Nonlinear causal discovery from observational data imposes strict identifiability assumptions on the formulation of structural equations utilized in the data generating process. The evaluation of structure learning methods under assumption violations requires a rigorous and interpretable approach, which quantifies both the structural similarity of the estimation with the ground truth and the capacity of the discovered graphs to be used for causal inference. Motivated by the lack of unified performance assessment framework, we introduce an interpretable, six-dimensional evaluation metric, i.e., distance to optimal solution (DOS), which is specifically tailored to the field of causal discovery. Furthermore, this is the first research to assess the performance of structure learning algorithms from seven different families on increasing percentage of non-identifiable, nonlinear causal patterns, inspired by real-world processes. Our large-scale simulation study, which incorporates seven experimental factors, shows that besides causal order-based methods, amortized causal discovery delivers results with comparatively high proximity to the optimal solution.

Lempel-Ziv complexity (LZC) is a key measure for detecting the irregularity and complexity of nonlinear time series and has seen various improvements in recent decades. However, existing LZC-based metrics, such as Permutation Lempel-Ziv complexity (PLZC) and Dispersion-Entropy based Lempel-Ziv complexity (DELZC), focus mainly on patterns of independent embedding vectors, often overlooking the transition patterns within the time series. To address this gap, this paper introduces a novel LZC-based method called Bidirectional Transition Dispersion Entropy-based Lempel-Ziv complexity (BT-DELZC). Leveraging Markov chain theory, this method integrates a bidirectional transition network framework with DELZC to better capture dynamic signal information. Additionally, an improved hierarchical decomposition algorithm is used to extract features from various frequency components of the time series. The proposed BT-DELZC method is first evaluated through four simulated experiments, demonstrating its robustness and effectiveness in characterizing nonlinear time series. Additionally, two fault-bearing diagnosis experiments are conducted by combining the hierarchical BT-DELZC method with various classifiers from the machine learning domain. The results indicate that BT-DELZC achieves the highest accuracy across both datasets, significantly outperforming existing methods such as LZC, PLZC, and DELZC in extracting features related to fault bearings.

Spectral clustering is a popular clustering method. It first maps data into the spectral embedding space and then uses Kmeans to find clusters. However, the two decoupled steps prohibit joint optimization for the optimal solution. In addition, it needs to construct the similarity graph for samples, which suffers from the curse of dimensionality when the data are high-dimensional. To address these two challenges, we introduce \textbf{D}eep \textbf{S}pectral \textbf{C}lustering (\textbf{DSC}), which consists of two main modules: the spectral embedding module and the greedy Kmeans module. The former module learns to efficiently embed raw samples into the spectral embedding space using deep neural networks and power iteration. The latter module improves the cluster structures of Kmeans on the learned spectral embeddings by a greedy optimization strategy, which iteratively reveals the direction of the worst cluster structures and optimizes embeddings in this direction. To jointly optimize spectral embeddings and clustering, we seamlessly integrate the two modules and optimize them in an end-to-end manner. Experimental results on seven real-world datasets demonstrate that DSC achieves state-of-the-art clustering performance.

Recommender systems are a critical component of e-commercewebsites. The rapid development of online social networking services provides an opportunity to explore social networks together with information used in traditional recommender systems, such as customer demographics, product characteristics, and transactions. It also provides more applications for recommender systems. To tackle this social network-based recommendation problem, previous studies generally built trust models in light of the social influence theory. This study inspects a spectrumof social network theories to systematicallymodel themultiple facets of a social network and infer user preferences. In order to effectively make use of these heterogonous theories, we take a kernel-based machine learning paradigm, design and select kernels describing individual similarities according to social network theories, and employ a non-linear multiple kernel learning algorithm to combine the kernels into a unified model. This design also enables us to consider multiple theories' interactions in assessing individual behaviors. We evaluate our proposed approach on a real-world movie review data set. The experiments show that our approach provides more accurate recommendations than trust-based methods and the collaborative filtering approach. Further analysis shows that kernels derived from contagion theory and homophily theory contribute a larger portion of the model.

Heterogeneity is a fundamental and challenging issue in federated learning, especially for the graph data due to the complex relationships among the graph nodes. To deal with the heterogeneity, lots of existing methods perform the weighted federation based on their calculated similarities between pairwise clients (i.e., subgraphs). However, their inter-subgraph similarities estimated with the outputs of local models are less reliable, because the final outputs of local models may not comprehensively represent the real distribution of subgraph data. In addition, they ignore the critical intra-heterogeneity which usually exists within each subgraph itself. To address these issues, we propose a novel Federated learning method by integrally modeling the Inter-Intra Heterogeneity (FedIIH). For the inter-subgraph relationship, we propose a novel hierarchical variational model to infer the whole distribution of subgraph data in a multi-level form, so that we can accurately characterize the inter-subgraph similarities with the global perspective. For the intra-heterogeneity, we disentangle the subgraph into multiple latent factors and partition the model parameters into multiple parts, where each part corresponds to a single latent factor. Our FedIIH not only properly computes the distribution similarities between subgraphs, but also learns disentangled representations that are robust to irrelevant factors within subgraphs, so that it successfully considers the inter- and intra- heterogeneity simultaneously. Extensive experiments on six homophilic and five heterophilic graph datasets in both non-overlapping and overlapping settings demonstrate the effectiveness of our method when compared with nine state-of-the-art methods. Specifically, FedIIH averagely outperforms the second-best method by a large margin of 5.79% on all heterophilic datasets.

Unsupervised visible-infrared person re-identification (USL-VI-ReID) is of great research and practical significance yet remains challenging due to the absence of annotations. Existing approaches aim to learn modality-invariant representations in an unsupervised setting. However, these methods often encounter label noise within and across modalities due to suboptimal clustering results and considerable modality discrepancies, which impedes effective training. To address these challenges, we propose a straightforward yet effective solution for USL-VI-ReID by mitigating universal label noise using neighbor information. Specifically, we introduce the Neighbor-guided Universal Label Calibration (N-ULC) module, which replaces explicit hard pseudo labels in both homogeneous and heterogeneous spaces with soft labels derived from neighboring samples to reduce label noise. Additionally, we present the Neighbor-guided Dynamic Weighting (N-DW) module to enhance training stability by minimizing the influence of unreliable samples. Extensive experiments on the RegDB and SYSU-MM01 datasets demonstrate that our method outperforms existing USL-VI-Figure 1: Illustration of the motivation of our method.

Predicting future bus trip chains for an existing user is of great significance for operators of public transit systems. Existing methods always treat this task as a time-series prediction problem, but the 1-dimensional time series structure cannot express the complex relationship between trips. To better capture the inherent patterns in bus travel behavior, this paper proposes a novel approach that synthesizes future bus trip chains based on those from similar days. Key similarity patterns are defined and tested using real-world data, and a similarity function is then developed to capture these patterns. Afterwards, a graph is constructed where each day is represented as a node and edge weight reflects the similarity between days. Besides, the trips on a given day can be regarded as labels for each node, transferring the bus trip chain prediction problem to a semi-supervised classification problem on a graph. To address this, we propose several methods and validate them on a real-world dataset of 10000 bus users, achieving state-of-the-art prediction results. Analyzing the parameters of similarity function reveals some interesting bus usage patterns, allowing us can to cluster bus users into three types: repeat-dominated, evolve-dominate and repeat-evolve balanced. In summary, our work demonstrates the effectiveness of similarity-based prediction for bus trip chains and provides a new perspective for analyzing individual bus travel patterns. The code for our prediction model is publicly available.

Despite being an essential tool across engineering and finance, Monte Carlo simulation can be computationally intensive, especially in largescale, path-dependent problems that hinder straightforward parallelization. A natural alternative is to replace simulation with machine learning or surrogate prediction, though this introduces challenges in understanding the resulting errors. We introduce a Prediction-Enhanced Monte Carlo (PEMC) framework where we leverage machine learning prediction as control variates, thus maintaining unbiased evaluations instead of the direct use of ML predictors. Traditional control variate methods require knowledge of means and focus on per-sample variance reduction. In contrast, PEMC aims at overall cost-aware variance reduction, eliminating the need for mean knowledge. PEMC leverages pre-trained neural architectures to construct effective control variates and replaces computationally expensive sample-path generation with efficient neural network evaluations. This allows PEMC to address scenarios where no good control variates are known.

This work presents an omics-driven modeling pipeline that integrates machine-learning tools to facilitate the dynamic modeling of multiscale biological systems. Random forests and permutation feature importance are proposed to mine omics datasets, guiding feature selection and dimensionality reduction for dynamic modeling. Continuous and differentiable machine-learning functions can be trained to link the reduced omics feature set to key components of the dynamic model, resulting in a hybrid model. As proof of concept, we apply this framework to a high-dimensional proteomics dataset of $\textit{Saccharomyces cerevisiae}$. After identifying key intracellular proteins that correlate with cell growth, targeted dynamic experiments are designed, and key model parameters are captured as functions of the selected proteins using Gaussian processes. This approach captures the dynamic behavior of yeast strains under varying proteome profiles while estimating the uncertainty in the hybrid model's predictions. The outlined modeling framework is adaptable to other scenarios, such as integrating additional layers of omics data for more advanced multiscale biological systems, or employing alternative machine-learning methods to handle larger datasets. Overall, this study outlines a strategy for leveraging omics data to inform multiscale dynamic modeling in systems biology and bioprocess engineering.

The drug development process is a critical challenge in the pharmaceutical industry due to its time-consuming nature and the need to discover new drug potentials to address various ailments. The initial step in drug development, drug target identification, often consumes considerable time. While valid, traditional methods such as in vivo and in vitro approaches are limited in their ability to analyze vast amounts of data efficiently, leading to wasteful outcomes. To expedite and streamline drug development, an increasing reliance on computer-aided drug design (CADD) approaches has merged. These sophisticated in silico methods offer a promising avenue for efficiently identifying viable drug candidates, thus providing pharmaceutical firms with significant opportunities to uncover new prospective drug targets. The main goal of this work is to review in silico methods used in the drug development process with a focus on identifying therapeutic targets linked to specific diseases at the genetic or protein level. This article thoroughly discusses A-to-Z in silico techniques, which are essential for identifying the targets of bioactive compounds and their potential therapeutic effects. This review intends to improve drug discovery processes by illuminating the state of these cutting-edge approaches, thereby maximizing the effectiveness and duration of clinical trials for novel drug target investigation.