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.
arXiv:2606. 06117v1 Announce Type: cross Abstract: We introduce pVR, a topological machine learning framework for alignment-free genomic sequence classification that combines $p$-adic numbers with topological data analysis.
The paper introduces Murmur2Vec, a lightweight, alignment‑free embedding that uses k‑mer counts hashed with MurmurHash to create a compact representation for biological sequences. It provides a full theoretical analysis, including bias/variance formulas, a Johnson–Lindenstrauss‑style concentration bound, and an excess‑risk bound that clarifies the trade‑off between hash‑table size and classifier performance. Empirically, Murmur2Vec matches or surpasses a fine‑tuned 650M‑parameter ESM‑2 protein language model across several classification tasks, including SARS‑CoV‑2 spike lineage and HIV‑1 Env subtype identification.
arXiv:2606. 14737v1 Announce Type: cross Abstract: Molecular dynamics (MD) simulations generate trajectories in a high-dimensional configuration space whose analysis critically depends on molecular descriptors, typically handcrafted observables or learned kinetic embeddings.
arXiv:2511. 04873v2 Announce Type: replace-cross Abstract: Prototype selection methods compress a training set, but the existing taxonomy of condensation, edition, hybrid, competence-based, optimization-based, and clustering-based families does not include methods that operate on the multi-scale topological structure of the data.
arXiv:2512.23348v3 Announce Type: replace-cross Abstract: We introduce a data-analysis framework based on filtrations of finite topological spaces. Starting from a finite metric data set, we construc...
arXiv:2606. 06342v1 Announce Type: cross Abstract: Topological Data Analysis (TDA) offers a principled, intrinsic lens for comparing neural representations.
arXiv:2505. 04346v2 Announce Type: replace Abstract: Clustering aims at partitioning data points into groups of similar objects without knowing about the class labels.
HoloAegis is a minimally parametric topological inference framework that uses frozen representations to map text onto the unit sphere and makes decisions via Gibbs‑Boltzmann free‑energy differences over pre‑computed anchor centroids. On a frozen three‑benchmark protocol, it matches WildGuard‑7B on toxicity, outperforms it on harmful behaviors, but underperforms on oversafety detection, while ShieldGemma‑2B fails on indirect harms. The study demonstrates that geometric guardrails can substitute for LLM judges in some cases and must defer to them in others, with anchor banks reducing score variance and boundary displacement.
arXiv:2607. 20657v1 Announce Type: cross Abstract: Unique and rapid classification of knots and links is an open mathematical problem that is relevant to a range of (bio)physical systems, including polymer melts, DNA, and proteins.
arXiv:2607. 25680v1 Announce Type: cross Abstract: We propose Rashomon Alignment (RA), a new measure to assess functional similarity between two models.
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.
COMPLEX is a closed‑form, training‑free embedding for multiparameter persistence modules that provides both an upper and a lower Lipschitz bound, enabling faithful feature representations. By slicing modules along a near‑diagonal net and embedding each slice with the certified PLACE/PALACE landmark map, the method guarantees that separated modules remain separated in the embedding. On Orbit benchmarks and molecular graph tasks, COMPLEX achieves state‑of‑the‑art accuracy, outperforming existing landmark, transformer, and graph‑based approaches.