arXiv subjects

Zhiqian Chen

Publications and source records attributed to Zhiqian Chen.

At least 19 recordsLinked to original sources

arXiv2026

From Causal Plausibility to Causal Reliability: Evaluating LLMs as Calibrated Direct Causal-Edge Classifiers

Large language models (LLMs) are increasingly used to provide prior causal knowledge for structural causal discovery, yet whether their direct-edge judgments and confidence can be trusted remains unclear. We systematically evaluate 12 instruction-tuned open-weight models across six benchmark causal graphs, five prompting strategies, and four confidence sources: verbalized, logit-based, cross-prompt agreement, and cross-model agreement. Under our language-only pairwise protocol, our evaluation yields three key findings. (i) LLM-based causal judgments are strongly recall-dominant: models predict overly dense graphs with many false-positive edges, while prompting mainly shifts the precision-recall trade-off rather than resolving overprediction. Gains from model scale diminish on the largest graphs and do not eliminate miscalibration. (ii) LLMs often capture causal relatedness without reliably identifying directness or orientation. Relative to published reference graphs, models misclassify 40.0% of indirect and 36.0% of reversed non-edges as direct edges, versus 28.2% of other non-edges. Moreover, 80.8% and 84.6% of these false positives receive verbalized confidence of at least 80%, revealing substantial overconfidence in structurally incorrect predictions. (iii) Conventional confidence estimates are unreliable, whereas agreement offers a more promising signal. Logit-based confidence frequently collapses near 1.0 regardless of correctness, while cross-prompt and cross-model agreement achieve better mean calibration and discrimination, though their advantages are not statistically significant after Holm correction. A benchmark-familiarity audit further identifies potential familiarity in five model-dataset pairs, all involving AsiaM. Overall, our results suggest LLMs are better viewed as sources of externally validated soft causal priors than as direct evidence of causal structure.

cs.LG↗

arXiv2026

MasterSet: A Large-Scale Benchmark for Must-Cite Citation Recommendation in the AI/ML Literature

The explosive growth of AI and machine learning literature -- with venues like NeurIPS and ICLR now accepting thousands of papers annually -- has made comprehensive citation coverage increasingly difficult for researchers. While citation recommendation has been studied for over a decade, existing systems primarily focus on broad relevance rather than identifying the critical set of ``must-cite'' papers: direct experimental baselines, foundational methods, and core dependencies whose omission would misrepresent a contribution's novelty or undermine reproducibility. We introduce MasterSet, a large-scale benchmark specifically designed to evaluate must-cite recommendation in the AI/ML domain. MasterSet incorporates over 150,000 papers collected from official conference proceedings/websites of 15 leading venues, serving as a comprehensive candidate pool for retrieval. We annotate citations with a three-tier labeling scheme: (I) experimental baseline status, (II) core relevance (1--5 scale), and (III) intra-paper mention frequency. Our annotation pipeline leverages an LLM-based judge, validated by human experts on a stratified sample. The benchmark task requires retrieving must-cite papers from the candidate pool given only a query paper's title and abstract, evaluated by Recall@$K$. We establish baselines using sparse retrieval, dense scientific embeddings, and graph-based methods, demonstrating that must-cite retrieval remains a challenging open problem.

cs.IR↗

arXiv2026

MOTGNN: Interpretable Graph Neural Networks for Multi-Omics Disease Classification

Integrating multi-omics data, such as DNA methylation, mRNA expression, and microRNA (miRNA) expression, offers a comprehensive view of the biological mechanisms underlying disease. However, the high dimensionality of multi-omics data, the heterogeneity across modalities, and the lack of reliable biological interaction networks make meaningful integration challenging. In addition, many existing models rely on handcrafted similarity graphs, are vulnerable to class imbalance, and often lack built-in interpretability, limiting their usefulness in biomedical applications. We propose Multi-Omics integration with Tree-generated Graph Neural Network (MOTGNN), a novel and interpretable framework for binary disease classification. MOTGNN employs eXtreme Gradient Boosting (XGBoost) for omics-specific supervised graph construction, followed by modality-specific Graph Neural Networks (GNNs) for hierarchical representation learning, and a deep feedforward network for cross-omics integration. Across three real-world disease datasets, MOTGNN outperforms state-of-the-art baselines by 5-10% in accuracy, ROC-AUC, and F1-score, and remains robust to severe class imbalance. The model maintains computational efficiency through the use of sparse graphs and provides built-in interpretability, revealing both top-ranked biomarkers and the relative contributions of each omics modality. These results highlight the potential of MOTGNN to improve both predictive accuracy and interpretability in multi-omics disease modeling.

cs.LG↗

arXiv2026

TF-DWGNet: A Directed Weighted Graph Neural Network with Tensor Fusion for Multi-Omics Cancer Subtype Classification

Integration and analysis of multi-omics data provide valuable insights for improving cancer subtype classification. However, such data are inherently heterogeneous, high-dimensional, and exhibit complex intra- and inter-modality dependencies. Graph neural networks (GNNs) offer a principled framework for modeling these structures, but existing approaches often rely on prior knowledge or predefined similarity networks that produce undirected or unweighted graphs and fail to capture task-specific directionality and interaction strength. Interpretability at both the modality and feature levels also remains limited. To address these challenges, we propose TF-DWGNet, a novel Graph Neural Network framework that combines tree-based Directed Weighted graph construction with Tensor Fusion for multiclass cancer subtype classification. TF-DWGNet introduces two key innovations: (i) a supervised tree-based strategy that constructs directed, weighted graphs tailored to each omics modality, and (ii) a tensor fusion mechanism that captures unimodal, bimodal, and trimodal interactions using low-rank decomposition for computational efficiency. Experiments on three real-world cancer datasets demonstrate that TF-DWGNet consistently outperforms state-of-the-art baselines across multiple metrics and statistical tests. In addition, the model provides biologically meaningful insights through modality-level contribution scores and ranked feature importance. These results highlight that TF-DWGNet is an effective and interpretable solution for multi-omics integration in cancer research.

q-bio.QM↗

arXiv2025

Filter-And-Refine: A MLLM Based Cascade System for Industrial-Scale Video Content Moderation

Effective content moderation is essential for video platforms to safeguard user experience and uphold community standards. While traditional video classification models effectively handle well-defined moderation tasks, they struggle with complicated scenarios such as implicit harmful content and contextual ambiguity. Multimodal large language models (MLLMs) offer a promising solution to these limitations with their superior cross-modal reasoning and contextual understanding. However, two key challenges hinder their industrial adoption. First, the high computational cost of MLLMs makes full-scale deployment impractical. Second, adapting generative models for discriminative classification remains an open research problem. In this paper, we first introduce an efficient method to transform a generative MLLM into a multimodal classifier using minimal discriminative training data. To enable industry-scale deployment, we then propose a router-ranking cascade system that integrates MLLMs with a lightweight router model. Offline experiments demonstrate that our MLLM-based approach improves F1 score by 66.50% over traditional classifiers while requiring only 2% of the fine-tuning data. Online evaluations show that our system increases automatic content moderation volume by 41%, while the cascading deployment reduces computational cost to only 1.5% of direct full-scale deployment.

cs.LG↗

arXiv2025

Embedding-based Retrieval in Multimodal Content Moderation

Video understanding plays a fundamental role for content moderation on short video platforms, enabling the detection of inappropriate content. While classification remains the dominant approach for content moderation, it often struggles in scenarios requiring rapid and cost-efficient responses, such as trend adaptation and urgent escalations. To address this issue, we introduce an Embedding-Based Retrieval (EBR) method designed to complement traditional classification approaches. We first leverage a Supervised Contrastive Learning (SCL) framework to train a suite of foundation embedding models, including both single-modal and multi-modal architectures. Our models demonstrate superior performance over established contrastive learning methods such as CLIP and MoCo. Building on these embedding models, we design and implement the embedding-based retrieval system that integrates embedding generation and video retrieval to enable efficient and effective trend handling. Comprehensive offline experiments on 25 diverse emerging trends show that EBR improves ROC-AUC from 0.85 to 0.99 and PR-AUC from 0.35 to 0.95. Further online experiments reveal that EBR increases action rates by 10.32% and reduces operational costs by over 80%, while also enhancing interpretability and flexibility compared to classification-based solutions.

cs.IR↗

arXiv2024

Network Interdiction Goes Neural

Network interdiction problems are combinatorial optimization problems involving two players: one aims to solve an optimization problem on a network, while the other seeks to modify the network to thwart the first player's objectives. Such problems typically emerge in an attacker-defender context, encompassing areas such as military operations, disease spread analysis, and communication network management. The primary bottleneck in network interdiction arises from the high time complexity of using conventional exact solvers and the challenges associated with devising efficient heuristic solvers. GNNs, recognized as a cutting-edge methodology, have shown significant effectiveness in addressing single-level CO problems on graphs, such as the traveling salesman problem, graph matching, and graph edit distance. Nevertheless, network interdiction presents a bi-level optimization challenge, which current GNNs find difficult to manage. To address this gap, we represent network interdiction problems as Mixed-Integer Linear Programming (MILP) instances, then apply a multipartite GNN with sufficient representational capacity to learn these formulations. This approach ensures that our neural network is more compatible with the mathematical algorithms designed to solve network interdiction problems, resulting in improved generalization. Through two distinct tasks, we demonstrate that our proposed method outperforms theoretical baseline models and provides advantages over traditional exact solvers.

cs.AI↗

arXiv2024

Bayesian-Guided Generation of Synthetic Microbiomes with Minimized Pathogenicity

Synthetic microbiomes offer new possibilities for modulating microbiota, to address the barriers in multidtug resistance (MDR) research. We present a Bayesian optimization approach to enable efficient searching over the space of synthetic microbiome variants to identify candidates predictive of reduced MDR. Microbiome datasets were encoded into a low-dimensional latent space using autoencoders. Sampling from this space allowed generation of synthetic microbiome signatures. Bayesian optimization was then implemented to select variants for biological screening to maximize identification of designs with restricted MDR pathogens based on minimal samples. Four acquisition functions were evaluated: expected improvement, upper confidence bound, Thompson sampling, and probability of improvement. Based on each strategy, synthetic samples were prioritized according to their MDR detection. Expected improvement, upper confidence bound, and probability of improvement consistently produced synthetic microbiome candidates with significantly fewer searches than Thompson sampling. By combining deep latent space mapping and Bayesian learning for efficient guided screening, this study demonstrated the feasibility of creating bespoke synthetic microbiomes with customized MDR profiles.

q-bio.QM↗

arXiv2024

Multiple-Source Localization from a Single-Snapshot Observation Using Graph Bayesian Optimization

Due to the significance of its various applications, source localization has garnered considerable attention as one of the most important means to confront diffusion hazards. Multi-source localization from a single-snapshot observation is especially relevant due to its prevalence. However, the inherent complexities of this problem, such as limited information, interactions among sources, and dependence on diffusion models, pose challenges to resolution. Current methods typically utilize heuristics and greedy selection, and they are usually bonded with one diffusion model. Consequently, their effectiveness is constrained. To address these limitations, we propose a simulation-based method termed BOSouL. Bayesian optimization (BO) is adopted to approximate the results for its sample efficiency. A surrogate function models uncertainty from the limited information. It takes sets of nodes as the input instead of individual nodes. BOSouL can incorporate any diffusion model in the data acquisition process through simulations. Empirical studies demonstrate that its performance is robust across graph structures and diffusion models. The code is available at https://github.com/XGraph-Team/BOSouL.

cs.LG↗

arXiv2024

Graph Bayesian Optimization for Multiplex Influence Maximization

Influence maximization (IM) is the problem of identifying a limited number of initial influential users within a social network to maximize the number of influenced users. However, previous research has mostly focused on individual information propagation, neglecting the simultaneous and interactive dissemination of multiple information items. In reality, when users encounter a piece of information, such as a smartphone product, they often associate it with related products in their minds, such as earphones or computers from the same brand. Additionally, information platforms frequently recommend related content to users, amplifying this cascading effect and leading to multiplex influence diffusion. This paper first formulates the Multiplex Influence Maximization (Multi-IM) problem using multiplex diffusion models with an information association mechanism. In this problem, the seed set is a combination of influential users and information. To effectively manage the combinatorial complexity, we propose Graph Bayesian Optimization for Multi-IM (GBIM). The multiplex diffusion process is thoroughly investigated using a highly effective global kernelized attention message-passing module. This module, in conjunction with Bayesian linear regression (BLR), produces a scalable surrogate model. A data acquisition module incorporating the exploration-exploitation trade-off is developed to optimize the seed set further. Extensive experiments on synthetic and real-world datasets have proven our proposed framework effective. The code is available at https://github.com/zirui-yuan/GBIM.

cs.SI↗

arXiv2024

Deep Sensitivity Analysis for Objective-Oriented Combinatorial Optimization

Pathogen control is a critical aspect of modern poultry farming, providing important benefits for both public health and productivity. Effective poultry management measures to reduce pathogen levels in poultry flocks promote food safety by lowering risks of food-borne illnesses. They also support animal health and welfare by preventing infectious diseases that can rapidly spread and impact flock growth, egg production, and overall health. This study frames the search for optimal management practices that minimize the presence of multiple pathogens as a combinatorial optimization problem. Specifically, we model the various possible combinations of management settings as a solution space that can be efficiently explored to identify configurations that optimally reduce pathogen levels. This design incorporates a neural network feedback-based method that combines feature explanations with global sensitivity analysis to ensure combinatorial optimization in multiobjective settings. Our preliminary experiments have promising results when applied to two real-world agricultural datasets. While further validation is still needed, these early experimental findings demonstrate the potential of the model to derive targeted feature interactions that adaptively optimize pathogen control under varying real-world constraints.

cs.LG↗

arXiv2024

Towards Interpreting Multi-Objective Feature Associations

Understanding how multiple features are associated and contribute to a specific objective is as important as understanding how each feature contributes to a particular outcome. Interpretability of a single feature in a prediction may be handled in multiple ways; however, in a multi-objective prediction, it is difficult to obtain interpretability of a combination of feature values. To address this issue, we propose an objective specific feature interaction design using multi-labels to find the optimal combination of features in agricultural settings. One of the novel aspects of this design is the identification of a method that integrates feature explanations with global sensitivity analysis in order to ensure combinatorial optimization in multi-objective settings. We have demonstrated in our preliminary experiments that an approximate combination of feature values can be found to achieve the desired outcome using two agricultural datasets: one with pre-harvest poultry farm practices for multi-drug resistance presence, and one with post-harvest poultry farm practices for food-borne pathogens. In our combinatorial optimization approach, all three pathogens are taken into consideration simultaneously to account for the interaction between conditions that favor different types of pathogen growth. These results indicate that explanation-based approaches are capable of identifying combinations of features that reduce pathogen presence in fewer iterations than a baseline.

cs.LG↗

arXiv2023

Bridging the Gap between Spatial and Spectral Domains: A Unified Framework for Graph Neural Networks

Deep learning's performance has been extensively recognized recently. Graph neural networks (GNNs) are designed to deal with graph-structural data that classical deep learning does not easily manage. Since most GNNs were created using distinct theories, direct comparisons are impossible. Prior research has primarily concentrated on categorizing existing models, with little attention paid to their intrinsic connections. The purpose of this study is to establish a unified framework that integrates GNNs based on spectral graph and approximation theory. The framework incorporates a strong integration between spatial- and spectral-based GNNs while tightly associating approaches that exist within each respective domain.

cs.LG↗

arXiv2023

XFlow: Benchmarking Flow Behaviors over Graphs

The occurrence of diffusion on a graph is a prevalent and significant phenomenon, as evidenced by the spread of rumors, influenza-like viruses, smart grid failures, and similar events. Comprehending the behaviors of flow is a formidable task, due to the intricate interplay between the distribution of seeds that initiate flow propagation, the propagation model, and the topology of the graph. The study of networks encompasses a diverse range of academic disciplines, including mathematics, physics, social science, and computer science. This interdisciplinary nature of network research is characterized by a high degree of specialization and compartmentalization, and the cooperation facilitated by them is inadequate. From a machine learning standpoint, there is a deficiency in a cohesive platform for assessing algorithms across various domains. One of the primary obstacles to current research in this field is the absence of a comprehensive curated benchmark suite to study the flow behaviors under network scenarios. To address this disparity, we propose the implementation of a novel benchmark suite that encompasses a variety of tasks, baseline models, graph datasets, and evaluation tools. In addition, we present a comprehensive analytical framework that offers a generalized approach to numerous flow-related tasks across diverse domains, serving as a blueprint and roadmap. Drawing upon the outcomes of our empirical investigation, we analyze the advantages and disadvantages of current foundational models, and we underscore potential avenues for further study. The datasets, code, and baseline models have been made available for the public at: https://github.com/XGraphing/XFlow

cs.SI↗

arXiv2023

Understanding Influence Maximization via Higher-Order Decomposition

Given its vast application on online social networks, Influence Maximization (IM) has garnered considerable attention over the last couple of decades. Due to the intricacy of IM, most current research concentrates on estimating the first-order contribution of the nodes to select a seed set, disregarding the higher-order interplay between different seeds. Consequently, the actual influence spread frequently deviates from expectations, and it remains unclear how the seed set quantitatively contributes to this deviation. To address this deficiency, this work dissects the influence exerted on individual seeds and their higher-order interactions utilizing the Sobol index, a variance-based sensitivity analysis. To adapt to IM contexts, seed selection is phrased as binary variables and split into distributions of varying orders. Based on our analysis with various Sobol indices, an IM algorithm dubbed SIM is proposed to improve the performance of current IM algorithms by over-selecting nodes followed by strategic pruning. A case study is carried out to demonstrate that the explanation of the impact effect can dependably identify the key higher-order interactions among seeds. SIM is empirically proved to be superior in effectiveness and competitive in efficiency by experiments on synthetic and real-world graphs.

cs.SI↗

arXiv2022

Deep representation learning: Fundamentals, Perspectives, Applications, and Open Challenges

Machine Learning algorithms have had a profound impact on the field of computer science over the past few decades. These algorithms performance is greatly influenced by the representations that are derived from the data in the learning process. The representations learned in a successful learning process should be concise, discrete, meaningful, and able to be applied across a variety of tasks. A recent effort has been directed toward developing Deep Learning models, which have proven to be particularly effective at capturing high-dimensional, non-linear, and multi-modal characteristics. In this work, we discuss the principles and developments that have been made in the process of learning representations, and converting them into desirable applications. In addition, for each framework or model, the key issues and open challenges, as well as the advantages, are examined.

cs.LG↗

arXiv2022

Memetic algorithms for Spatial Partitioning problems

Spatial optimization problems (SOPs) are characterized by spatial relationships governing the decision variables, objectives, and/or constraint functions. In this article, we focus on a specific type of SOP called spatial partitioning, which is a combinatorial problem due to the presence of discrete spatial units. Exact optimization methods do not scale with the size of the problem, especially within practicable time limits. This motivated us to develop population-based metaheuristics for solving such SOPs. However, the search operators employed by these population-based methods are mostly designed for real-parameter continuous optimization problems. For adapting these methods to SOPs, we apply domain knowledge in designing spatially-aware search operators for efficiently searching through the discrete search space while preserving the spatial constraints. To this end, we put forward a simple yet effective algorithm called swarm-based spatial memetic algorithm (SPATIAL) and test it on the school (re)districting problem. Detailed experimental investigations are performed on real-world datasets to evaluate the performance of SPATIAL. Besides, ablation studies are performed to understand the role of the individual components of SPATIAL. Additionally, we discuss how SPATIAL~is helpful in the real-life planning process and its applicability to different scenarios and motivate future research directions.

math.OC↗

arXiv2022

Demystifying Graph Convolution with a Simple Concatenation

Graph convolution (GConv) is a widely used technique that has been demonstrated to be extremely effective for graph learning applications, most notably node categorization. On the other hand, many GConv-based models do not quantify the effect of graph topology and node features on performance, and are even surpassed by some models that do not consider graph structure or node properties. We quantify the information overlap between graph topology, node features, and labels in order to determine graph convolution's representation power in the node classification task. In this work, we first determine the linear separability of graph convoluted features using analysis of variance. Mutual information is used to acquire a better understanding of the possible non-linear relationship between graph topology, node features, and labels. Our theoretical analysis demonstrates that a simple and efficient graph operation that concatenates only graph topology and node properties consistently outperforms conventional graph convolution, especially in the heterophily case. Extensive empirical research utilizing a synthetic dataset and real-world benchmarks demonstrates that graph concatenation is a simple but more flexible alternative to graph convolution.

cs.LG↗