predictions to replace the standard graph convolution network, enabling EGRC-Net to scale effectively. Through extensive experiments conducted on nine widely-used benchmark datasets, we demonstrate that our proposed methods consistently outperform several state-of-the-art approaches. Notably, EGRC-Net achieves an improvement of more than 11.99\% in Adjusted Rand Index (ARI) over the best baseline on the DBLP dataset. Furthermore, our scalable approach exhibits a 10.73% gain in ARI while reducing memory usage by 33.73% and decreasing running time by 19.71%. The code for EGRC-Net will be made publicly available at \url{https://github.com/ZhihaoPENG-CityU/EGRC-Net}.

Due to domain shifts, machine learning systems typically struggle to generalize well to new domains that differ from those of training data, which is what domain generalization (DG) aims to address. Although a variety of DG methods have been proposed, most of them fall short in interpretability and require domain labels, which are not available in many real-world scenarios. This paper presents a novel DG method, called HMOE: Hypernetwork-based Mixture of Experts (MoE), which does not rely on domain labels and is more interpretable. MoE proves effective in identifying heterogeneous patterns in data. For the DG problem, heterogeneity arises exactly from domain shifts. HMOE employs hypernetworks taking vectors as input to generate the weights of experts, which promotes knowledge sharing among experts and enables the exploration of their similarities in a low-dimensional vector space. We benchmark HMOE against other DG methods under a fair evaluation framework -- DomainBed. Our extensive experiments show that HMOE can effectively separate mixed-domain data into distinct clusters that are surprisingly more consistent with human intuition than original domain labels. Using self-learned domain information, HMOE achieves state-of-the-art results on most datasets and significantly surpasses other DG methods in average accuracy across all datasets.

Large medical imaging data sets are becoming increasingly available, but ensuring sample quality without significant artefacts is challenging. Existing methods for identifying imperfections in medical imaging rely on data-intensive approaches, compounded by a scarcity of artefact-rich scans for training machine learning models in clinical research. To tackle this problem, we propose a framework with four main components: 1) artefact generators inspired by magnetic resonance physics to corrupt brain MRI scans and augment a training dataset, 2) abstract and engineered features to represent images compactly, 3) a feature selection process depending on the artefact class to improve classification, and 4) SVM classifiers to identify artefacts. Our contributions are threefold: first, physics-based artefact generators produce synthetic brain MRI scans with controlled artefacts for data augmentation. This will avoid the labour-intensive collection and labelling process of scans with rare artefacts. Second, we propose a pool of abstract and engineered image features to identify 9 different artefacts for structural MRI. Finally, we use an artefact-based feature selection block that, for each class of artefacts, finds the set of features providing the best classification performance. We performed validation experiments on a large data set of scans with artificially-generated artefacts, and in a multiple sclerosis clinical trial where real artefacts were identified by experts, showing that the proposed pipeline outperforms traditional methods. In particular, our data augmentation increases performance by up to 12.5 percentage points on accuracy, precision, and recall. The computational efficiency of our pipeline enables potential real-time deployment, promising high-throughput clinical applications through automated image-processing pipelines driven by quality control systems.

In this paper, we address the problem of dynamic network embedding, that is, representing the nodes of a dynamic network as evolving vectors within a low-dimensional space. While the field of static network embedding is wide and established, the field of dynamic network embedding is comparatively in its infancy. We propose that a wide class of established static network embedding methods can be used to produce interpretable and powerful dynamic network embeddings when they are applied to the dilated unfolded adjacency matrix. We provide a theoretical guarantee that, regardless of embedding dimension, these unfolded methods will produce stable embeddings, meaning that nodes with identical latent behaviour will be exchangeable, regardless of their position in time or space. We additionally define a hypothesis testing framework which can be used to evaluate the quality of a dynamic network embedding by testing for planted structure in simulated networks. Using this, we demonstrate that, even in trivial cases, unstable methods are often either conservative or encode incorrect structure. In contrast, we demonstrate that our suite of stable unfolded methods are not only more interpretable but also more powerful in comparison to their unstable counterparts.

In the rapidly evolving realm of machine learning, algorithm effectiveness often faces limitations due to data quality and availability. Traditional approaches grapple with data sharing due to legal and privacy concerns. The federated learning framework addresses this challenge. Federated learning is a decentralized approach where model training occurs on client sides, preserving privacy by keeping data localized. Instead of sending raw data to a central server, only model updates are exchanged, enhancing data security. We apply this framework to Sparse Principal Component Analysis (SPCA) in this work. SPCA aims to attain sparse component loadings while maximizing data variance for improved interpretability. Beside the L1 norm regularization term in conventional SPCA, we add a smoothing function to facilitate gradient-based optimization methods. Moreover, in order to improve computational efficiency, we introduce a least squares approximation to original SPCA. This enables analytic solutions on the optimization processes, leading to substantial computational improvements. Within the federated framework, we formulate SPCA as a consensus optimization problem, which can be solved using the Alternating Direction Method of Multipliers (ADMM). Our extensive experiments involve both IID and non-IID random features across various data owners. Results on synthetic and public datasets affirm the efficacy of our federated SPCA approach.

How best to model structurally heterogeneous processes is a foundational question in the social, health and behavioral sciences. Recently, Fisher et al., (2022) introduced the multi-VAR approach for simultaneously estimating multiple-subject multivariate time series characterized by common and individualizing features using penalized estimation. This approach differs from many popular modeling approaches for multiple-subject time series in that qualitative and quantitative differences in a large number of individual dynamics are well-accommodated. The current work extends the multi-VAR framework to include new adaptive weighting schemes that greatly improve estimation performance. In a small set of simulation studies we compare adaptive multi-VAR with these new penalty weights to common alternative estimators in terms of path recovery and bias. Furthermore, we provide toy examples and code demonstrating the utility of multi-VAR under different heterogeneity regimes using the multivar package for R (Fisher, 2022).

We propose a novel methodology for forecasting spatio-temporal data using supervised semi-nonnegative matrix factorization (SSNMF) with frequency regularization. Matrix factorization is employed to decompose spatio-temporal data into spatial and temporal components. To improve clarity in the temporal patterns, we introduce a nonnegativity constraint on the time domain along with regularization in the frequency domain. Specifically, regularization in the frequency domain involves selecting features in the frequency space, making an interpretation in the frequency domain more convenient. We propose two methods in the frequency domain: soft and hard regularizations, and provide convergence guarantees to first-order stationary points of the corresponding constrained optimization problem. While our primary motivation stems from geophysical data analysis based on GRACE (Gravity Recovery and Climate Experiment) data, our methodology has the potential for wider application. Consequently, when applying our methodology to GRACE data, we find that the results with the proposed methodology are comparable to previous research in the field of geophysical sciences but offer clearer interpretability.