Disco: Densely-overlapping Cell Instance Segmentation via Adjacency-aware Collaborative Coloring

Accurate cell instance segmentation is foundational for digital pathology analysis. Existing methods based on contour detection and distance mapping still face significant challenges in processing complex and dense cellular regions. Graph coloring-based methods provide a new paradigm for this task, yet the effectiveness of this paradigm in real-world scenarios with dense overlaps and complex topologies has not been verified. Addressing this issue, we release a large-scale dataset GBC-FS 2025, which contains highly complex and dense sub-cellular nuclear arrangements. We conduct the first systematic analysis of the chromatic properties of cell adjacency graphs across four diverse datasets and reveal an important discovery: most real-world cell graphs are non-bipartite, with a high prevalence of odd-length cycles (predominantly triangles). This makes simple 2-coloring theory insufficient for handling complex tissues, while higher-chromaticity models would cause representational redundancy and optimization difficulties. Building on this observation of complex real-world contexts, we propose Disco (Densely-overlapping Cell Instance Segmentation via Adjacency-aware COllaborative Coloring), an adjacency-aware framework based on the "divide and conquer" principle. It uniquely combines a data-driven topological labeling strategy with a constrained deep learning system to resolve complex adjacency conflicts. First, "Explicit Marking" strategy transforms the topological challenge into a learnable classification task by recursively decomposing the cell graph and isolating a "conflict set." Second, "Implicit Disambiguation" mechanism resolves ambiguities in conflict regions by enforcing feature dissimilarity between different instances, enabling the model to learn separable feature representations.

PAMAS: Self-Adaptive Multi-Agent System with Perspective Aggregation for Misinformation Detection

Misinformation on social media poses a critical threat to information credibility, as its diverse and context-dependent nature complicates detection. Large language model-empowered multi-agent systems (MAS) present a promising paradigm that enables cooperative reasoning and collective intelligence to combat this threat. However, conventional MAS suffer from an information-drowning problem, where abundant truthful content overwhelms sparse and weak deceptive cues. With full input access, agents tend to focus on dominant patterns, and inter-agent communication further amplifies this bias. To tackle this issue, we propose PAMAS, a multi-agent framework with perspective aggregation, which employs hierarchical, perspective-aware aggregation to highlight anomaly cues and alleviate information drowning. PAMAS organizes agents into three roles: Auditors, Coordinators, and a Decision-Maker. Auditors capture anomaly cues from specialized feature subsets; Coordinators aggregate their perspectives to enhance coverage while maintaining diversity; and the Decision-Maker, equipped with evolving memory and full contextual access, synthesizes all subordinate insights to produce the final judgment. Furthermore, to improve efficiency in multi-agent collaboration, PAMAS incorporates self-adaptive mechanisms for dynamic topology optimization and routing-based inference, enhancing both efficiency and scalability. Extensive experiments on multiple benchmark datasets demonstrate that PAMAS achieves superior accuracy and efficiency, offering a scalable and trustworthy way for misinformation detection.

TopoPrune: Robust Data Pruning via Unified Latent Space Topology

Geometric data pruning methods, while practical for leveraging pretrained models, are fundamentally unstable. Their reliance on extrinsic geometry renders them highly sensitive to latent space perturbations, causing performance to degrade during cross-architecture transfer or in the presence of feature noise. We introduce TopoPrune, a framework which resolves this challenge by leveraging topology to capture the stable, intrinsic structure of data. TopoPrune operates at two scales, (1) utilizing a topology-aware manifold approximation to establish a global low-dimensional embedding of the dataset. Subsequently, (2) it employs differentiable persistent homology to perform a local topological optimization on the manifold embeddings, ranking samples by their structural complexity. We demonstrate that our unified dual-scale topological approach ensures high accuracy and precision, particularly at significant dataset pruning rates (e.g., 90%). Furthermore, through the inherent stability properties of topology, TopoPrune is (a) exceptionally robust to noise perturbations of latent feature embeddings and (b) demonstrates superior transferability across diverse network architectures. This study demonstrates a promising avenue towards stable and principled topology-based frameworks for robust data-efficient learning.

Learning Multi-type heterogeneous interacting particle systems

We propose a framework for the joint inference of network topology, multi-type interaction kernels, and latent type assignments in heterogeneous interacting particle systems from multi-trajectory data. This learning task is a challenging non-convex mixed-integer optimization problem, which we address through a novel three-stage approach. First, we leverage shared structure across agent interactions to recover a low-rank embedding of the system parameters via matrix sensing. Second, we identify discrete interaction types by clustering within the learned embedding. Third, we recover the network weight matrix and kernel coefficients through matrix factorization and a post-processing refinement. We provide theoretical guarantees with estimation error bounds under a Restricted Isometry Property (RIP) assumption and establish conditions for the exact recovery of interaction types based on cluster separability. Numerical experiments on synthetic datasets, including heterogeneous predator-prey systems, demonstrate that our method yields an accurate reconstruction of the underlying dynamics and is robust to noise.

DSFC-Net: A Dual-Encoder Spatial and Frequency Co-Awareness Network for Rural Road Extraction

Accurate extraction of rural roads from high-resolution remote sensing imagery is essential for infrastructure planning and sustainable development. However, this task presents unique challenges in rural settings due to several factors. These include high intra-class variability and low inter-class separability from diverse surface materials, frequent vegetation occlusions that disrupt spatial continuity, and narrow road widths that exacerbate detection difficulties. Existing methods, primarily optimized for structured urban environments, often underperform in these scenarios as they overlook such distinctive characteristics. To address these challenges, we propose DSFC-Net, a dual-encoder framework that synergistically fuses spatial and frequency-domain information. Specifically, a CNN branch is employed to capture fine-grained local road boundaries and short-range continuity, while a novel Spatial-Frequency Hybrid Transformer (SFT) is introduced to robustly model global topological dependencies against vegetation occlusions. Distinct from standard attention mechanisms that suffer from frequency bias, the SFT incorporates a Cross-Frequency Interaction Attention (CFIA) module that explicitly decouples high- and low-frequency information via a Laplacian Pyramid strategy. This design enables the dynamic interaction between spatial details and frequency-aware global contexts, effectively preserving the connectivity of narrow roads. Furthermore, a Channel Feature Fusion Module (CFFM) is proposed to bridge the two branches by adaptively recalibrating channel-wise feature responses, seamlessly integrating local textures with global semantics for accurate segmentation. Comprehensive experiments on the WHU-RuR+, DeepGlobe, and Massachusetts datasets validate the superiority of DSFC-Net over state-of-the-art approaches.

Disentangling multispecific antibody function with graph neural networks

Multispecific antibodies offer transformative therapeutic potential by engaging multiple epitopes simultaneously, yet their efficacy is an emergent property governed by complex molecular architectures. Rational design is often bottlenecked by the inability to predict how subtle changes in domain topology influence functional outcomes, a challenge exacerbated by the scarcity of comprehensive experimental data. Here, we introduce a computational framework to address part of this gap. First, we present a generative method for creating large-scale, realistic synthetic functional landscapes that capture non-linear interactions where biological activity depends on domain connectivity. Second, we propose a graph neural network architecture that explicitly encodes these topological constraints, distinguishing between format configurations that appear identical to sequence-only models. We demonstrate that this model, trained on synthetic landscapes, recapitulates complex functional properties and, via transfer learning, has the potential to achieve high predictive accuracy on limited biological datasets. We showcase the model's utility by optimizing trade-offs between efficacy and toxicity in trispecific T-cell engagers and retrieving optimal common light chains. This work provides a robust benchmarking environment for disentangling the combinatorial complexity of multispecifics, accelerating the design of next-generation therapeutics.

Test-Time Adaptation for Anomaly Segmentation via Topology-Aware Optimal Transport Chaining

Deep topological data analysis (TDA) offers a principled framework for capturing structural invariants such as connectivity and cycles that persist across scales, making it a natural fit for anomaly segmentation (AS). Unlike thresholdbased binarisation, which produces brittle masks under distribution shift, TDA allows anomalies to be characterised as disruptions to global structure rather than local fluctuations. We introduce TopoOT, a topology-aware optimal transport (OT) framework that integrates multi-filtration persistence diagrams (PDs) with test-time adaptation (TTA). Our key innovation is Optimal Transport Chaining, which sequentially aligns PDs across thresholds and filtrations, yielding geodesic stability scores that identify features consistently preserved across scales. These stabilityaware pseudo-labels supervise a lightweight head trained online with OT-consistency and contrastive objectives, ensuring robust adaptation under domain shift. Across standard 2D and 3D anomaly detection benchmarks, TopoOT achieves state-of-the-art performance, outperforming the most competitive methods by up to +24.1% mean F1 on 2D datasets and +10.2% on 3D AS benchmarks.

Trigger Optimization and Event Classification for Dark Matter Searches in the CYGNO Experiment Using Machine Learning

The CYGNO experiment employs an optical-readout Time Projection Chamber (TPC) to search for rare low-energy interactions using finely resolved scintillation images. While the optical readout provides rich topological information, it produces large, sparse megapixel images that challenge real-time triggering, data reduction, and background discrimination. We summarize two complementary machine-learning approaches developed within CYGNO. First, we present a fast and fully unsupervised strategy for online data reduction based on reconstruction-based anomaly detection. A convolutional autoencoder trained exclusively on pedestal images (i.e. frames acquired with GEM amplification disabled) learns the detector noise morphology and highlights particle-induced structures through localized reconstruction residuals, from which compact Regions of Interest (ROIs) are extracted. On real prototype data, the selected configuration retains (93.0 +/- 0.2)% of reconstructed signal intensity while discarding (97.8 +/- 0.1)% of the image area, with ~25 ms per-frame inference time on a consumer GPU. Second, we report a weakly supervised application of the Classification Without Labels (CWoLa) framework to data acquired with an Americium--Beryllium neutron source. Using only mixed AmBe and standard datasets (no event-level labels), a convolutional classifier learns to identify nuclear-recoil-like topologies. The achieved performance approaches the theoretical limit imposed by the mixture composition and isolates a high-score population with compact, approximately circular morphologies consistent with nuclear recoils.

Explaining Synergistic Effects in Social Recommendations

In social recommenders, the inherent nonlinearity and opacity of synergistic effects across multiple social networks hinders users from understanding how diverse information is leveraged for recommendations, consequently diminishing explainability. However, existing explainers can only identify the topological information in social networks that significantly influences recommendations, failing to further explain the synergistic effects among this information. Inspired by existing findings that synergistic effects enhance mutual information between inputs and predictions to generate information gain, we extend this discovery to graph data. We quantify graph information gain to identify subgraphs embodying synergistic effects. Based on the theoretical insights, we propose SemExplainer, which explains synergistic effects by identifying subgraphs that embody them. SemExplainer first extracts explanatory subgraphs from multi-view social networks to generate preliminary importance explanations for recommendations. A conditional entropy optimization strategy to maximize information gain is developed, thereby further identifying subgraphs that embody synergistic effects from explanatory subgraphs. Finally, SemExplainer searches for paths from users to recommended items within the synergistic subgraphs to generate explanations for the recommendations. Extensive experiments on three datasets demonstrate the superiority of SemExplainer over baseline methods, providing superior explanations of synergistic effects.

DREAM: Dual-Standard Semantic Homogeneity with Dynamic Optimization for Graph Learning with Label Noise

Graph neural networks (GNNs) have been widely used in various graph machine learning scenarios. Existing literature primarily assumes well-annotated training graphs, while the reliability of labels is not guaranteed in real-world scenarios. Recently, efforts have been made to address the problem of graph learning with label noise. However, existing methods often (i) struggle to distinguish between reliable and unreliable nodes, and (ii) overlook the relational information embedded in the graph topology. To tackle this problem, this paper proposes a novel method, Dual-Standard Semantic Homogeneity with Dynamic Optimization (DREAM), for reliable, relation-informed optimization on graphs with label noise. Specifically, we design a relation-informed dynamic optimization framework that iteratively reevaluates the reliability of each labeled node in the graph during the optimization process according to the relation of the target node and other nodes. To measure this relation comprehensively, we propose a dual-standard selection strategy that selects a set of anchor nodes based on both node proximity and graph topology. Subsequently, we compute the semantic homogeneity between the target node and the anchor nodes, which serves as guidance for optimization. We also provide a rigorous theoretical analysis to justify the design of DREAM. Extensive experiments are performed on six graph datasets across various domains under three types of graph label noise against competing baselines, and the results demonstrate the effectiveness of the proposed DREAM.