arXiv subjects

Xizhe Zhang

Publications and source records attributed to Xizhe Zhang.

At least 19 recordsLinked to original sources

arXiv2026

Counterfactual Evaluation of Temporal Observation Protocols

We study counterfactual protocol evaluation: whether data collected under a realised observation protocol determine the predictive value of alternatives that were never deployed. Protocol value is the population $R^2$ of the Bayes-optimal predictor of a fixed trajectory-level target from the measurements an alternative would collect. We show that even infinite benchmark data need not determine this value: distinct latent covariance structures can induce the same benchmark measurement--target law while assigning different values to the same alternative. We develop a value-specific identification theory in which only latent ambiguity that changes the alternative's value matters. For linear targets, invisible covariance directions certify non-identification, while targeted measurements can restore identification without recovering the full latent covariance; an exact permutation construction extends the result to nonlinear aggregate targets. With finite dense calibration data, uniform error bounds control protocol-selection regret and distinguishable value gaps. Exact marginal gains then support cost-constrained, target-aware observation design. Simulations and retrospective analyses of Sleep-EDF and Long-Term AF show that broad temporal-layout differences can be more reliably distinguished than fine placements selected from finite data. Together, these results connect identification, calibration resolution and observation design for undeployed protocols.

cs.LG↗

arXiv2026

The Label Defines the Timescale: Trait-State Limits of Temporal-Aggregate Learning

Machine-learning benchmarks often pair a label that aggregates a long temporal horizon with input observed through one or a few short windows. Their apparent performance ceiling may therefore be an acquisition-protocol ceiling rather than a model-capacity ceiling. We study labels of the form $Θ_{g,T}=T^{-1}\int_0^T g\{Z(t)\}\,\mathrm{d}t$ when the latent Gaussian process contains both a stable individual trait and a correlated within-individual state. An exact protocol-conditioned Bayes-risk identity provides a common tool. First, we decompose label variance into an $O(1)$ trait component and an $O(T^{-1})$ state component, explaining why a snapshot can retain cross-sectional predictability while poorly tracking within-person change. Second, we derive task-dependent effective temporal spans: mean labels depend on the ordinary correlation time, whereas occupation-time labels depend on an entire spectrum of higher-order correlation times. Third, state-driven occupation-label variance is maximal when the stable trait lies at the threshold; window efficiency decays much more slowly away from that boundary. Under an equal segment budget, exact risks and Monte Carlo experiments show that repeated segments at one time rapidly saturate, whereas temporally dispersed observations continue to increase state explainability. The trait ceiling uses quantities available from ordinary test-retest data; only the state ceiling requires short-lag temporal calibration. The results distinguish architectural limits from protocol limits and show that the label, rather than duration or segment count alone, defines the relevant timescale.

stat.ML↗

arXiv2026

Noise-Robust Box-Supervised Infrared Small Target Detection via Physics-Inspired Soft Label Optimization

Infrared small target detection (IRSTD) commonly relies on pixel-level mask supervision. Such annotations, however, are costly and inherently uncertain because infrared targets have blurred boundaries and weak textures. We formulate box-supervised IRSTD as a problem distinct from generic box-to-mask segmentation and point-supervised IRSTD. Its central challenge is to construct stable pixel-level soft supervision from highly contaminated boxes. To this end, we propose Hotspot-Anchored Label Optimization (HALO). HALO localizes a radiometric anchor inside each box under local background-statistics constraints, then synthesizes a Physically Anchored Gaussian (PAG) soft label around the anchor. This turns noisy box supervision into continuous, pixel-level soft labels. The entire process is performed offline before training, remains decoupled from the detector backbone, and requires no online label updates. Experiments on public datasets show that HALO is competitive with representative box-supervised methods under standard tight boxes. Under looser or shifted box annotations that better approximate real scenarios, HALO is substantially more robust while remaining consistent across backbones. We further introduce a contamination-aware operating-regime analysis to characterize the effective boundary of this class of methods and reveal how intrinsic signal-to-clutter ratio relates to performance.

cs.CV↗

arXiv2026

Module control in youth symptom networks across COVID-19

The COVID-19 pandemic exposed young people to a prolonged and evolving societal stressor, yet it remains unclear whether symptom networks were reorganized or whether control was redistributed across a conserved modular scaffold. Here we analysed repeated cross-sectional data on 47 self-reported mental-health symptoms from 14,181 U.S. young adults aged 18-24 years across five COVID-19 phases between 2020 and 2023. For each phase, we estimated Gaussian graphical models, identified symptom communities, and characterized minimum-dominating-set-based module control. Symptom networks showed broadly conserved community organization across phases, indicating a stable mesoscale scaffold despite marked temporal variation. By contrast, intermodule control shifted from an early configuration centered on stress-related symptoms to a later, more distributed pattern spanning emotional, cognitive and social domains. Resampling analyses showed high stability for node strength and moderate stability for module-to-module control, whereas average within-module control was less robust. These findings suggest that prolonged crisis may preserve the modular architecture of youth psychopathology while redistributing control across symptom domains, and they identify intermodule control as a comparatively robust mesoscale feature for cross-phase comparison.

q-bio.QM↗

arXiv2025

Optimized Control of Duplex Networks

Many real-world complex systems can be modeled as multiplex networks, where each layer represents a distinct set of interactions among the same entities. Controlling such systems-steering them toward desired states using external inputs-is crucial across many domains. However, existing network control theory largely focuses on single-layer networks, and applying separate controls to each layer of a multiplex system often leads to redundant sets of driver nodes, increasing cost and complexity. To address this challenge, we formulate the Universal Minimum Union Driver Set (MinUDS) problem for duplex networks. The goal is to find the smallest set of driver nodes that can simultaneously control both layers. We propose a novel algorithm, Shortest Cross-Layer Augmenting Path Search (CLAP-S). This method introduces the concept of a Cross-Layer Augmenting Path (CLAP) and efficiently explores the combinatorial space of control configurations. CLAP-S iteratively realigns each layer's Minimum Driver Set (MDS) to maximize their overlap. We prove the algorithm's global optimality and demonstrate its efficiency on both synthetic networks and real-world multiplex systems. The results show that CLAP-S consistently outperforms baseline approaches by significantly reducing the number of required driver nodes and cutting computational time by an order of magnitude. This work provides a powerful, general-purpose tool for optimizing control strategies in multi-layer networks, enabling more economical interventions in diverse fields.

eess.SY↗

arXiv2025

Heatmap Guided Query Transformers for Robust Astrocyte Detection across Immunostains and Resolutions

Astrocytes are critical glial cells whose altered morphology and density are hallmarks of many neurological disorders. However, their intricate branching and stain dependent variability make automated detection of histological images a highly challenging task. To address these challenges, we propose a hybrid CNN Transformer detector that combines local feature extraction with global contextual reasoning. A heatmap guided query mechanism generates spatially grounded anchors for small and faint astrocytes, while a lightweight Transformer module improves discrimination in dense clusters. Evaluated on ALDH1L1 and GFAP stained astrocyte datasets, the model consistently outperformed Faster R-CNN, YOLOv11 and DETR, achieving higher sensitivity with fewer false positives, as confirmed by FROC analysis. These results highlight the potential of hybrid CNN Transformer architectures for robust astrocyte detection and provide a foundation for advanced computational pathology tools.

cs.CV↗

arXiv2025

Adaptive control of dynamic networks

Real-world network systems are inherently dynamic, with network topologies undergoing continuous changes over time. Previous works often focus on static networks or rely on complete prior knowledge of evolving topologies, whereas real-world networks typically undergo stochastic structural changes that are difficult to predict in advance. To address this challenge, we define the adaptive control problem and propose an adaptive control algorithm to reduce the extra control cost caused by driver node switching. We introduce a node-level adaptive control metric to capture both the stability and consistency of each node across historical topologies. By integrating this metric with a partial matching repair strategy, our algorithm adjusts the minimum driver node set in real time at each snapshot, while minimizing unnecessary reconfigurations between consecutive time steps. Extensive experiments on synthetic and real-world dynamic networks demonstrate that the proposed adaptive control algorithm significantly outperforms the existing algorithm, reducing the switching cost by an average of 22% in synthetic networks and 19\% in real-world networks, without requiring foreknowledge of the future evolution of the network. These findings extend the theoretical scope of dynamic network controllability and open new avenues for practical applications in transportation, social, and molecular regulatory systems.

eess.SY↗

arXiv2025

From Cancer Drivers to Cancer Keepers: Paradigm Shift and Clinical Implications

Cancer research has traditionally focused on identifying driver genes, those with mutations that initiate tumorigenesis. The Cancer Driver Gene (CDG) paradigm, further supported by the observation of oncogene addiction in tumors, has successfully guided the development of targeted therapies. However, the limitations of this driver-centric view, highlighted by the broad emergence of frequent therapeutic resistance, the presence of driver mutations in healthy tissues or individuals, and the lack of identifiable drivers in many tumors, call for a shift in perspective and clinical practice. The latest network controllability perspective on cancer cells introduced the concept of Cancer Keeper Genes (CKGs) and a CKG-based paradigm for cancer therapeutics. The new concept encompasses the concept of non-oncogene addiction, emphasizing reliance on non-mutated pathways crucial for maintaining oncogenic cellular states. Here, we explore the transition towards a system-level understanding of cancer based on the CKG paradigm, emphasizing the essential role of genes required for tumor maintenance, irrespective of their initiating function or mutational capacity. We discuss clinical implications of this paradigm shift, highlighting the progress made so far and potential of targeting non-driver CKGs, genes involved in processes like DNA damage response, proteostasis, and metabolism, as a promising strategy to overcome therapeutic challenges and achieve more durable cancer control. Targeting these maintenance vulnerabilities represents a critical evolution in precision oncology, moving towards therapies designed to dismantle the networks sustaining malignancies.

q-bio.MN↗

arXiv2025

GridRoute: A Benchmark for LLM-Based Route Planning with Cardinal Movement in Grid Environments

Recent advancements in Large Language Models (LLMs) have demonstrated their potential in planning and reasoning tasks, offering a flexible alternative to classical pathfinding algorithms. However, most existing studies focus on LLMs' independent reasoning capabilities and overlook the potential synergy between LLMs and traditional algorithms. To fill this gap, we propose a comprehensive evaluation benchmark GridRoute to assess how LLMs can take advantage of traditional algorithms. We also propose a novel hybrid prompting technique called Algorithm of Thought (AoT), which introduces traditional algorithms' guidance into prompting. Our benchmark evaluates six LLMs ranging from 7B to 72B parameters across various map sizes, assessing their performance in correctness, optimality, and efficiency in grid environments with varying sizes. Our results show that AoT significantly boosts performance across all model sizes, particularly in larger or more complex environments, suggesting a promising approach to addressing path planning challenges. Our code is open-sourced at https://github.com/LinChance/GridRoute.

cs.AI↗

arXiv2025

Faces of the Mind: Unveiling Mental Health States Through Facial Expressions in 11,427 Adolescents

Mood disorders such as depression and anxiety often manifest through facial expressions, but existing machine learning algorithms designed to assess these disorders have been hindered by small datasets and limited real-world applicability. To address this gap, we analyzed facial videos of 11,427 participants - a dataset two orders of magnitude larger than those used in previous studies - including standardized facial expression videos and psychological assessments of depression, anxiety, and stress. However, scaling up the dataset introduces significant challenges due to increased symptom heterogeneity, making it difficult for models to learn accurate representations. To address this, we introduced the Symptom Discrepancy Index (SDI), a novel metric for quantifying dataset heterogeneity caused by variability in individual symptoms among samples with identical total scores. By removing the 10% most heterogeneous cases as identified by the SDI, we raised the F1 scores of all models from approximately 50% to 80%. Notably, comparable performance gains were observed within both the retained and excluded subsets. These findings demonstrate symptom heterogeneity, not model capacity, as the principal bottleneck in large scale automated assessment and provide a general solution that is readily applicable to other psychometric data sets.

cs.CV↗

arXiv2024

Module control of network analysis in psychopathology

The network approach to characterizing psychopathology departs from traditional latent categorical and dimensional approaches. Causal interplay among symptoms contributed to dynamic psychopathology system. Therefore, analyzing the symptom clusters is critical for understanding mental disorders. Furthermore, despite extensive research studying the topological features of symptom networks, the control relationships between symptoms remain largely unclear. Here, we present a novel systematizing concept, module control, to analyze the control principle of the symptom network at a module level. We introduce Module Control Network (MCN) to identify key modules that regulate the network's behavior. By applying our approach to a multivariate psychological dataset, we discover that non-emotional modules, such as sleep-related and stress-related modules, are the primary controlling modules in the symptom network. Our findings indicate that module control can expose central symptom cluster governing psychopathology network, offering novel insights into the underlying mechanisms of mental disorders and individualized approach to psychological interventions.

q-bio.NC↗

arXiv2023

Exploring the relationship between response time sequence in scale answering process and severity of insomnia: a machine learning approach

Objectives: The study aims to investigate the relationship between insomnia and response time. Additionally, it aims to develop a machine learning model to predict the presence of insomnia in participants using response time data. Methods: A mobile application was designed to administer scale tests and collect response time data from 2729 participants. The relationship between symptom severity and response time was explored, and a machine learning model was developed to predict the presence of insomnia. Results: The result revealed a statistically significant difference (p<.001) in the total response time between participants with or without insomnia symptoms. A correlation was observed between the severity of specific insomnia aspects and response times at the individual questions level. The machine learning model demonstrated a high predictive accuracy of 0.743 in predicting insomnia symptoms based on response time data. Conclusions: These findings highlight the potential utility of response time data to evaluate cognitive and psychological measures, demonstrating the effectiveness of using response time as a diagnostic tool in the assessment of insomnia.

cs.LG↗

arXiv2023

Attention-Based Acoustic Feature Fusion Network for Depression Detection

Depression, a common mental disorder, significantly influences individuals and imposes considerable societal impacts. The complexity and heterogeneity of the disorder necessitate prompt and effective detection, which nonetheless, poses a difficult challenge. This situation highlights an urgent requirement for improved detection methods. Exploiting auditory data through advanced machine learning paradigms presents promising research directions. Yet, existing techniques mainly rely on single-dimensional feature models, potentially neglecting the abundance of information hidden in various speech characteristics. To rectify this, we present the novel Attention-Based Acoustic Feature Fusion Network (ABAFnet) for depression detection. ABAFnet combines four different acoustic features into a comprehensive deep learning model, thereby effectively integrating and blending multi-tiered features. We present a novel weight adjustment module for late fusion that boosts performance by efficaciously synthesizing these features. The effectiveness of our approach is confirmed via extensive validation on two clinical speech databases, CNRAC and CS-NRAC, thereby outperforming previous methods in depression detection and subtype classification. Further in-depth analysis confirms the key role of each feature and highlights the importance of MFCCrelated features in speech-based depression detection.

cs.SD↗

arXiv2023

Total controllability analysis discovers explainable drugs for Covid-19 treatment

Network medicine has been pursued for Covid-19 drug repurposing. One such approach adopts structural controllability, a theory for controlling a network (the cell). Motivated to protect the cell from viral infections, we extended this theory to total controllability and introduced a new concept of control hubs. Perturbation to any control hub renders the cell uncontrollable by exogenous stimuli, e.g., viral infections, so control hubs are ideal drug targets. We developed an efficient algorithm for finding all control hubs and applied it to the largest homogenous human protein-protein interaction network. Our new method outperforms several popular gene-selection methods, including that based on structural controllability. The final 65 druggable control hubs are enriched with functions of cell proliferation, regulation of apoptosis, and responses to cellular stress and nutrient levels, revealing critical pathways induced by SARS-CoV-2. These druggable control hubs led to drugs in 4 major categories: antiviral and anti-inflammatory agents, drugs on central nerve systems, and dietary supplements and hormones that boost immunity. Their functions also provided deep insights into the therapeutic mechanisms of the drugs for Covid-19 therapy, making the new approach an explainable drug repurposing method. A remarkable example is Fostamatinib that has been shown to lower mortality, shorten the length of ICU stay, and reduce disease severity of hospitalized Covid-19 patients. The drug targets 10 control hubs, 9 of which are kinases that play key roles in cell differentiation and programmed death. One such kinase is RIPK1 that directly interacts with viral protein nsp12, the RdRp of the virus. The study produced many control hubs that were not targets of existing drugs but were enriched with proteins on membranes and the NF-$κ$B pathway, so are excellent candidate targets for new drugs.

q-bio.MN↗

arXiv2023

NetMoST: A network-based machine learning approach for subtyping schizophrenia using polygenic SNP allele biomarkers

Subtyping neuropsychiatric disorders like schizophrenia is essential for improving the diagnosis and treatment of complex diseases. Subtyping schizophrenia is challenging because it is polygenic and genetically heterogeneous, rendering the standard symptom-based diagnosis often unreliable and unrepeatable. We developed a novel network-based machine-learning approach, netMoST, to subtyping psychiatric disorders. NetMoST identifies polygenic risk SNP-allele modules from genome-wide genotyping data as polygenic haplotype biomarkers (PHBs) for disease subtyping. We applied netMoST to subtype a cohort of schizophrenia subjects into three distinct biotypes with differentiable genetic, neuroimaging and functional characteristics. The PHBs of the first biotype (36.9% of all patients) were related to neurodevelopment and cognition, the PHBs of the second biotype (28.4%) were enriched for neuroimmune functions, and the PHBs of the third biotype (34.7%) were associated with the transport of calcium ions and neurotransmitters. Neuroimaging patterns provided additional support to the new biotypes, with unique regional homogeneity (ReHo) patterns observed in the brains of each biotype compared with healthy controls. Our findings demonstrated netMoST's capability for uncovering novel biotypes of complex diseases such as schizophrenia. The results also showed the power of exploring polygenic allelic patterns that transcend the conventional GWAS approaches.

q-bio.MN↗

arXiv2022

Identification of cancer-keeping genes as therapeutic targets by finding network control hubs

Finding cancer driver genes has been a focal theme of cancer research and clinical studies. One of the recent approaches is based on network structural controllability that focuses on finding a control scheme and driver genes that can steer the cell from an arbitrary state to a designated state. While theoretically sound, this approach is impractical for many reasons, e.g., the control scheme is often not unique and half of the nodes may be driver genes for the cell. We developed a novel approach that transcends structural controllability. Instead of considering driver genes for one control scheme, we considered control hub genes that reside in the middle of a control path of every control scheme. Control hubs are the most vulnerable spots for controlling the cell and exogenous stimuli on them may render the cell uncontrollable. We adopted control hubs as cancer-keep genes (CKGs) and applied them to a gene regulatory network of bladder cancer (BLCA). All the genes on the cell cycle and p53 singling pathways in BLCA are CKGs, confirming the importance of these genes and the two pathways in cancer. A smaller set of 35 sensitive CKGs (sCKGs) for BLCA was identified by removing network links. Six sCKGs (RPS6KA3, FGFR3, N-cadherin (CDH2), EP300, caspase-1, and FN1) were subjected to small-interferencing-RNA knockdown in four cell lines to validate their effects on the proliferation or migration of cancer cells. Knocking down RPS6KA3 in a mouse model of BLCA significantly inhibited the growth of tumor xenografts in the mouse model. Combined, our results demonstrated the value of CKGs as therapeutic targets for cancer therapy and the potential of CKGs as an effective means for studying and characterizing cancer etiology.

q-bio.MN↗

arXiv2022

Response to: Significance and stability of deep learning-based identification of subtypes within major psychiatric disorders. Molecular Psychiatry (2022)

Recently, Winter and Hahn [1] commented on our work on identifying subtypes of major psychiatry disorders (MPDs) based on neurobiological features using machine learning [2]. They questioned the generalizability of our methods and the statistical significance, stability, and overfitting of the results, and proposed a pipeline for disease subtyping. We appreciate their earnest consideration of our work, however, we need to point out their misconceptions of basic machine-learning concepts and delineate some key issues involved.

cs.LG↗

arXiv2022

Control hubs of complex networks and a polynomial-time identification algorithm

Unveiling the underlying control principles of complex networks is one of the ultimate goals of network science. We introduce a novel concept, control hub, to reveal a cornerstone of the control structure of a network. The control hubs of a network are the nodes that lie in the middle of a control path in every control scheme of the network. We present a theorem based on graph theory for identifying control hubs without computing all control schemes. We develop an algorithm to identify all control hubs in O(N0.5L) time complexity for a network of N nodes and L links.

cs.DM↗