Topology

Identifying where to innovate in a dense technical domain - such as operating systems or hardware/software co-design - is fundamentally a search problem in a high-dimensional knowledge space. Existing approaches rely on keyword search, citation proximity, or human intuition, none of which formalise the notion of an unexplored region that is simultaneously relevant to a target goal and absent from prior art. We present Topological Void Analysis (TVA), a mathematical framework that defines topological voids as triads (A, B, C) in a dense-sparse hybrid embedding space. A void requires three conditions: (i) both concepts A and B are semantically cohesive with domain anchor C; (ii) their pairwise similarity falls within a calibrated marginality band - avoiding both obvious combinations and unrelated noise; and (iii) they share a sparse lexical bridge while the geodesic midpoint on the embedding hypersphere is unoccupied. Applied to ~140k indexed documents, TVA generates 2,128 invention candidates across 96 targets; 90% survive automated quality filtering, yielding 191 REVISE and 1 APPROVE verdict from four-specialist adversarial review (0.05% end-to-end). Two case studies demonstrate the framework surfaces non-obvious connective tissue rather than merely obvious related pairs.

Persistent homology (PH) encodes global information, such as cycles, and is thus increasingly integrated into graph neural networks (GNNs). PH methods in GNNs typically traverse an increasing sequence of subgraphs. In this work, we first expose limitations of this inclusion procedure. To remedy these shortcomings, we analyze contractions as a principled topological operation, in particular, for graph representation learning. We study the persistence of contraction sequences, which we call Contraction Homology (CH). We establish that forward PH and CH differ in expressivity. We then introduce Hourglass Persistence, a class of topological descriptors that interleave a sequence of inclusions and contractions to boost expressivity, learnability, and stability. We also study related families parametrized by two paradigms. We also discuss how our framework extends to simplicial and cellular networks. We further design efficient algorithms that are pluggable into end-to-end differentiable GNN pipelines, enabling consistent empirical improvements over many PH methods across standard real-world graph datasets. Code is available at \href{https://github.com/Aalto-QuML/Hourglass}{this https URL}.

Scaling vision-language models into Visual Multiagent Systems (VMAS) is hindered by two coupled issues. First, communication topologies are fixed before inference, leaving them blind to visual content and query context; second, agent reasoning abilities remain static during deployment. These issues reinforce each other: a rigid topology fails to leverage richer agent expertise, while static agents lack incentives to specialize for a given query. We address this with SkillGraph, a joint framework that evolves both agent expertise and communication topology. Within this framework, a Multimodal Graph Transformer (MMGT) encodes visual tokens, instruction semantics and active skill embeddings to predict a query-conditioned collaboration graph, replacing hand-crafted routing with dynamic, content-aware information flow. Complementing this, a Skill Designer distills and refines reasoning heuristics from failure cases, constructing a self-evolving multimodal Skill Bank. Crucially, updated skill embeddings are fed back into the MMGT, enabling the topology to adapt alongside capability growth. Experiments show that SkillGraph achieves consistent improvements across four benchmarks, five common MAS structures and four base models. Code is available at https://github.com/niez233/skillgraph.

Text-attributed graphs integrate semantic information of node texts with topological structure, offering significant value in various applications such as document classification and information extraction. Existing approaches typically encode textual content using language models (LMs), followed by graph neural networks (GNNs) to process structural information. However, during the LM-based text encoding phase, most methods not only perform semantic interaction solely at the word-token granularity, but also neglect the structural dependencies among texts from different nodes. In this work, we propose DuConTE, a dual-granularity text encoder with topology-constrained attention. The model employs a cascaded architecture of two pretrained LMs, encoding semantics first at the word-token granularity and then at the node granularity. During the self-attention computation in each LM, we dynamically adjust the attention mask matrix based on node connectivity, guiding the model to learn semantic correlations informed by the graph structure. Furthermore, when composing node representations from word-token embeddings, we separately evaluate the importance of tokens under the center-node context and the neighborhood context, enabling the capture of more contextually relevant semantic information. Extensive experiments on multiple benchmark datasets demonstrate that DuConTE achieves state-of-the-art performance on the majority of them.

Transformers encode structure in sequences via an expanding contextual history. However, their purely feedforward architecture fundamentally limits dynamic state tracking. State tracking -- the iterative updating of latent variables reflecting an evolving environment -- involves inherently sequential dependencies that feedforward networks struggle to maintain. Consequently, feedforward models push evolving state representations deeper into their layer stack with each new input step, rendering information inaccessible in shallow layers and ultimately exhausting the model's depth. While this depth limit can be bypassed by dynamic depth models and by explicit or latent thinking that externalizes state representations, these solutions are computationally and memory inefficient. In this article, we argue that temporally extended cognition requires refocusing from explicit thought traces to implicit activation dynamics via recurrent architectures. We introduce a taxonomy of recurrent and continuous-thought transformer architectures, categorizing them by their recurrence axis (depth versus step) and their ratio of input tokens to recurrence steps. Finally, we outline promising research directions, including enhanced state-space models and coarse-grained recurrence, to better integrate state tracking into modern foundation models.

Category-level object pose estimation is fundamental for embodied intelligence, yet achieving robust generalization to unseen instances remains challenging. However, existing methods mainly rely on simple feature extraction and aggregation, which struggle to capture category-shared topological structures and conduct semantic keypoint modeling, limiting their generalization. To address these, we propose a \textbf{T}opology-Aware Learning with \textbf{S}emantic \textbf{M}amba for Category-Level \textbf{P}ose Estimation framework (TSM-Pose). Specifically, we introduce a Topology Extractor to capture the global topological representation of the point cloud, which is integrated into local geometry features and enables robust category-level structural representation. Simultaneously, we propose a Mamba-based Global Semantic Aggregator that injects semantics priors into keypoints to enhance their expressiveness and leverages multiple TwinMamba blocks to model long-range dependencies for more effective global feature aggregation. Extensive experiments on three benchmark datasets (REAL275, CAMERA25, and HouseCat6D) demonstrate that TSM-Pose outperforms existing state-of-the-art methods.

The spectral kernel field equation R[k] = T[k] lacks a conservation-law analog. We prove (i) the fixed-point flow is strictly volume-expanding (tr DF > 0), precluding automatic conservation, and (ii) the conservation deficit per mode equals the Hessian stability margin exactly: D_m = -Delta'. Closing the deficit requires a scene-side compensating contribution, which we formalise as the distinction dynamics equation dc/dt = G[c, h_t], with MaxCal-optimal realisation G_opt. On fixed-topology 3D surface graphs we derive a conditional topology-preserving compression theorem: retaining k >= beta_0 + beta_1 modes (under a spectral-ordering assumption) preserves all Betti-number charges; we include a worked short-cycle counterexample (figure-eight) calibrating when the assumption fails. A triple necessary spectral diagnostic -- Fiedler-mode concentration, elevated curl energy, anomalous beta_1 -- is derived for planetary drainage networks at O(N) cost. Two internal real-data sequences serve as preliminary consistency checks; full benchmarks and adaptive-topology extensions are deferred.

We present the Global Neural World Model (GNWM), a self-stabilizing framework that achieves topological quantization through balanced continuous entropy constraints. Operating as a continuous, action-conditioned Joint-Embedding Predictive Architecture (JEPA), the GNWM maps environments onto a discrete 2D grid, enforcing translational equivariance without pixel-level reconstruction. Our results show this architecture prevents manifold drift during autoregressive rollouts by using grid ``snapping'' as a native error-correction mechanism. Furthermore, by training via maximum entropy exploration (random walks), the model learns generalized transition dynamics rather than memorizing specific expert trajectories. We validate the GNWM across passive observation, active agent control, and abstract sequence regimes, demonstrating its capacity to act not just as a spatial physics simulator, but as a causal discovery model capable of organizing continuous, predictable concepts into structured topological maps.

Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological structures involving branching paths, converging flows, and cyclic dependencies, their reasoning capabilities degrade sharply, even on tasks as basic as counting endpoints. Existing benchmarks fail to probe this gap, focusing on semantic comprehension rather than structural reasoning. We introduce ReactBench, a benchmark that reveals fundamental limitations in structural reasoning through chemical reaction diagrams. These real-world scientific diagrams offer an ideal testbed because they naturally span diverse structures from linear chains to cyclic graphs, while requiring both precise local recognition and coherent global reasoning. Our benchmark comprises 1,618 expert-annotated QA pairs across four hierarchical task dimensions. Extensive evaluation across 24 MLLMs reveals a significant performance gap exceeding 30% between anchor-based tasks and holistic structural reasoning tasks. Controlled ablations confirm this bottleneck lies in reasoning, not perception. These findings expose a fundamental deficit in structural understanding and establish directions for advancing visual reasoning.

Three-dimensional (3D) fingerprint recognition and identification offer several advantages over traditional two-dimensional (2D) recognition systems. The contactless nature of 3D fingerprints enhances hygiene and security, reducing the risk of contamination and spoofing. In addition to surface ridge and valley patterns, 3D fingerprints capture depth, curvature, and shape information, enabling the development of more precise and robust authentication systems. Despite recent advancements, significant challenges remain. The topological height of fingerprint pixels complicates the extraction of ridge and valley patterns. Furthermore, registration issues limit the acquisition process, requiring consistent direction and orientation across all samples. To address these challenges, this paper introduces a method that unwraps 3D fingerprints, represented as 3D point clouds, using B-spline curve fitting to mitigate height variation and reduce registration limitations. The unwrapped point cloud is then converted into a grayscale image by mapping the relative heights of the points. This grayscale image is subsequently used for recognition through conventional 2D fingerprint identification methods. The proposed approach demonstrated superior performance in 3D fingerprint recognition, achieving Equal Error Rates (EERs) of 0.2072%, 0.26%, and 0.22% across three experiments, outperforming existing methods. Additionally, the method surpassed 3D fingerprint flattening technique in both recognition and identification during cross-session experiments, achieving an EER of 1.50% when fingerprints with varying registrations were included.

This work simulates the developmental process of cortical neurogenesis, initiating from a single stem cell and governed by gene regulatory rules derived from mouse single-cell transcriptomic data. The developmental process spontaneously generates a heterogeneous population of 5,000 cells, yet yields only 85 mature neurons - merely 1.7% of the total population. These 85 neurons form a densely interconnected core of 200,400 synapses, corresponding to an average degree of 4,715 per neuron. At iteration zero, this minimal circuit performs at chance level on MNIST. However, after a single epoch of standard training, accuracy surges to over 90% - a gain exceeding 80 percentage points - with typical runs falling in the 89-94% range depending on developmental stochasticity. The identical circuit, without any architectural modification or data augmentation, achieves 40.53% on CIFAR-10 after one epoch. These findings demonstrate that developmental rules sculpt a domain-general topological substrate exceptionally amenable to rapid learning, suggesting that biological developmental processes inherently encode powerful structural priors for efficient computation.

Building extraction from optical Remote Sensing (RS) imagery suffers from performance degradation under real-world hazy and low-light conditions. However, existing optical methods and benchmarks focus primarily on ideal clear-weather conditions. While SAR offers all-weather sensing, its side-looking geometry causes geometric distortions. To address these challenges, we introduce HaLoBuilding, the first optical benchmark specifically designed for building extraction under hazy and low-light conditions. By leveraging a same-scene multitemporal pairing strategy, we ensure pixel-level label alignment and high fidelity even under extreme degradation. Building upon this benchmark, we propose HaLoBuild-Net, a novel end-to-end framework for building extraction in adverse RS scenarios. At its core, we develop a Spatial-Frequency Focus Module (SFFM) to effectively mitigate meteorological interference on building features by coupling large receptive field attention with frequency-aware channel reweighting guided by stable low-frequency anchors. Additionally, a Global Multi-scale Guidance Module (GMGM) provides global semantic constraints to anchor building topologies, while a Mutual-Guided Fusion Module (MGFM) implements bidirectional semantic-spatial calibration to suppress shallow noise and sharpen weather-induced blurred boundaries. Extensive experiments demonstrate that HaLoBuild-Net significantly outperforms state-of-the-art methods and conventional cascaded restoration-segmentation paradigms on the HaLoBuilding dataset, while maintaining robust generalization on WHU, INRIA, and LoveDA datasets. The source code and datasets are publicly available at: https://github.com/AeroVILab-AHU/HaLoBuilding.

Skeleton-based action recognition is widely applied in sensor-based systems, including human-computer interaction and intelligent surveillance. However, typical sensors produce sparse and discrete joint coordinates, often leading to the loss of fine-grained spatiotemporal information during dynamic movements. Furthermore, predefined physical topologies restrict modeling potential long-range dependencies. To address these challenges, we propose KGS-GCN, which integrates kinematics-driven Gaussian splatting and probabilistic topology within a graph convolutional network. A Gaussian splatting module constructs anisotropic covariance matrices by extracting instantaneous joint velocity vectors, rendering sparse skeleton sequences into multi-view continuous heatmaps rich in spatiotemporal semantics. Additionally, a probabilistic topology construction strategy transcends physical connectivity limitations by utilizing the Bhattacharyya distance to quantify statistical correlations between joint Gaussian distributions, generating an adaptive prior adjacency matrix. Finally, the lightweight multi-view rendering branch and topological GCN backbone are unified through a visual context gating mechanism, enabling seamless fusion of continuous dynamic cues with structural priors while maintaining high computational efficiency, requiring only 1.4M parameters and 1.3 GFLOPs. Extensive experiments on multiple benchmark datasets demonstrate that KGS-GCN significantly enhances the modeling of complex spatiotemporal dynamics and achieves competitive performance at low computational cost, establishing an efficient paradigm for improving the perceptual robustness of low-fidelity sensor data.

Accurate prediction of multivariate time series is essential for emerging network intelligent control, observability, and management functions. Existing statistical-based and shallow machine learning models have shown limited prediction capabilities on multivariate time series. They prioritize improvements in average prediction accuracy, while overlooking heterogeneous dependency structures and performance variability across individual time series. Recent advances in large language models have introduced new directions for multivariate time series forecasting; however, their application in conjunction with explicit structural dependency modeling remains relatively underexplored, especially in networked environments. In this paper, we present a topology-aware learning framework for large-scale network traffic prediction that explicitly models both temporal dynamics and structural dependencies in multivariate network time series. We first investigate a graph attention model designed to capture topology-induced correlations among network traffic time series. We then evaluate a fine-tuned large language model-based representations for improved generalization across heterogeneous traffic patterns. To further address the diversity of cross-correlations in high-dimensional traffic data, we introduce a clustering-based preprocessing stage that groups traffic flows with similar dependency characteristics prior to model training, reducing input complexity and improving learning stability. Experiments on real backbone traffic data show consistent improvements over statistical and recurrent neural network baselines. In addition to average accuracy, we evaluate performance across individual time series and observe reduced variability in prediction quality.

Persistent entropy is a scalar summary of persistence barcodes widely used to detect regime changes, yet there is no account of when a structural change in a barcode must produce a detectable change in entropy. We establish a model-agnostic theorem supplying such conditions. Treating persistence diagrams as random objects indexed by a control parameter, we identify a dispersion-condensation mechanism in the normalized persistence weights and derive an explicit lower bound on the entropy difference between the two regimes, valid with high probability at finite sample size and insensitive to the absolute scale of bar lifetimes. We also give a procedure for verifying the hypotheses on empirical barcodes. Applied to convolutional networks, the criterion shows that the circular organization of learned filters reported by Gabrielsson and Carlsson emerges through a sharp topological phase transition, and locates its onset: within a few hundred iterations on MNIST, but an order of magnitude later on CIFAR-10. The same criterion detects the Kuramoto synchronization and Vicsek order-disorder transitions.

Multi-agent systems face a fundamental architectural flaw: agent identity is bound to network location. When agents migrate between providers, scale across instances, or federate across organizations, URI-based identity schemes break references, fragment audit trails, and require centralized coordination. We propose the agent:// URI scheme, which decouples identity from topology through three orthogonal components: a trust root establishing organizational authority, a hierarchical capability path enabling semantic discovery, and a sortable unique identifier providing stable reference. The scheme enables capability-based discovery through DHT key derivation, where queries return agents by what they do rather than where they are. Trust-root scoping prevents cross-organization pollution while permitting federation when desired. Cryptographic attestation via PASETO tokens binds capability claims to agent identity, enabling verification without real-time contact with the issuing authority. We evaluate the scheme across four dimensions: capability expressiveness (100% coverage on 369 production tools with zero collision), discovery precision (F1=1.0 across 10,000 agents), identity stability (formal proofs of migration invariance), and performance (all operations under 5 microseconds). The agent:// URI scheme provides a formally-specified, practically-evaluated foundation for decentralized agent identity and capability-based discovery.

Clustering is a cornerstone of modern data analysis. Detecting clusters in exploratory data analyses (EDA) requires algorithms that make few assumptions about the data. Density-based clustering algorithms are particularly well-suited for EDA because they describe high-density regions, assuming only that a density exists. Applying density-based clustering algorithms in practice, however, requires selecting appropriate hyperparameters, which is difficult without prior knowledge of the data distribution. For example, DBSCAN requires selecting a density threshold, and HDBSCAN* relies on a minimum cluster size parameter. In this work, we propose Persistent Leaves Spatial Clustering for Applications with Noise (PLSCAN), a multiscale density-based clustering algorithm that replaces HDBSCAN*'s fixed minimum cluster size pruning of a mutual-reachability linkage hierarchy with a persistence-based cluster selection procedure. Effectively, PLSCAN identifies all minimum cluster sizes for which HDBSCAN* produces stable (leaf) clusters. In concept, PLSCAN applies scale-space clustering principles and is equivalent to persistent homology on a novel metric space. We compare its performance to HDBSCAN* on several real-world datasets, demonstrating that it achieves a higher median ARI, is less sensitive to changes in the number of mutual reachability neighbours, and has higher stability under resampling. Additionally, we compare PLSCAN's computational costs to $k$-Means++, demonstrating competitive run-times on low-dimensional datasets. At higher dimensions, run times scale more similarly to HDBSCAN*.

Reinforcement learning has enabled impressive locomotion skills on articulated robots, but common policy representations remain only weakly aligned with robot physics. Generic networks ignore kinematic structure, while graph-based policies encode connectivity without specifying how physical quantities transform across symmetric body parts. We introduce a morphological symmetry graph representation for locomotion policy learning and instantiate it in MS-PPO. Starting from the robot's topological graph, our representation augments each observation and action space with the permutation and sign transformations induced by morphological symmetry. This yields a symmetry-equivariant graph actor and a symmetry-invariant graph critic, enforcing the desired policy and value constraints by construction rather than through reward shaping or data augmentation. We evaluate MS-PPO on a variety of locomotion tasks using both Unitree Go2 quadruped and Unitree G1 humanoid, including command tracking, asymmetric joint failures, out-of-distribution command generalization, and zero-shot sim-to-real deployment. Experiments show improved symmetry generalization, robustness, sample efficiency, and model efficiency over topology- and symmetry-aware baselines.

The advent of the big data paradigm has transformed how industries manage and analyze information, ushering in an era of unprecedented data volume, velocity, and variety. Within this landscape, mixed-data clustering has become a critical challenge, requiring innovative methods that can effectively exploit heterogeneous data types, including numerical and categorical variables. Traditional clustering techniques, typically designed for homogeneous datasets, often struggle to capture the additional complexity introduced by mixed data, underscoring the need for approaches specifically tailored to this setting. Hierarchical and explainable algorithms are particularly valuable in this context, as they provide structured, interpretable clustering results that support informed decision-making. This paper introduces a clustering method grounded in pretopological spaces. In addition, benchmarking against classical numerical clustering algorithms and existing pretopological approaches yields insights into the performance and effectiveness of the proposed method within the big data paradigm.

The existing method of GS-PowerOpt solves the non-convex optimization problem of the form $\max_{\boldsymbol{x} \in \mathbb{R}^d} f(\boldsymbol{x})$ through maximizing a Gaussian-smoothed surrogate $F_{N,σ}(\boldsymbolμ) = \mathbb{E}_{\boldsymbol{x}\sim\mathcal{N}(\boldsymbolμ,σ^2 I_d)}[e^{N f(\boldsymbol{x})}]$. We analyze the role of the smoothing radius $σ>0$ and identify a limitation of the fixed-$σ$ design used in GS-PowerOpt. Specifically, $σ$ induces an inherent exploration--refinement tradeoff: a larger $σ$ improves global exploration and finite-time surrogate optimization, but may distort the location of the surrogate maximizer; in contrast, a smaller $σ$ better preserves local structure but can weaken gradient signals away from high-value regions. To address this limitation, we propose GS-PowerHP, a power-smoothed homotopy method with an incrementally decaying $σ$ schedule. The proposed mechanism uses larger smoothing radii in early iterations to maintain informative gradient signals when the iterate is far from high-value regions, and gradually decreases $σ$ to improve local refinement near the maximizer. We provide theoretical results showing that this decaying schedule improves the exploration--refinement tradeoff of fixed-$σ$ power smoothing. Empirically, GS-PowerHP consistently outperforms the fixed-$σ$ baseline and exhibits robust performance across different optimization tasks, including adversarial attacks on ImageNet ($d=150{,}528$), where it substantially improves over other smoothing-based zeroth-order methods.

Topological mapping offers a compact and robust representation for navigation, but progress in the field is hindered by the lack of standardized evaluation metrics, datasets, and protocols. Existing systems are assessed using different environments and criteria, preventing fair and reproducible comparisons. Moreover, a key challenge - perceptual aliasing - remains under-quantified, despite its strong influence on system performance. We address these gaps by (1) formalizing topological consistency as the fundamental property of topological maps and showing that localization accuracy provides an efficient and interpretable surrogate metric, and (2) proposing the first quantitative measure of dataset ambiguity to enable fair comparisons across environments. To support this protocol, we curate a diverse benchmark dataset with calibrated ambiguity levels, implement and release deep-learned baseline systems, and evaluate them alongside classical methods. Our experiments and analysis yield new insights into the limitations of current approaches under perceptual aliasing. All datasets, baselines, and evaluation tools are fully open-sourced to foster consistent and reproducible research in topological mapping.

Swarm-based optimization algorithms have demonstrated remarkable success in solving complex problems, yet their widespread adoption remains limited due to poor transparency in how algorithmic components influence performance. This work presents a multi-faceted explainability framework for Particle Swarm Optimization (PSO) through two complementary perspectives: landscape-based and algorithmic explainability. From the landscape-based perspective, we develop a comprehensive characterization framework using Exploratory Landscape Analysis (ELA) to quantify problem difficulty, multimodality, and ruggedness, extracting ELA meta-features, dispersion measures, and information content statistics, while a machine learning approach employing Decision Tree and Random Forest classifiers enables prediction of optimal topology-specific hyperparameter configurations for unseen problems. From the algorithmic explainability perspective, we integrate IOHxplainer for temporal convergence profiling and Search Trajectory Networks (STN) for spatial navigation mapping, proposing three novel STN metrics-Connectivity Density, Fragmentation Score, and Search Efficiency-that enhance visual explainability by quantifying topology-specific search organization and transition effectiveness. Through systematic experimentation across 24 benchmark functions in multiple dimensions with Star, Ring, and Von Neumann topologies, we establish practical guidelines for topology selection and parameter configuration. Our findings uncover the black-box nature of PSO, providing greater transparency and interpretability to swarm intelligence systems. The source code is available at https://github.com/GitNitin02/ioh_pso.

We propose persistent discrete homology as a tool for topological data analysis and discuss its advantages over the existing methods. In particular, we provide empirical evidence that persistent discrete homology is more noise-resistant than persistent homology of the Vietoris-Rips complex for data coming from non-metric settings.

Equivariant network architectures are a well-established tool for predicting invariant or equivariant quantities. However, almost all learning problems considered in this context feature a global symmetry, i.e. each point of the underlying space is transformed with the same group element, as opposed to a local ``gauge'' symmetry, where each point is transformed with a different group element, exponentially enlarging the size of the symmetry group. Gauge equivariant networks have so far mainly been applied to problems in quantum chromodynamics. Here, we introduce a novel application domain for gauge-equivariant networks in the theory of topological condensed matter physics. We use gauge equivariant networks to predict topological invariants (Chern numbers) of multiband topological insulators. The gauge symmetry of the network guarantees that the predicted quantity is a topological invariant. We introduce a novel gauge equivariant normalization layer to stabilize the training and prove a universal approximation theorem for our setup. We train on samples with trivial Chern number only but show that our models generalize to samples with non-trivial Chern number. We provide various ablations of our setup. Our code is available at https://github.com/sitronsea/GENet/tree/main.

We investigate the structure of Kazhdan-Lusztig polynomials of the symmetric group by leveraging computational approaches from big data, including exploratory and topological data analysis, applied to the polynomials for symmetric groups of up to 11 strands.

In artificial-intelligence-aided signal processing, existing deep learning models often exhibit a black-box structure. Here, conceptually beyond spectral analysis, we demonstrate that topological methods not only effectively capture intrinsic and complex structural information but can also enhance neural networks. We provide a transparent methodology, TopCap, to capture topological features inherent in time series for basic machine learning. Compared to prior approaches, we obtain descriptors that probe finer information such as the vibration of a time series. Notably, in classifying voiced and voiceless consonants, TopCap achieves an accuracy consistently standing in comparison with neural network models. Moreover, by integrating TopCap features into those neural networks, our approach improves upon state-of-the-art methods in terms of robustness against noise, as well as accuracy, stability, convergence of loss function, and interpretability.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Despite their widespread use, the principles governing the organisation of syntactic dependency trees remain poorly understood. I analyse dependency trees from 124 typologically, genetically, and geographically diverse languages. Their topology departs systematically from randomness. Relative to uniformly sampled random trees, dependency trees exhibit greater structural robustness and lower branching heterogeneity. I propose that these universal regularities emerge naturally from incremental grammatical encoding. I model this process using sublinear preferential attachment. The model accurately reproduces the observed topology. More generally, the results demonstrate how a universal statistical property of syntax can emerge from a simple, cognitively motivated generative process. They further illustrate a broader principle of efficiency by construction: communicatively efficient syntactic structures can emerge without direct optimisation for communication.

Quantitative assessment of muscle MRI is crucial for monitoring neuromuscular disorders (NMD). This study introduces an automated radiomic phenotyping framework based on original features engineered across five main architectural domains: quantitative morphometry, spatial distribution, geometric shape, interactions between progressive fat replacement stages, and graph-based topology. Utilizing 1184 MRI scans from the CoMPaSS-NMD project, we map the complex 3D architecture of heterogeneous intramuscular lipodegeneration into objective, morphologically interpretable biomarkers. We introduce a graph-based skeletonization of fat infiltrates to quantify muscle architectural changes, establishing a multi-dimensional extension of traditional, spatially-agnostic volume metrics by mapping topological networks across the entire 3D muscle volume. Statistical screening via non-parametric Kruskal-Wallis analysis confirmed the discriminative power of these novel descriptors across the genetic hierarchy. Notably, topological network metrics (e.g., SF1_Skel_Nodes, $\epsilon^2$ = 0.2656) and interface dynamics metrics (e.g., SF2_To_SF1_Dist_Min, $\epsilon^2$ = 0.2092) demonstrated substantial effect sizes, providing deeper structural insights than classical volumetric assessments. Post-hoc pairwise evaluations and UMAP projections further indicated the capability of these topological and 3D geometric invariants to capture disease-specific macroscopic infiltration patterns. These results demonstrate that global architectural features represent a highly promising class of biomarkers for differential diagnosis, offering new avenues for tracking longitudinal disease dynamics in neuromuscular diagnostics. The developed automated feature extraction pipeline is integrated and available within the MUSCAT (MUSCle fAt Topology) library.