Topology of a Smile: Persistent Homology in Dental Imaging

CBCT (Cone Beam Computed Tomography) scans provide detailed three-dimensional images, widely used in dentistry for diagnostic and treatment planning tasks. While invaluable, analyzing and documenting these scans is labor-intensive, prompting efforts to automate key steps like the classification and segmentation of anatomical structures to identify tooth types and associated pathologies. In this article, we propose an approach to automation that leverages persistent homology, a framework from topological data analysis that studies the shape of data by identifying features like connected components, holes, and voids across multiple scales. Persistent homology, together with a support vector machine, allows us to classify teeth in a CBCT scan and to perform diagnostics. Our method advances the state of the art, reaching average accuracy scores of 97.67% for tooth-labeling and 96.77% for diagnostic tasks, outperforming a CNN trained on the same data with accuracy of 70.27% and 86.67%, respectively.

PHINN-EEG: Topological Time-Series Analysis of Dream-State EEG -- Dynamic Betti Curves for Dream Content Classification and Topology-Conditioned Neural Signal Synthesis

Current electroencephalography (EEG)-based dream detection relies on power spectral density (PSD) and statistical moment features, achieving a state-of-the-art area under the receiver operating characteristic curve (AUC) of approximately 0.70 on the DREAM database (Wong et al., 2025, Nature Communications). We introduce PHINN-EEG (Persistent Homology Inspired Neural Network for EEG), the first topological time-series framework for dream mentation analysis. Using sliding-window Takens delay embeddings and Vietoris-Rips filtrations on multichannel pre-awakening EEG epochs, we extract Dynamic Betti Curves that characterize the geometric architecture of neural activity, not merely its energy. These topological invariants, combined with topology-conditioned flow matching, are analytically projected to outperform existing PSD and catch22 benchmarks, targeting AUC = 0.82-0.90 on the 1,462-awakening open-access subset of the DREAM database (drawn from a full registry of 3,191 total awakenings from 263 participants across 20 independent laboratories). We further introduce a topology-conditioned rectified flow model for dream-state EEG synthesis-with a spectral-conditioned flow model of comparable feature dimensionality as an additional ablation baseline to isolate the value of topological conditioning specifically-and propose a set of candidate Betti transition archetypes linking topology to phenomenological dream report categories, presented as an exploratory hypothesis space pending empirical validation. If validated, this work represents a paradigm shift from spectral energy to phase-space geometry in neural rare-event detection, with potential future implications for wearable BCI dream monitoring.

Topological Shape Representation for Aneurysm -- Bifurcation Detection

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.

TopoAgent: An Agentic Framework for Automated Topology Learning in Medical Imaging

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.

Magnitude-Based Features for Multispecies Spatial Data

Multispecies spatial data arise in many applications where interactions between different entities are central to system behaviour, including biomedical imaging, geospatial analysis, and species ecology. Despite their importance, relatively few quantitative tools exist to capture such interactions. In this work, we propose magnitude-based features for the analysis of multispecies spatial data. Magnitude is a real-valued invariant of finite metric spaces that can be interpreted as an effective number of points, incorporating both spatial configuration and scale. We develop global and local magnitude feature vectors and demonstrate their utility on synthetic tumour microenvironment data, and in tissue microarray data from human colorectal cancer samples. Locally, the method identifies distinct neighbourhood types and reveals spatial heterogeneity; in the model, this includes radial patterns associated with different qualitative outcomes of the simulations, while in the real-world data it reflects the importance of tertiary lymphoid structure-like interactions between B and T cell populations. Globally, the approach recovers known classifications of long-term simulation outcomes across parameter regimes in synthetic data, and suggests important roles for CD4+ T cells and CD163+ macrophages in distinguishing patients with favourable Crohn's like reactions from unfavourable diffuse immune infiltration. Together, these results suggest that magnitude-based features provide a powerful and flexible tool for the analysis of multispecies spatial data.

$p$-adic Bi-Filtrations for Topological Machine Learning on Genomic Sequences

We introduce pVR, a topological machine learning framework for alignment-free genomic sequence classification that combines $p$-adic numbers with topological data analysis. Each DNA sequence is encoded along two complementary axes: a $p$-adic distance on $k$-mer prefixes, which captures hierarchical positional structure, and a compositional $L_1$ distance on $k$-mer frequencies, which captures local sequence content. The two distances jointly parameterise a bi-filtered Vietoris--Rips complex, and per-sequence topological summaries from this bi-filtration serve as features for standard machine learning classifiers. We establish theoretical guarantees for the construction: stability under metric perturbations and invariance to the choice of prime, alongside a result that explains why a single $p$-adic axis is topologically uninformative and why the bi-filtration recovers nontrivial homology. On twelve genomic benchmarks ($28$ to $500$ sequences, $3$ to $7$ classes), pVR outperforms four established alignment-free baselines on three of six low-sample datasets, with gains of up to $21$ percentage points; it underperforms only on a SARS-CoV-2 variant benchmark whose point-mutation divergence violates the hierarchical assumption, and all methods saturate in the large-sample regime. pVR also outperforms zero-shot frozen embeddings from the 500M-parameter Nucleotide Transformer v2 by $6.7$ to $11.4$ percentage points on three low-sample benchmarks. The pVR codebase is publicly available at https://github.com/MAHI-Group/pVR.