Topology

When computing sub/super-level-set persistent homology (PH), the effect of noise may introduce millions of (short-lived) topological generators, presenting an obstacle to both the computation of PH of large 3D images, and any analysis of PH that incorporates the number of generators. As such, it is often necessary to denoise the data before computing its PH. We analyze the PH of synthetic 3D images of porous media in the presence of spatially uncorrelated noise, and perform a comparative analysis of various topological measures (e.g. bottleneck distance, Wasserstein distance, persistence statistics and persistence images) to assess their robustness to both noise and the denoising process (i.e. adding spatially uncorrelated Gaussian noise, and denoising by either a Gaussian convolution or a machine learning approach).

We present two approaches for predicting tennis match outcomes using topological data analysis and graph theory on ATP singles matches from 2000-2025. The first method applies lower-star filtration to player competitive networks, extracting topological features through persistent homology using four summary methods (VAB, HNAV, HWNAV, OW-HNPV) combined with Modified Band Depth analysis. Algorithmic optimizations including ego graph approximations and triangle elimination enable analysis of about 66k matches. Our Random Forest model achieves 66.2% accuracy (AUC = 0.719) using topological, graph-theoretic, and ranking features. Feature importance analysis reveals that rankings contribute 36.3%, centralities 25.5%, and TDA features 24.0%, with topological features providing complementary signal. When rankings are unavailable, the topology-only model maintains 63.56% accuracy, demonstrating that network-derived features alone capture meaningful competitive structure. The second method uses a modified Katz similarity index with temporal edge weighting, achieving 62.48% accuracy on held-out test data. This work represents the first application of lower-star filtration to tennis prediction, provides systematic comparison of four topological summary methods in sports analytics, and demonstrates that TDA can achieve above-chance prediction using network topology alone while providing additional value when combined with traditional features.

Automatic feature engineering (AutoFE) for tabular data requires discovering informative transformations from a large program space. Existing approaches suffer from three limitations: classical methods rely on fixed operator libraries with limited expressivity, LLM-based methods generate proposals from static prompts without retaining search experience, and evolutionary methods use fixed migration policies that ignore task-specific cross-family transfer utility. We introduce TOPOFE, a framework that formulates AutoFE as graph-structured multi-island evolutionary program search. The transformation space is partitioned into semantically coherent families, each explored by an island through LLM-guided mutation and crossover. Each island maintains a Prompt Adaptation Memory that accumulates accept/reject feedback to steer proposals toward productive regions without parameter updates. To coordinate global exploration, TOPOFE dynamically learns a directed topology graph whose edge weights encode transfer utility between transformation families. Cross-island transfer is triggered by adaptive saturation detection and performed through LLM-mediated hybrid synthesis, enabling discovery of compositional feature programs that cannot emerge from isolated local search. Experiments on 29 tabular datasets show that TOPOFE consistently outperforms most state-of-the-art AutoFE methods on classification and regression tasks. Beyond predictive performance, TOPOFE produces feature sets with lower redundancy and higher representational coverage, while the learned topology graph acquires meaningful task-specific transfer structure correlated with downstream gains. The discovered feature programs transfer reliably across diverse predictors and LLM backbones, demonstrating that improvements arise from TOPOFE's structured search and adaptive coordination rather than backbone-specific generation capability.

Self-Organizing Maps (SOMs) have long been used as exploratory tools for high-dimensional data: they organize objects into a two-dimensional topology that reveals clusters, gradients, sparse regions, dense regions, and boundaries. Yet, in modern data systems, SOMs are typically trained and visualized outside the DBMS, disconnected from the relational data they summarize. We introduce the abstraction of a queryable data map: a learned topological artifact consisting of representatives, neighborhood relations, object assignments, and derived summaries. We instantiate this idea with MapDB, a lightweight prototype that makes SOM artifacts queryable so users can explore data topology without leaving the database. Experimental study shows that SOM training is feasible at moderate analytical scale, that map queries are interactive after materialization, and that SOM regions provide meaningful targets for exploratory SQL.

Topological maps are key outputs of autonomous driving perception systems, delivering essential road information for path planning. They identify instances such as centerlines and traffic signs, along with their connectivity relationships. Due to the lack of explicit markings for centerlines in real-world environments, the detection of centerline instances remains a significant challenge. To tackle this problem, we propose HGeo-TopoMap, which leverages an explicit prior map and implicit spatial relations to hierarchically boost topological mapping. First, a geometric adaptive learning module is designed for the road structure map obtained via inverse perspective mapping. This module discretely encodes semantic and spatial features from the map, followed by a prior-mask attention mechanism that selectively focuses on informative regions. Then, a geometric consistency learning module is devised, which leverages the geometric properties and spatial relationships of centerlines. Built on the geometry-aware decoder, it enforces spatial consistency by aligning features of centerline instances with identical geometric orientations. The proposed method is evaluated on the OpenLane-V2 dataset across the centerline, lane segment, and robustness benchmarks. Beyond substantial improvements in topological mapping accuracy, the proposed method offers the benefit of enhanced robustness, consistently outperforming baselines under both standard and challenging conditions. The source code and model weights will be made publicly available at https://github.com/lynn-yu/HGeo-TopoMap.

Computer aided design (CAD) is ubiquitous: virtually any modern object was designed using editable CAD tools. However, with the shortage of available CAD datasets in its native editable and parametric format, boundary representation (B-Rep), it is ever more important to develop data-efficient methods for this domain. We present a new self-supervised pretraining task, Masked Topology Modeling (MTM), that leverages the face-adjacency graph, an induced structure unique to B-reps that the encoder can be asked to reconstruct. MTM masks a fraction of edges and trains a small head to predict each masked edge's convexity and curve type from the encoder's post-message-passing face features. We combine MTM with a MoCo-style momentum-queue contrastive learning over B-rep-aware augmentations, a BFS-connected face-region masked-reconstruction objective, and pretraining on the ABC dataset and our new procedurally generated dataset to show strong performance on a number of benchmarks.

A second order finite volume scheme rests on two local quantities: a gradient reconstructed in each cell, and a limiter which scales it down where the reconstruction would overshoot. Both are set by fixed formulas, and on coarse unstructured meshes a small network can supply better values. But a network is free to output anything, and the usual safeguard is a penalty in the training loss, which discourages inadmissible states without preventing them. We replace the penalty by a hard constraint. The network still sets both quantities, and every value it can produce lies inside safe bounds: its stencil weights cannot cancel a neighbour, and its limiter is capped by the local flow. The flux, the wall treatment and the time step are not learned and carry their own guarantees. Admissibility therefore holds for every value of the weights rather than as an outcome of training, and no negative density or pressure occurred in any computation reported here. Because the scheme is safe whatever the network does, we could ask what the network contributes. We test it on supersonic channel flow over an obstacle, including the forward facing step of Woodward and Colella. Learning lowers the error by 38% on an unseen geometry and 29% on an unseen obstacle topology, measured against the same scheme with the network switched off. The method aims at the accuracy of a fine mesh for the cost of a coarse one, and refining once improves the error fourfold while multiplying the run time by eight. Learning secures half of this improvement for a sixth of this time. All of this comes from one of the two quantities the network sets. The gradient reconstruction reproduces the full effect on its own, and the limiter accounts for about a tenth as much. This also explains why the gain fades beyond the Mach numbers the weights were trained on.

The Traffic Assignment Problem is a fundamental but computationally expensive component of transportation planning. While Graph Neural Networks have emerged as fast, data-driven surrogates, their practical deployment is severely constrained by a spatial generalization gap. Standard models rely on transductive feature initializations that tie travel demand to fixed network topologies, preventing seamless transfer to new urban environments. To overcome this structural limitation, this research proposes a network-agnostic initialization layer, termed Geometrically Unconstrained Inductive Demand EmbeDding (GUIDED). By injecting travel demand as a scalar attribute on auxiliary virtual links rather than as specific node features, this modular framework standardizes the input space regardless of network scale. Extensive experimental evaluation across multiple urban topologies demonstrates that a Heterogeneous Graph Attention Network (HetGAT) model integrated with the proposed GUIDED layer maintains state-of-the-art predictive accuracy on single-network tasks, while demonstrating superior robustness to out-of-distribution demand patterns and maintaining a distinct performance advantage over the baseline even under severe data scarcity. Notably, the proposed feature initialization enables highly parameter-efficient domain adaptation for inter-network transfer learning without artificial input homogenization, establishing a robust foundation for truly inductive models. At the same time, the optimized scatter operations of the initialization layer yield an approximate 50% reduction in training time per epoch compared to the baseline approach. Furthermore, while demonstrated on vehicular traffic, this fundamental abstraction of spatial topology provides a versatile blueprint for generalized origin-destination spatial problems, such as freight logistics and multimodal network optimization.

TabPFN is a transformer-based foundation model for tabular prediction that performs inference without task-specific training by conditioning on a support set and query inputs. Despite its strong empirical performance, its internal behavior on structurally difficult tabular geometries remains poorly understood. We study this behavior using zigzag persistent homology, treating TabPFN layer representations as evolving point clouds. We construct a controlled benchmark of synthetic tabular tasks with known true probabilities and varied intrinsic topology, including warped circles, tori, spheres, Hopf links, trefoil knots, and Swiss rolls. Across these tasks, we find that the topology of TabPFN's internal representation geometry is strongly associated with dataset-level reliability; for example, the zeroth homology group $H_0$ fragmentation count correlates positively with mean absolute residual across controlled tasks, and this association strengthens in a high-resolution warped circle case study at large sample size. Harder geometries induce a dual topological signature: increased $H_1$ loop activity and increased $H_0$ fragmentation, while the $H_1$ persistence becomes shorter-lived. These descriptors correlate with Bayes error, mean absolute residuals, and overconfidence. Our results suggest that zigzag persistence diagnoses the reliability of the inferred in-context task geometry and provides a context-level view of when TabPFN operates in topologically stressed regimes.

Background. Predicting conversion from mild cognitive impairment (MCI) to Alzheimer's disease (AD) is central to trial enrichment and care planning, yet existing models provide no individual-level uncertainty estimates and rarely include transparent leakage audits. We introduce the first application of persistent homology to longitudinal clinical trajectory point clouds for this task, and the first split-conformal individual risk guarantee for any AD-conversion model. Methods. We analysed 741 MCI subjects (240 converters, 32.4%) from ADNI with a uniform 4-year follow-up cap. Five leakage sources were corrected; without them a naive pipeline achieved AUC=0.934, inflated by +0.075. Vietoris-Rips persistent homology and sublevel-set proxies were combined with trajectory slopes and engineered features (76 total) in a stacking ensemble evaluated by 5-fold cross-validation. Results. Cox and Random Survival Forest models with TDA features achieved concordance C=0.799 and C=0.826 versus C=0.753 and C=0.812 without (+0.045 and +0.014). The primary nested AUC is 0.840 (same-fold bound 0.866); external AUC was 0.879 on a zero-overlap ADNI-2/GO/3 cohort. H0 persistence entropy was the top SHAP feature and significantly associated with APOE4 dosage (Spearman r=-0.191, p<0.0001, Bonferroni-corrected). Cross-conformal coverage was 90.4%+-2.2% (target 90%); empirical external coverage 96.9%. Maximum fairness gap in false-negative rate across seven subgroups was 0.092. Conclusions. We propose H0 persistence entropy as a topological biomarker of cognitive decline and demonstrate that a leakage-audited, conformally calibrated pipeline reaches competitive accuracy with individual-level uncertainty quantification not previously available for this task.

Extracting structured, parametric 3D representations from raw images remains a fundamental challenge in computer vision and graphics. While recent advancements in the 3D Gaussian Splatting (3DGS) pipeline integrate planar primitives to yield compact and editable geometry, these approaches typically treat planes as isolated, discrete sets. This lack of topological connectivity hinders robust geometric reasoning, leading to fragmented reconstructions and misaligned boundaries that fall short of the precision for rigorous spatial analysis and professional design workflows. To address this, we introduce TopoGS, the first 3DGS framework to explicitly integrate both planar and topological constraints for coherent 3D reconstruction. Specifically, we extract global 2D topological relationships from multi-view image segmentations and anchor Gaussian primitives to these structural elements. This formulation enables the joint optimization of plane parameters, rendering fidelity, and topological adjacency. By enforcing strict multi-view consistency alongside these topological constraints, our method significantly mitigates geometric misalignments and produces connected, structured 3D models. Extensive evaluations on the ScanNet++ dataset demonstrate that TopoGS achieves state-of-the-art performance, providing a highly robust solution for generating accurate, topologically sound, and visually faithful scene representations.

Protein fold classification can be approached via sequence-based representations or structural descriptors, but direct comparisons between lightweight handcrafted descriptors and pretrained protein language model embeddings remain limited. We investigate discrete Ricci curvature on Calpha contact graphs as a lightweight structural descriptor for fold classification. Each protein domain is represented by a 22-dimensional fixed-length feature derived from summary statistics and quantiles of Ollivier-Ricci and Forman-Ricci edge curvature distributions. We evaluate on CATH top-10 Topology classification and on the ASTRAL 40%-identity SCOPe top-10 Fold benchmark, comparing against geometry, contact-graph statistics, persistent homology, and mean-pooled ESM-2 (150M) baselines. On both datasets, lightweight structural descriptors substantially outperform mean-pooled ESM-2 embeddings, with a larger performance gap on the ASTRAL 40% SCOPe benchmark. Ricci alone uses 22 dimensions, or 3.4% of the ESM-2 baseline dimensionality, and already outperforms mean-pooled ESM-2 on both datasets. Combining Ricci with persistent homology yields the strongest performance, achieving macro-F1 of 0.71 on CATH and 0.68 on SCOPe with a 112-dimensional feature vector. These results identify a regime where lightweight interpretable graph descriptors offer a practical alternative to pretrained protein language model embeddings.

We propose SPECS, a genetic algorithm for automated analog circuit synthesis with joint topology and sizing optimization. SPECS is inspired by NeuroEvolution of Augmenting Topologies (NEAT), an evolutionary algorithm originally developed to synthesize neural networks. By reformulating the genome representation and adapting the genetic operators to the analog circuit domain, we successfully transfer the core principles of NEAT to analog circuit synthesis. Circuit-specific wiring constraints are incorporated to ensure valid and physically meaningful designs throughout the evolutionary process, and speciation is used to preserve innovation while maintaining population diversity. We evaluate the proposed method on a set of computational circuit synthesis tasks consisting of square, cube, square root, and cube root functions. Experimental results demonstrate that SPECS outperforms benchmark methods across all tasks in both solution quality and reliability. The synthesized circuits and their schematics are available in the supplementary repository.

Many datasets encountered across a wide range of domains possess rich geometric and topological structure that is difficult to capture using conventional vector-based representations. Quantum machine learning offers the possibility of processing high-dimensional data in Hilbert spaces, but its practical success depends critically on how classical data is encoded into quantum states. We introduce \emph{quantum topological data encoding} (QTDE), a general framework for encoding topological information into quantum states via topology-driven quantum evolution. Our method generalises an existing topology-driven quantum encoding framework to higher-dimensional data. We test the proposed method on clique-complexes classification tasks, and provide preliminary evidence that topology-driven quantum representations can capture discriminative information beyond that available through direct comparisons of classical topological descriptors. The proposed quantum representations consistently outperform a baseline based on direct comparisons of the combinatorial Laplacians describing the underlying topological structure. We indicate several areas of application where the framework can be used to provide a more efficient and reliable data representation.

Single-task fine-tuning of graph neural networks (GNNs) for power grid problems exhibits a systematic failure mode: models that achieve the lowest in-distribution error degrade the most under topology shift. We term this topology overfitting: the tendency of task-specific gradient signals to encode relational structure particular to the training topologies rather than the underlying physics, causing models to fail on unseen grids despite strong in-distribution performance. To expose and address this failure mode, we introduce MxGPS (Multiplex GPS), a multiplex graph transformer that runs K task-specialised GPS branches over a shared node encoder, jointly trained on Static State Estimation (SSE) and AC Power Flow (PF) via a self-supervised pre-training and multi-task fine-tuning protocol, with a cross-branch attention module evaluated in ablation. The joint SSE+PF objective forces the shared encoder to simultaneously satisfy complementary gradient signals, preventing it from overfitting to topology-specific relational structure. Under a 3-fold sliding-window cross-validation spanning four unseen topologies (14-, 24-, 162-, and 300-bus), MxGPS attains 0% boundary violation rate (BVR) on all four zero-shot Power Flow topologies. Critically, models with substantially lower in-distribution PF error degrade by 190% to 1400% under topology shift, whereas MxGPS degrades by only 39%, an inversion that directly implicates topology overfitting as the failure mechanism rather than insufficient model capacity. With only 1.6M parameters (12x fewer than the GridFM reference baseline), MxGPS demonstrates that multi-task joint training is a principled and parameter-efficient mechanism for topology-agnostic generalisation in power grid foundation models.

Generating high-quality triangle meshes is essential for film, gaming, and interactive 3D applications. Mainstream methods rely on mesh serialization and autoregressive processes, which stuggles in effective inference and is sensitive to error accumulation. In this paper, we present Nexus, a diffusion method that achieves holistic mesh generation via decoupled vertex and topology generation. First, we view mesh vertices as sparse voxels organized as an octree and adopt a diffusion model to generate the vertices in a coarse-to-fine manner. Second, for topology modeling, we propose Spacetime Interval, as an extension of Spacetime Distance to encode arbitrary edge and face topology into continuous per-vertex embeddings. It allows for a global and efficient recovery of complex topology. We then employ a diffusion model to generate the continuous embeddings on the generated vertices. Extensive experiments on the Objaverse and Toys4K datasets and in-the-wild images demonstrate that our method outperforms state-of-the-art autoregressive and two-stage baselines, effectively circumventing the inherent limitations of sequential mesh modeling. A blind user study from 3D practitioners confirms strong perceptual preference for our results.

Although topological mapping and navigation have been studied extensively, the specific role and downstream effect of loop closures in purely topological representations has received relatively little attention. Importantly, loop closure over topological maps is distinct from loop closure over globally referenced trajectories and metric maps. Building on recent denser topologies grounded in pixel-level, relative 3D geometry, we propose PixelLoop which introduces loop closures directly in pixel space. Unlike sparse image-level edges or pose-graph corrections in SLAM, our pixel-level closures act as dense topological shortcuts that alter planning connectivity and cost propagation rather than merely aligning coordinates. This dense connectivity enables stable any-point-to-any-point navigation and produces costmaps that align accurately with geometric shortest paths. In particular, we showcase the distinct advantage of applying loop closures to fine-grained pixel topologies rather than image-level topologies. Across extensive simulated experiments, PixelLoop achieves over 35% absolute improvement in both Success Rate and SPL compared to image-relative baselines, with the largest gains in scenarios requiring shortcut exploitation. Results are further validated through real-world mobile robot deployments, demonstrating that dense pixel-level loop closures provide a practical and robust foundation for topological visual navigation. Project Page: https://pixelloop-nav.github.io/

Machine-learned surrogates for the AC power flow (ACPF) problem amortize the cost of repeated solves on a fixed network, but lose one to two orders of magnitude of accuracy when a line outage changes the topology. This degradation is an operator shift. The altered admittance matrix changes the input-to-output map, so identical inputs yield a different output distribution. Existing methods correct this with target-topology data and per-topology gradient steps. We ask whether the correction can instead be made statistical and gradient-free. We propose In-Context Whitening (ICW), which trains an ACPF surrogate in an output space whitened by the base topology's first two moments, and adapts it to an unseen N-1 or N-2 topology by re-estimating that whitening from a few hundred solved cases on the new topology. This adaptation is gradient-free, weight-free, and architecture-agnostic. We prove that among affine whiteners the unique choice that preserves the coordinate-wise semantics of the physical output vector is ZCA whitening, so within efficient invertible corrections, two moments are sufficient. Across the IEEE 30-, 118-, and 300-bus systems under N-1 and N-2 contingencies, ICW reduces overall error by 6$\times$ to 28$\times$ over frozen surrogates (up to 54$\times$ per-quantity under N-2) and cuts worst-bus power-balance mismatch by up to 30$\times$, with consistent gains across three backbones. At deployment scale it matches or beats gradient-based adaptation in accuracy while adapting 21$\times$ to 34$\times$ faster, with a cost that parallelizes on commodity CPU cores rather than requiring one GPU per contingency.

Dexterous grasp generation across robot hands is challenging because hands differ in kinematic topology, actuation dimensions, and native command spaces. We introduce GraspGraphNet, a topology-aware grasp generation framework that represents each hand as a URDF-derived kinematic graph and directly generates executable palm poses and joint configurations. GraspGraphNet combines hierarchical object surface encoding, differentiable forward kinematics, and dynamic world-edge message passing to model evolving robot-object interactions. It applies conditional flow matching directly in executable palm-pose and joint-state space, avoiding post-processing optimization, inverse kinematics, and retargeting. Using a shared model trained on Barrett Hand, Allegro Hand, and Shadow Hand, GraspGraphNet achieves an average success rate of 83.48% with 40ms inference time per grasp on a 40-object benchmark. Without retraining, the same model achieves 72.70% success on controlled finger-removal variants, demonstrating robustness to hand-topology variations. These results suggest that graph-structured hand representations can effectively support dexterous grasp generation across robot hands with different kinematic structures. Project: https://lysees.github.io/graspgraphnet-page

Efficient exploration and target search in large-scale unknown environments remain challenging for aerial robots due to the demands of broad spatial coverage, fine-grained perception, and real-time decision-making. This paper presents SLIDER, a lightweight and memory-efficient framework that avoids reliance on globally dense maps by combining a local sliding map with sparse global history information. A novel observation quality evaluation method is proposed, leveraging historical poses and sensor models to assess point cloud data in real-time, enabling efficient frontier detection. To support scalable and responsive planning, an incremental viewpoint clustering strategy dynamically adapts to local updates, significantly reducing the number of candidate targets and decreasing computational load. A sparse global topological map is incrementally maintained to assist global planning and cost evaluation. Extensive simulations and real-world experiments demonstrate that the proposed system outperforms state-of-the-art methods in memory usage, decision latency, and search efficiency.

Input--output feedback linearization fails at decoupling singularities, where the decoupling matrix loses rank, the relative degree is lost, and the linearizing control becomes unbounded. This paper develops a singularity-robust trajectory-tracking controller for square nonlinear control-affine systems that tracks through isolated decoupling singularities with bounded control. The method recasts tracking as real-time arc-length homotopy continuation, equivalently a continuous-time Newton/Davidenko flow, and replaces the inverse decoupling matrix by the least-norm Moore--Penrose solution of an augmented matrix $A=[Λ\mid b]$, where $b$ is the homotopy direction. A transversality condition $w^T b \ne 0$, with $w$ in the left null space of the decoupling matrix, keeps the augmented matrix full row rank through a generic rank-one loss. The resulting flow agrees with feedback linearization away from the singular set, tracks with $O(1/k)$ error, and re-locks after each crossing. The theory also characterizes the reflection-versus-branch-crossing dichotomy at Whitney folds and relates the reflection case to a Filippov sliding mode. Extensions cover dynamic relative-degree-one minimum-phase systems and arbitrary relative degree via filtered-error reduction. Simulations include a redundant 2-DOF manipulator, relative-degree-one and relative-degree-two plants, and a dual-active-bridge series-resonant DC/DC converter, where the method performs bounded inversion across buck/boost and resonance singularities while preserving zero-voltage soft switching.

Motion blending in character animation enables the synthesis of new motions by interpolating between existing examples. Current methods are typically restricted to fixed skeleton topologies, requiring identical or near-identical skeletal structures across characters. We present a novel framework for motion blending across heterogeneous skeletons. The proposed architecture combines a semantic encoder, which extracts per-frame latent representations of the motion state, with a diffusion-based decoder, which reconstructs character-specific motion conditioned on this latent code. At inference, blended motions are obtained by interpolating the latent representations of two input motions. We train and evaluate the method on the Truebones Zoo dataset using motions defined on both same and distinct skeleton topologies, demonstrating the ability to achieve smooth and plausible blending in a variety of scenarios.

Archive-based exploration methods such as Go-Explore select which visited state to return to using visitation rarity, and frontier methods return to the boundary of the unknown; neither asks whether the unexplored region behind a boundary is enterable at all. Exploration is not just about finding reward - it is about collecting a structurally complete experience for downstream learning and planning. We introduce TopoExplore, which augments Go-Explore cell selection with a periodic topological pass: enclosed unexplored regions (voids) of the visited-set occupancy grid are detected by flood fill (the H1 classes of its cubical complex), and a decaying selection bonus is placed only on their strict entrances (gap or door cells), so sealed regions are never targeted and entered regions retire. On a controlled 18-environment MiniGrid suite (15 seeds, frozen hyperparameters) TopoExplore attains a 1.52x geometric-mean speedup in median steps-to-first-entry over its exact Go-Explore ablation, versus 1.37x for a frontier baseline; frontier exploration degrades when sealed decoy structure appears (0.83-1.48x on decoy environments vs. 1.65-2.11x for TopoExplore), while TopoExplore holds its largest win on hard multi-interaction doors (10.9x). We report an honest negative on Montezuma's Revenge - without wall knowledge, unreachable occupancy artifacts capture the bonus and performance degrades as it grows, isolating the wall-aware entrance test as the load-bearing component - and a preliminary positive on HM3D scanned buildings, where the speedup over Go-Explore tracks scene difficulty (r=0.69) even as frontier selection dominates blanket coverage. The evidence supports a deliberately scoped claim: topology-aware selection pays off where enclosed structure must be discriminated, and remains competitive at open coverage, where frontier methods are strongest, despite not being tuned for that regime.

We present, to our knowledge, the first adaptation of Pauli Correlation Encoding (PCE) to quantum topological data analysis, reformulating Betti number estimation as a depth-efficient variational optimization over a compressed qubit register. From a Takens embedding and Vietoris--Rips filtration of S&P500 returns, we extract combinatorial Laplacians and recast null-space counting as a continuous-PCE Rayleigh-quotient minimization with variational deflation, encoding $n_k$ simplex indices into $O(n_k^{1/κ})$ qubits with shallow, ancilla-free circuits. Because the resulting loss is rational rather than bilinear in the correlators, the barren-plateau bound of\cite{Sciorilli25} does not transfer; empirically the gradient variance decays only polynomially, with no exponential barren plateau, over $n=4$--$12$ qubits. The classical stage matches ripser~\cite{bauer2021ripser} on all 190 sliding windows (2007-2009). On the real market Laplacians ($β_1=1$--$22$), warm-starting from a classical null-space surrogate allows PCE-VQE to recover $β_1$ exactly at every scale, placing the obstacle in the optimisation landscape rather than the encoding. Chronologically split classification gives in-regime ROC AUC $0.818$, but out-of-distribution evaluation on the 2020 COVID shock and 2022 rate cycle (AUC $0.009$, $0.515$) shows the calibration does not generalize across crisis regimes.

Graph Neural Networks (GNNs) provide a learning-based framework for approximating graph quantities that are expensive to compute exactly. This paper investigates GNNs for scalable approximation of betweenness and closeness centrality, formulated as a node-ranking problem. Exact centrality values are used as supervision, and ranking quality is evaluated using Kendall's tau rank correlation. We study whether message-passing GNNs can learn transferable structural representations across different graph topologies rather than only fitting the distribution used during training. On unseen Erdos renyi graphs, the proposed models achieve tau = 0.851 for betweenness and tau = 0.894 for closeness. A large-scale betweenness model trained on graphs with N = 5,000 nodes achieves tau = 0.938, demonstrating scalability. Mixed-distribution training on Erdos renyi, Barabasi-Albert, and Gaussian Random Partition graphs improves betweenness transfer across graph families. In contrast, closeness centrality remains more sensitive to community-structured graphs and shows reduced transfer to real-world topologies. Finally, GNN inference achieves up to a 97.7x speedup over exact computation. These results show that mixed-distribution training can improve structural transfer in GNN-based centrality approximation, while identifying closeness centrality's sensitivity to topology as an open challenge.

This study harnesses topological analysis in an attempt to reveal structure in the dynamics of a crowd. Topology and in particular persistent homology characterizes relational structures in data through the number of connected components and holes, that is, a loop of pairwise connection with no connections across it. We apply this universal data analysis method to a simulated time series of individual pedestrian positions of a crowd moving through a wide corridor -- either uni- or bidirectional. We consider two pedestrians to be connected, when they are sufficiently close. This approach leads to two matrices containing the persistence signatures for the whole time series, so-called CROCKERs. Despite the high level of data abstraction, the CROCKERs' first two principal components on time-delayed positional data show a clear separation of the different parameter configurations. This holds up to symmetry. Our results support our claim that persistent homology is a useful tool to characterize crowd dynamics without introducing any prior assumptions about the detectable spatio-temporal patterns.

Automated detection of intracranial aneurysms (IAs) from CT angiography (CTA) is severely hindered by high false-positive rates. Convolutional neural networks (CNNs) rely on local pixel intensities, causing systematic confusion between saccular aneurysms and vascular bifurcations - a problem especially acute for small lesions (<3 mm), where detection sensitivity falls below 60%. We propose a plug-and-play, topology-aware false-positive reduction framework evaluating the Smooth Euler Characteristic Transform (SECT) - a directional representation encoding global 3D vascular geometry independently of intensity - against persistence-based summaries (Persistence Images and Landscapes), tested on a stratified subset of the RSNA 2025 dataset. SECT achieves an AUC of 0.943, substantially outperforming direction-agnostic methods (AUC ~0.68), and exhibits a clinical performance inversion: it excels on the sub-3 mm cohort, maintaining 0.943 AUC and 78.5% sensitivity at 95% specificity. The representation is also scanner-agnostic, achieving 0.927 mean AUC under leave-one-scanner-out (LOGO) validation across four manufacturers. By capturing asymmetric geometric invariants rather than intensity profiles, SECT reliably resolves the primary structural confounder in IA detection, positioning it as a robust downstream filter for hybrid deep-learning diagnostic pipelines.

Unsupervised graph clustering is a fundamental technique for uncovering underlying semantic patterns in large-scale networks. Although Graph Contrastive Learning has demonstrated promising performance, existing methods often suffer from the "structural isolation" issue during mini-batch training, making it challenging to capture cohesive community structures that characterize the global topological distribution. To address these challenges, we propose SCISE, a Scalable unsupervised graph Clustering framework that preserves structural Integrity by synergizing community-aware sampling with constrained Structural Entropy. Specifically, we first introduce the Structural Entropy Community Constraint operator (SECC), which optimizes structural information within a constrained solution space to mitigate community fragmentation and enhance partition cohesion. Second, to prevent global information loss during batch training, we design a Community-Aware Sampling Expansion (CSampE) mechanism that incorporates the community context of target nodes into sampling batches, effectively breaking structural barriers and preserving topological integrity. Finally, we devise a Structural Contrastive Learning (StructCL) module that refines edge weights based on intra-batch structural similarity, guiding the encoder to learn representations in a higher-order structural space. Extensive experiments on six mainstream benchmark datasets demonstrate that SCISE significantly outperforms state-of-the-art algorithms, with ablation studies and robustness analyses further validating its effectiveness and reliability for real-world large-scale graphs.

Over-the-air (OTA) aggregation exploits the superposition property of wireless multiple-access channels to aggregate model updates from multiple devices within a single transmission slot, significantly reducing communication latency. While OTA computation has been extensively studied for centralized federated learning (FL), its integration with decentralized federated learning (DFL) remains largely unexplored, and principled communication topology selection is absent from existing work. We present AIRPLAN, a query-optimized topology selection framework for Over-the-Air Decentralized Federated Learning (OTA-DFL). AIRPLAN establishes a formal equivalence between OTA-DFL and distributed query processing, enabling topology selection to be formulated as a cost-based query optimization problem. Using privacy-preserving Count-Min Sketch statistics, AIRPLAN estimates workload characteristics, evaluates a graph-aware cost model across candidate topologies, and selects the communication graph that minimizes training cost while satisfying a target accuracy SLA. Experiments across five graph families, three vision benchmarks, four client scales, and multiple SNR settings show that AIRPLAN matches the oracle-optimal topology in 91.4% of workloads while introducing less than 1.8% overhead. We further derive theoretical error bounds for topology-aware sparsification, demonstrating that well-connected topologies better tolerate aggressive compression. AIRPLAN introduces a systems-oriented perspective that bridges wireless federated learning and distributed query optimization.

The growing number of medical vision foundation models highlights the need for effective model selection. However, mainstream selection methods rely on exhaustive fine-tuning, which is computationally expensive. Most of the existing Transferability Estimation (TE) metrics are primarily designed for image-level classification. They fail to preserve spatial relationships and fine-grained boundary details, which are crucial for the segmentation task. Additionally, while image-level tasks typically process a single feature vector per input, dense prediction tasks in 3D medical imaging require voxel-wise evaluation against dense annotations. To bridge these gaps, we propose a \textit{non-parametric, topology-driven} framework that estimates transferability directly from the alignment between the sparse 1-skeleton graph of dense features and semantic labels via Minimum Spanning Trees (MST). We decouple the alignment into two complementary geometric scales: Local Boundary-Aware Topological Consistency (LBTC) to assess boundary separability, where we prove that the MST leakage rate serves as a finite-sample lower bound on the Bayes error; and Global Representation Topology Divergence (GRTD) to evaluate the overall anatomical layout. Crucially, we formally justify a counterintuitive mechanism: Although without fine-tuning, the randomly initialized segmentation decoder acts as a topology-preserving spatial projector, reducing the variance of pairwise distance estimates and stabilizing global alignment evaluation. Fused via a task-adaptive gating mechanism, these dual metrics adapt to diverse clinical complexities. Evaluated on a large-scale benchmark of 114,000 3D medical volumes across diverse anatomical tasks, our topological framework achieves state-of-the-art transferability estimation with an average weighted Kendall (outperforming by 0.36) while accelerating evaluation by 56 times.

Sleep physiology arises from the coordinated dynamics of the central nervous system (CNS) and autonomic nervous system (ANS), as reflected by multimodal polysomnography signals including EEG, EOG, EMG, ECG, and respiration. However, existing sleep foundation models often fuse heterogeneous biosignals in a topology-agnostic manner, overlooking their physiological organization. We introduce Omni-Sleep, a sleep foundation model that uses the CNS/ANS partition as a physiological prior for topology-constrained representation learning. Omni-Sleep learns structured representations through three objectives: intra-system consistency, which captures shared subsystem-level factors within neural and cardio-respiratory signals; inter-system synchronization, which aligns subsystem trajectories to model brain--body dynamics; and latent-space masked temporal modeling, which captures long-horizon sleep dynamics. Pre-trained on over 100,000 hours of multi-center multimodal PSG data, Omni-Sleep is evaluated on sleep staging and multi-disease classification. Across datasets and modality-ablation settings, Omni-Sleep outperforms strong foundation-model baselines, showing improved label efficiency, cross-dataset generalization, and robustness to missing modalities. These results highlight the value of physiological hierarchy for generalizable sleep representation learning. Code is available at https://github.com/AutoBrain-sleep/OmniSleep.

Topological data analysis (TDA) is a machine learning technique that uses topology to extract patterns from data and has shown the potential to exhibit quantum advantage. A key concept in TDA is persistent homology, which measures the robustness of topological information at different lengthscales. In this paper, we introduce and study the problem of normalized persistence, a practically motivated and easily interpretable version of persistent homology that counts the fraction of holes that persist at different lengthscales. We prove that a variant of normalized persistence is $\mathsf{DQC}_1$-hard and contained in $\mathsf{BQP}$, giving evidence of an exponential quantum speedup for TDA under the standard assumption that $\mathsf{DQC}_1 \not\subseteq \mathsf{BPP}$. These are the first $\mathsf{DQC}_1$-hardness results that are directly applicable to TDA instances. We also find a close connection between normalized persistence and the complexity of estimating spectral quantities in the low-energy subspace of local Hamiltonians. We study a family of such problems, including a low-energy normalized subtrace and spectral density. We show that these are $\mathsf{DQC}_1$-hard for $O(1)$-local Hamiltonians, strengthening previous results that required log-local interactions. We also introduce a variant of $\mathsf{DQC}_1$ with perfect completeness ($\mathsf{SDQC}_1$) to characterize the hardness of problems normalized by an exact kernel. This includes normalized persistence for $O(1)$-local Hamiltonians, which we show is $\mathsf{SDQC}_1$-hard.

Modeling motion for articulated objects of arbitrary skeleton topology remains difficult: existing motion generators target a fixed human skeleton, and prior adaptations either fail to share a vocabulary across rigs or discard motion detail through global pooling. Our key observation is that while joint-level motion does not correspond cleanly across species, motion of functional joint groups does: a human arm, a wolf foreleg, and a bird wing share motion structure despite differing joint counts and connectivity, a correspondence that joint names (e.g., "forearm", "wing_L1") partially expose even when topology does not. We introduce SAMoR (Skeleton-Aware Motion Representation for Articulated Objects), a cross-topology motion representation that encodes each motion segment as a small fixed number ($K=8$) of part tokens shared across arbitrary skeletons. A graph-transformer encoder consumes per-joint motion features, kinematic graph structure, and joint-name embeddings, then compresses them into part-level tokens via cross-attention pooling and residual vector quantization, yielding a discrete motion codebook shared across rigs. To keep the part queries from collapsing into redundant global representations, we introduce a topology-agnostic attention supervision loss, with joint-name dropout to reduce over-reliance on text labels. We curate a heterogeneous corpus from HumanML3D, Truebones Zoo, and animated Objaverse-XL assets, and evaluate SAMoR on held-out characters with unseen skeletons. It supports accurate reconstruction and cross-topology transfer, and enables text-conditioned generation and part-wise editing via a MaskGIT token generator. SAMoR reaches $2.75 \times 10^{-2}$ normalized MPJPE on cross-topology reconstruction, $5.8\times$ below the strongest adapted variable-$J$ tokenizer baseline, while remaining competitive with fixed-skeleton specialists on HumanML3D.

High definition map generation is essential for autonomous driving, yet remains a labor-intensive process at scale. We present MapDreamer, a generative diffusion model that synthesizes lane-level vector maps with explicit topology directly from a single aerial image. MapDreamer learns a compact latent representation of lane centerlines and their topological relations using a variational autoencoder and predicts graphs with a transformer-based latent diffusion model. To align generated maps with the observed scene, we condition each denoising step on dense aerial features injected through cross-attention. To handle the varying number of lanes across scenes, we propose a lane cardinality module paired with background ghost lane latents, a learned buffer that prevents slot collapse during diffusion. Furthermore, we introduce a sliding-window global graph aggregation strategy that stitches local tiles into city-scale maps while preserving connectivity through encoded lane boundaries. Experiments on UrbanLaneGraph derived from Argoverse 2 show improved geometric and topological fidelity over non-generative baselines.

ROS 2 (Robot Operating System 2) has emerged as the de facto standard for modern robot software development, with middleware implementations such as the Data Distribution Service (DDS) and Zenoh forming the core infrastructure for distributed robotic communication. Despite their architectural flexibility, these middleware systems exhibit structural limitations, particularly under dynamic and resource-constrained wireless environments. This paper presents a systematic survey of ROS 2 middleware and introduces a conceptual framework to examine its architectural limits through three structural dimensions required by distributed robotic systems, namely Space, Time, and State. We first provide a structured analysis of middleware architecture and operational dynamics, including discovery, data exchange, and state management mechanisms. Building on this foundation, we formalize Time as temporal predictability for control loops, Space as spatial abstraction from physical topology to enable modular deployment, and State as contextual continuity despite dynamic node participation and intermittent connectivity. Through a comprehensive review of existing implementations and prior studies, we organize middleware research according to the structural trade-offs that arise among these dimensions. Under constrained wireless conditions, spatial abstraction can obscure network variability and weaken temporal guarantees, while mechanisms that preserve state continuity introduce computational and network overhead that competes with time-critical communication. These interactions reveal structural trade-offs that characterize the practical limits of contemporary robot middleware. By synthesizing architectural patterns and identifying gaps in current modeling and analysis approaches, this survey outlines a principled research roadmap for robust and scalable robotic middleware architectures.

We study layered models, including feedforward networks, ResNets, and transformers, by limiting each layer to a width of $d = 3$, i.e., $\mathbb{R}^3$ as representation space. This allows us to track how a neural network changes low-dimensional topological invariants through its layers. Just about any topological structure may be simplified or even trivialized by simply increasing dimension; e.g., any knot is equivalent to an unknot in $\mathbb{R}^4$. By restricting to $\mathbb{R}^3$, we not only isolate the effects of activation and depth from that of width, we work in a space that lends itself to easy visualization. We focus on linking number here, deferring other invariants like link groups, Milnor's $\barμ$-invariants, knot types, ambient cobordisms, to a sequel. We provide full proofs and empirical experiments to justify the following insights: When measured by their power to effect changes in linking numbers, the layer-skipping feature in ResNets is as powerful as the attention mechanism in transformers; both ResNets and transformers are strictly more powerful than feedforward neural networks with monotonic activations, which are in turn more powerful than invertible and flow-based models; but replacing monotonic activation with a nonmonotonic one elevates a feedforward network into the same expressivity class as ResNets and transformers. These results suggest that low-dimensional topology can be a useful tool to guide designs of AI architectures. We also generalize our results from $d = 3$ to arbitrary $d > 3$.

We introduce Point-supervised Multi-Object Tracking (PS-MOT) as a cost-effective alternative to traditional bounding box supervision, shifting the focus from spatial fitting to topological center-driven representation. However, PS-MOT faces challenges, e.g., spatial ambiguity and identity drift due to the lack of explicit geometric structure and scale constraints. To address these, we propose PS-Track, a hierarchical pipeline transitioning from points to instances across data, model, and loss levels. At the data level, we introduce Temporal-Feedback Prompting (TFP) to evolve points into temporally consistent pseudo-labels using negative spatial cues and motion priors. At the model level, we design the Point-Excited Wavelet Attention (PEWA) module, which leverages semantic correlations to activate high-frequency components, ``hallucinating'' object boundaries. At the loss level, Uncertainty-Guided Gaussian Learning (UGL) models pseudo-labels as probabilistic distributions, dynamically calibrating supervision intensity. Experiments on DanceTrack, EmboTrack, SportsMOT, and JRDB demonstrate that PS-Track provides a feasible and effective point-supervised alternative across diverse tracking scenarios, establishing a new state-of-the-art for point-supervised tracking. The source code is available at https://github.com/xifen523/PS-MOT.

Chatbots have become increasingly prevalent across various domains, offering automated assistance in many areas, especially mental health support. The training is done using extremely large datasets, which are sometimes not available in very specific domains. Moreover, it would sometimes be ideal to train the chatbot with personal information about the patients, which, of course, cannot be done on shared servers since it would violate patient confidentiality. Hence, being able to improve the performance of a chatbot, possibly trained locally and on a restricted dataset, without having to increase the dataset itself, would be extremely beneficial. In this work, we will enhance the input datasets using persistent homology (PH) vectorizations computed from the raw datasets themselves. Then we will compare, across several metrics, the performance of multiple chatbot models with or without the PH enhancement. Our experiments suggest that, while at times the PH enhancement is not particularly beneficial, it sometimes brings remarkable advantages for virtually no cost.

Topological data analysis (TDA), particularly persistent homology (PH), captures geometric structural properties in medical images (e.g., connected components, loops, shape characteristics), which conventional pixel-level deep learning approaches often neglect. While many topological descriptors are known for converting persistence diagrams (PDs) or raw images into topological feature vectors, existing methods mostly default to a single fixed descriptor (e.g., persistence images), leaving the diversity of topological representations largely unexplored. To the best of our knowledge, there is no known large language model (LLM)-based agentic framework that can automatically determine the most suitable topological descriptors for a given image dataset and produce the corresponding topological feature vectors for downstream tasks. To fill this gap, we propose \textbf{TopoAgent}, an LLM-based agentic framework that automates topology learning for medical image analysis.TopoAgent operates through a Perception--Reasoning--Action--Reflection loop supported by 21 domain-specific tools and dual memory that accumulates experience across runs. Its skill set is distilled from systematic evaluation of 15 topological descriptors across 26 datasets with six classifiers. TopoAgent analyzes input images and their topological characteristics, reasons about which topological descriptors best suit the input, and determines the optimal descriptor and its configuration, all without task-specific training.

Every existing vector database and agent memory framework treats memory as passive storage that agents query explicitly. No system propagates knowledge between agents through the memory layer itself. We introduce HyphaeDB, an agent-native memory infrastructure that reinterprets the Hierarchical Navigable Small World (HNSW) graph topology the data structure at the core of every modern vector database not as a search optimization, but as a communication fabric for multi-agent AI systems. In HyphaeDB, agents are nodes in the vector space with persistent positions, knowledge propagates via a gossip protocol through the graph's neighbor structure with energy-based attenuation, and emergent behaviors contradiction detection, pattern crystallization, and consensus formation arise from the combination of topology, propagation dynamics, and local interaction rules. We present the architecture built on three primitives (knowledge nodes, topology edges, and memory diffs), a multi-layer abstraction hierarchy with promotion via emergent consensus, and theoretical analysis grounding the system in small-world network theory, epidemic broadcast protocols, and swarm intelligence. We provide a reference implementation on PostgreSQL with pgvector and describe a concrete deployment in Swarm-Driven Development, a multi-agent software engineering methodology. HyphaeDB represents, to our knowledge, the first system to combine navigable small world topology with gossip-based knowledge propagation for multi-agent coordination.

Test-time adaptation (TTA) has emerged as a promising paradigm for mitigating distribution shifts in deep models. However, existing TTA approaches for anomaly segmentation remain limited by their reliance on pixel-level heuristics, such as confidence thresholding or entropy minimisation, which fail to preserve structural consistency under noise and texture variation. Moreover, they typically treat anomaly maps as flat intensity fields, ignoring the higher-order spatial relationships that characterise complex defect geometries. We introduce TopoTTA (Topological Test-Time Adaptation), a novel framework that integrates persistent homology, a tool from topological data analysis, into the TTA pipeline to enforce geometric and structural coherence during adaptation. By applying multi-level cubical complex filtration to anomaly score maps, TopoTTA derives robust topological pseudo-labels that guide a lightweight test-time classifier, enhancing segmentation quality without retraining the backbone model. The approach avoids reliance on method-specific raw-score thresholding for mask binarisation, preserves connectivity, and generalises across both 2D and 3D modalities. Extensive experiments across six standard benchmarks (MVTec AD, VisA, Real-IAD, MVTec 3D-AD, AnomalyShapeNet, and MVTec LOCO) demonstrate an average 15% F1 improvement over state-of-the-art unsupervised anomaly detection and segmentation methods, with the largest gains on anomalies exhibiting complex geometric or structural variations. These findings suggest that integrating topological reasoning into test-time adaptation provides a principled route to structure-aware generalisation, bridging the gap between geometric learning and robust adaptation.

Continuous attractor neural networks (CANNs) are the canonical computational framework for how the brain encodes continuous variables such as spatial position, head direction, and movement direction, and explain the activity of hippocampal place cells, entorhinal grid cells, and head-direction cells. CANN research, however, is fragmented: most results rest on lab-specific implementations, general-purpose simulators lack CANN-specific abstractions, and the path from spike trains to attractor geometry in real recordings lacks a standardized toolkit. Here, we present a comprehensive open-source toolkit that unifies the full CANN research workflow. It combines three tightly integrated components: 1) canns, a Python library on BrainPy/JAX that provides standardized 1D/2D CANNs, spike-frequency-adaptation variants, grid cell networks, hierarchical path-integration models, and brain-inspired attractor architectures, together with curated datasets, task generators, an analyzer module and trainer modules for biologically plausible plasticity; 2) canns-lib, a Rust acceleration backend delivering hundreds-of-times speedups for spatial-navigation workloads and modest gains for Ripser-based persistent homology; 3) ASA (Attractor Structure Analyzer), a PySide6 pipeline applying persistent homology and cohomology to experimental neural recordings to detect ring-like and toroidal attractor signatures in real data. The toolkit ships with full-detail reproducible pipelines that recover recent CANN results including SFA-driven anticipative tracking, theta sweeps in head-direction/place/grid systems, and hierarchical path integration.

Large language model (LLM) multi-agent systems increasingly depend not only on how individual agents reason, but also on how agents are connected. This paper introduces QueenBee Planner, a framework that treats inter-agent communication topology as a retrievable and self-improving design skill. A pool of worker agents, the task adapter, and the scoring function are frozen; only an outer LLM planner learns to generate temporal communication DAGs specifying who sends information to whom, in which round, who merges messages, and who emits the final answer. Execution traces are distilled into evidence-backed design rules with three actions: \emph{Preserve}, \emph{Modify}, and \emph{Avoid}. To prevent self-evolution from turning lucky runs or plausible but false explanations into policy, QueenBee uses held-out acceptance gates, variance-aware credit, motif-level attribution, transfer trust, insight falsification, and structural deduplication. We evaluate the method on Count-Frequency aggregation and Silo-Bench-style distributed coordination tasks. With fixed workers, self-evolved graph generation produces communication structures that improve over fixed topologies and cold generation. In the CF fulltest setting, the best generated graph reduces RMSE from 12.53 for the strongest fixed topology to 7.87 while also reducing messages, model calls, and token cost; Silo-style results show the same direction of improvement over cold and fixed-topology baselines. These results suggest that multi-agent systems can learn reusable architectural design knowledge rather than merely memorizing task answers.

We address the problem of inferring a directed network from nodal measurements generated by linear diffusion dynamics on the sought graph. Observations are modeled as the outputs of a graph convolutional filter, i.e., a polynomial (with unknown coefficients) of a local diffusion graph-shift operator encoding the latent graph topology, excited with an ensemble of independent graph signals with arbitrarily-correlated nodal components. Unlike prior efforts that considered undirected graphs and white signal excitations, here the graph-shift operator and the observations' covariance matrix are not simultaneously diagonalizable. In this challenging context, we first rely on measurements of the output signals along with prior statistical information on the inputs to identify the diffusion filter. Such system identification problem involves solving a system of quadratic matrix equations, which we show is identifiable under spectral-diversity assumptions on the input covariances. For algorithmic purposes we recast it as a smooth quadratic minimization subject to Stiefel manifold constraints. Subsequent identification of the network topology given the graph filter estimate boils down to finding a sparse and structurally admissible shift that commutes with the given filter, thus, forcing the latter to be a polynomial in the sought graph-shift operator. A joint graph filter and topology identification algorithm is also proposed, which alternates between the aforementioned steps in a mutually reinforcing fashion to offer improved sample complexity. Numerical tests corroborate the effectiveness of the proposed algorithms in recovering synthetic digraphs and real-data case studies, and illustrate their potential utility on urban mobility analyses as well as portfolio optimization.

Floods frequently impact regions around the world. Rapid and accurate flood detection is crucial for emergency response and timely mitigation of human and economic loss. The expanding availability of satellite data and advances in artificial intelligence have enhanced monitoring of environmental hazards, but many flood events remain challenging to detect because cloud cover obscures optical satellite imagery. Rambour et al. introduced the SEN12-FLOOD dataset and extracted per-image features using a ResNet-50 convolutional neural network backbone, then fed these features into a gated recurrent unit network to show that temporal information can substantially improve accuracy compared to single-image baselines. More recently, Chamatidis et al. showed that a vision transformer can achieve strong performance with popular convolutional architectures. However, these models typically function as opaque black boxes, making it difficult to interpret their decision boundaries, learned features, and internal reasoning, especially in safety-critical domains like remote sensing. In contrast, topological data analysis (TDA) provides a mathematically grounded framework for capturing global structural features of data. TDA has emerged as a powerful tool for analyzing complex imagery, especially imagery with geometrically interpretable structures, of which floods are a prime candidate. In this work, we systematically evaluate topological descriptors for flood detection using the open-source SEN12-FLOOD dataset. By extracting topological features from each image and incorporating them into neural networks, we demonstrate that topological descriptors carry meaningful flood signals independently and complement existing networks to yield more robust and interpretable flood detection systems.

Demonstration augmentation is proposed for cost-efficient data acquisition, but existing methods are fundamentally limited in deformable manipulation due to two challenges: (1) the state space is high-dimensional with physics-induced constraints, making valid configurations impossible to reach via low-dimensional pose perturbations; and (2) trajectory transfer is non-equivariant, as material points no longer move rigidly together under deformation. We present DeformGen, a dynamics-based augmentation framework that achieves topological diversity for deformable objects. For the state challenge, DeformGen expands the valid state distribution by applying localized physical disturbances and forward-simulating the dynamics to obtain topology-coherent, physically plausible deformable states. For the trajectory challenge, DeformGen transfers source manipulation trajectories via deformation-field warping, which lifts per-particle displacements into a continuous spatial function to adapt the end-effector trajectory consistently with the deformed geometry. In this way, our method jointly augments the state distribution and its associated manipulation behavior. Experiments on high-fidelity deformable manipulation benchmarks show that DeformGen generally improves policy learning compared with training on the original demonstrations alone and with rigid-style augmentation baselines.

Deep learning-based models have achieved state-of-the-art performance in Time Series Forecasting (TSF), yet their evaluation remains dominated by pointwise error metrics such as Mean Squared Error (MSE), which quantify numerical accuracy but overlook structural properties of the forecast signal, including recurrent dynamics, oscillatory behavior, and phase alignment. As a result, forecasts exhibiting over-smoothing, phase shifts, or frequency distortions may achieve favorable error scores despite substantial structural degradation. To address this limitation, we propose TopoCast, a topology-driven framework for evaluating structural fidelity in TSF. TopoCast reconstructs phase-space representations of forecast and ground-truth sequences using Takens delay embedding and applies persistent homology to characterize their intrinsic dynamics. We derive four complementary topological fidelity measures from persistence diagrams and aggregate them into a Topological Fidelity Score (TFS). We further introduce dominant cycle overlap, a novel metric that maps persistent topological features to the temporal domain to assess whether dominant oscillatory patterns occur at the correct time points. Combined with TFS, this yields the Localized Topological Fidelity Score (LTFS), a phase-aware measure that captures temporal localization errors invisible to existing evaluation metrics. Experiments on five Transformer architectures across three real-world benchmark datasets demonstrate that models with similar forecasting errors can exhibit markedly different structural fidelity profiles, revealing failure modes overlooked by conventional evaluation and highlighting the value of topology-aware forecast assessment.

Geospatial vector data quality is a foundational research topic in GIS, yet classic rule-based quality assessment algorithms often struggle with diverse urban morphologies and massive data volumes. Recently, Geospatial Artificial Intelligence (GeoAI) shows promising potential for automating geospatial analysis, while its application to native vector data remains largely underexplored. To fill this research gap, we proposed Topo4Vec, an automated GeoAI framework, designed for scalable vector data quality assessment via advanced Spatial Representation Learning (SRL). Specifically, Topo4Vec relax the labor-intensive manual annotation process via topological error simulation, such as overlapping polygons and street network connectivity errors e.g., overshoots and undershoots. Then, it leverages state-of-the-art SRL approaches to encode complex, native vector geometries (e.g., polylines and polygons) into a latent space where topological errors are isolated from valid ones. A systematic performance evaluation across three study areas (Los Angeles, Munich, and Singapore) demonstrates the effectiveness and robustness of Topo4Vec, achieving a peak accuracy of 0.99 for detecting overlapping building footprints and 0.60 for overshoots and undershoots in street networks. Moreover, lessons learned from Topo4Vec shed a promising light into a scalable and autonomous GeoAI approach for large-scale vector data consistency and quality monitoring within the fast-growing geospatial data ecosystems. The code and data used in the paper are made openly available in https://figshare.com/s/612148eeb4bccadbd715.

Ill-posed questions, including ambiguous, underspecified, or contradictory queries, may admit no valid answer or multiple plausible answers, posing a challenge for large language models (LLMs). Existing approaches largely analyze ill-posedness through model outputs and often focus on specific subclasses. We investigate whether diverse sources of ill-posedness can be represented within a unified topology of LLM internal states and whether this structure can be used to steer response behavior. We model the contextual hidden states of prompt tokens at each transformer layer as a point cloud and characterize its geometry using finite zero-dimensional persistent homology. Each layer is summarized by three compact descriptors: mean finite lifetime, normalized lifetime entropy, and largest-lifetime concentration. Concatenating these descriptors across layers yields a topology representation of the question. We further introduce topology-conditioned activation steering, which retrieves topologically similar examples and constructs query-specific activation interventions that encourage source-aware clarification or abstention. Across three open-weight LLMs, topology features consistently outperform prompt-based and pooled-hidden-state baselines for ill-posedness classification, improving average accuracy from $67.4\%$ to $78.9\%$ on AmbigQA, from $79.9\%$ to $88.5\%$ on SituatedQA, and from $57.6\%$ to $69.6\%$ on CLAMBER 9-way classification. Topology-conditioned steering increases the average total acceptable response rate from $61.4\%$ to $70.6\%$ and grounded acceptable responses from $11.9\%$ to $16.4\%$. These results show that persistent homology provides both an interpretable representation of ill-posedness and an effective mechanism for targeted response steering.

Thin-structure segmentation--power lines, cracks, lane markings at 1-3 pixel width--requires preserving connectivity that standard representations preclude: patching severs continuous structures and conventional superpixels merge thin targets into background before classification. Topology-aware losses penalize connectivity breaks at the objective level but cannot recover what the representation has already destroyed. We propose SEMIR, a framework that replaces the pixel lattice with a parameterized graph minor whose contraction map preserves thin-structure connectivity under the contraction criterion. The minor collapses millions of pixels into tens or hundreds of boundary-aligned supernodes, enabling full-resolution inference without patching at scales demonstrated up to 21 MP in this paper; a lightweight GNN classifies the reduced graph and an exact map lifts predictions to pixel resolution. One pipeline--identical architecture, features, loss, and GNN hyperparameters across all dataset--matches or exceeds domain-specific baselines on TTPLA (power lines), CrackSeg9k (pavement cracks), and SkyScapes Lane (aerial markings) on Dice, IoU, and Boundary F1 while reducing mask fragmentation by at least 4.6x relative to SLIC at matched inference.

While Diffusion Transformers (DiTs) have revolutionized high-fidelity video generation, their reliance on 3D full attention creates a quadratic computational bottleneck. Existing sparse methods face a dilemma: dynamic pruning suffers from prohibitive runtime overhead and memory fragmentation, while static heuristics fail to capture fine-grained dependencies. In this work, we propose ScalingAttention, a training-free framework grounded in a key inductive bias: while individual activations are input-dependent, the high-mass attention regions for each head rapidly converge to a stable, prompt-agnostic Intrinsic Sparse Topology. This topology is weight-encoded, scale-invariant, and efficient to extract. ScalingAttention decouples topology discovery from sparsity control via: (1) WEST (Weight-Encoded Sparse Topology), which extracts a robust block-sparse prior mask offline to eliminate runtime search; (2) FAST (Fidelity-Aware Sensitivity Tuning), which adaptively tunes head-wise sparsity based on diffusion fidelity requirements. To ensure practical acceleration, we co-design a hardware-aligned bit-wise block-sparse kernel. Experiments on Wan2.1 show up to 1.90X end-to-end speedup with superior fidelity, establishing a new Pareto frontier over state-of-the-art baselines.

We present an exploratory benchmark and quantum-inspired modeling prototype for fraud screening in dynamic financial transaction graphs. Coordinated fraud may not be visible from individual transactions alone, but may emerge as a multi-period relational pattern. We focus on sparse-ring fraud, a stylized pattern in which a completed directed cycle is distributed across several days, requiring models to integrate evidence across both time and graph structure. We study this problem using a synthetic transaction simulator with completed sparse-ring injections and broken-ring decoys. Daily directed transaction graphs are aggregated into rolling windows and represented using raw graph features, persistent-homology summaries, or hybrid feature vectors that combine both. We compare a gated recurrent unit (GRU) baseline with quantum-inspired Contextual Machine Learning (CML) as sequence-level classifiers. Because the benchmark uses synthetic data, a modest sample size, and sequence-level labels, the results are exploratory. Within this scope, topology-only summaries are too compressed to solve the supervised ring-completion task by themselves, largely because they remove account-pair identity and edge direction. The strongest results come from hybrid representations that combine identity-preserving graph features with topological summaries. These findings suggest that topology is most useful as a contextual layer over dynamic graph features, and that CML is a promising candidate model for fraud patterns whose evidence is distributed across temporal and relational context.

Enzyme substrate interaction (ESI) prediction is a fundamental computational task for biocatalyst discovery and reaction screening in large biochemical spaces. In practical settings, ESI prediction is challenged by sparse positive supervision and low-homology distribution shift, where test enzymes share limited sequence identity with those observed during training. To address these challenges, we propose RAMMESI, a retrieval-augmented multimodal framework for robust ESI prediction. RAMMESI learns explicit pairwise enzyme-substrate representations through directional cross-modal interaction modeling and adaptive fusion. To enhance robustness, RAMMESI retrieves neighboring enzymes at inference time, recombines them with the query substrate, and aggregates the resulting pairwise predictions as contextual evidence. To improve learning under sparse positive supervision, we further adopt an imbalance-aware weighted-BCE objective. Experiments on two ESI benchmarks under sequence-identity-aware splits demonstrate that RAMMESI achieves consistently strong performance, with particular advantages in more challenging low-identity regimes. In addition, the retrieval module improves multiple ESI backbones in a plug-and-play manner, suggesting that retrieval provides a general mechanism for improving robustness under homology shift.

While deep learning models achieve state-of-the-art performance in complex tasks, they remain brittle when faced with new environments or sensory deprivation. In contrast, biological systems exhibit remarkable tolerance to these challenges. We address this vulnerability by developing a recurrent neural network (RNN) whose architecture is directly derived from the synaptic-resolution brain connectome of the fruit fly Drosophila melanogaster. We demonstrate the feasibility of training the fly connectome neural network (FLYNN) to perform vision-based navigation in MuJoCo, achieving performance comparable to modern hand-crafted networks of similar parameter counts. Crucially, FLYNN exhibits superior resistance to out-of-distribution (OOD) data and tolerance to sensory loss without further training. It remained functional even under total vision loss while hand-crafted networks largely failed, even when specifically trained with camera dropout. Principal Component Analysis (PCA) of the internal state of FLYNN suggests that it exhibits a particularly high degree of representational modularity, which might be related to its robustness. Our work provides a new direction for designing resilient artificial agents following the topology of biological brains.

Fingerprints are the most widely deployed biometric. Verifying whether two impressions come from the same finger typically relies on minutiae, small landmarks such as skin ridge endings and bifurcations. These landmarks are extracted through a multi-stage pipeline of image enhancement, skeletonization, minutiae detection, and alignment. We investigate an alternative: using topological data analysis to represent the full pattern of skin ridges and valleys directly, bypassing minutiae detection and the downstream matching pipeline. We apply persistent homology, a topological tool that tracks how loops in the ridge pattern form and fill in across spatial scales, producing multi-scale summaries of ridge geometry. We develop and compare a range of verification methods on a standard benchmark dataset, FVC2000 DB1. Even the simplest topological summaries, with no trained parameters, substantially outperform geometry-only baselines. A trained method achieves an AUC of 0.91, while an optimal-transport method excels at the strictest false-accept thresholds, suggesting they capture different aspects of the ridge pattern. Fusing these two approaches yields the best performance at every low false-accept threshold we examine. Our results establish that these topological summaries capture substantial fingerprint identity information, far more effective for verification than raw pixel-level geometry. Because the entire pipeline is openly specified, it offers a transparent complement to minutiae-based systems, and we provide a modular framework for constructing, evaluating, and combining topological verification methods.

Real-time process monitoring requires methods that extract actionable information from high-dimensional time-series data. In this work, we present a new approach for process monitoring that combines tools of topological data analysis (TDA) and machine learning. In the proposed approach, we represent multivariate time-series data as manifolds and use topological descriptors to summarize the structure of such data; we then use a neural ordinary differential equation to learn the dynamic evolution of the topological structure of the system. Using real data from an industrial process, we show that this trajectory-based event detection approach is effective at detecting diverse types of events. We contrast this approach against reconstruction-based approaches such as principal component analysis and autoencoders and against a trajectory-based approach that uses Koopman autoencoders.

We present TriFlow, a new generative approach for producing compact 3D meshes with artist-like triangle topology directly from input geometry conditions such as signed distance fields. Our key insight is to represent mesh topology as a nearest-vertex vector field (NVF) defined over the surface, where each point encodes its association to the nearest triangle vertex in the local barycentric frame. We train a latent flow-matching model to synthesize this field, enabling topology generation conditioned on the input geometry. To extract a coherent mesh, we cluster surface regions using the generated NVF and guide a constrained quadric error metric (QEM) mesh simplification with topology-aware optimization. This yields output meshes that closely match the input geometry while exhibiting structured, artist-like connectivity. Experiments demonstrate that TriFlow achieves stronger generalization and significantly improved topology quality compared to state-of-the-art learning-based approaches, alongside 90% lower Chamfer Distance and an 8x speedup.

Large language models are commonly aligned through supervised fine-tuning, yet little is known about how their internal representations evolve during this process. We study alignment dynamics using persistent homology by tracking the topology of activation spaces throughout fine-tuning. Across four transformer language models ranging from 1B to 7B parameters and three alignment objectives corresponding to helpful, harmless, and mixed training data, we find that the majority of topological reorganization occurs during the earliest stages of training. A dense checkpoint analysis reveals a transient peak in topological activity followed by rapid stabilization. We further show that different alignment objectives induce distinguishable topological trajectories, while instruction-tuned and pretrained models exhibit qualitatively different patterns of evolution. Our results suggest that persistent homology provides a complementary perspective on alignment, revealing representation-level changes that are not apparent from behavioral metrics alone.

Accurate survival prediction is essential for personalized treatment planning in head and neck cancer, yet remains challenging due to the heterogeneous and high-dimensional nature of multimodal clinical data. While deep survival models have improved predictive performance over classical statistical approaches, existing methods typically rely on static fusion strategies or temporally agnostic modeling, limiting their ability to capture structured clinical workflows. In this work, we propose ChronoSurv, a heterogeneous hierarchical directed graph framework for multimodal survival analysis. ChronoSurv represents patient care as a progression-aware clinical trajectory using directed graphs aligned with key diagnostic steps. A hierarchical topology incorporates fine-grained, coarse, and global representations, further supporting flexible adaptation to missing modalities, while heterogeneous message passing models complex and asymmetric relationships across modalities and clinical steps. Experimental results on two public datasets demonstrate that ChronoSurv achieves state-of-the-art discriminative performance while maintaining statistically reliable calibration. Comprehensive ablation studies further confirm the contribution of each architectural component, highlighting the potential of trajectory-aware graph modeling for multimodal survival prediction.

A wide range of neurosymbolic (NeSy) systems compute one functional: a belief-weighted sum of a logical quantity over a space of $σ$-structures, of which weighted model counting, fuzzy logic, and probabilistic logic are special cases. This account is built on sets, and a set deliberately forgets two things that are important for NeSy: when two $σ$-structures are the same up to a symmetry of the theory, and how many distinct proofs witness a query. Types, in the sense of homotopy type theory, preserve this information and turn the functional into a belief-weighted homotopy cardinality, a notion of size that counts each object in inverse proportion to its symmetries. We develop the framework from scratch for NeSy systems, prove a conservativity theorem that recovers the classical functional when symmetries are trivial, and show that the symmetry our framework exposes is exactly the one behind reasoning shortcuts. The payoff is concrete: the shortcut-aware concept posterior that recent methods reach by ensembling or expressive density estimation is the only symmetry-invariant point of the confusion-set simplex, computable in closed form by averaging a single model over the symmetry group. On MNIST reasoning-shortcut benchmarks this single-model wrapper is better calibrated than a diversity-trained ensemble, while leaving label accuracy and identifiable concepts untouched. Code is freely available at https://github.com/bio-ontology-research-group/hott-nesy.