arXiv Computation and Language

Self-Supervised Lexical Representation Learning for Fast, Large-Scale Phylogenetic Inference

The paper presents a fully self‑supervised contrastive learning framework that learns lexical representations from raw IPA‑transcribed wordlists without any cognacy annotations or expert input. Using a dual contrastive objective—word‑level and language‑level losses—the model produces word representations that enable fast computation of pairwise language distances and the inference of a global phylogenetic tree for 3,399 language varieties. The resulting tree achieves a generalized quartet distance competitive with baselines while requiring only minutes of computation on a standard notebook GPU, and the representations also capture diachronic concept stability.

arXiv Machine Learning
Oct 9

RAGenome: Scaling Retrieval-Based Genomic Language Models to Long Contexts

RAGenome is a retrieval‑based genomic language model that extends pretraining to contexts 100 times longer than existing MSA‑based models, enabling it to capture both cross‑species evolutionary relationships and within‑species long‑range interactions. Trained on whole‑genome alignments from 100 vertebrates, it improves gene‑finding performance from 0.45 to 0.60 while staying competitive on evolutionary tasks such as prioritizing pathogenic variants. The model offers competitive performance at a fraction of the training cost, unifying evolutionary modeling and long‑range capabilities in a single scalable framework.

By Frederikke Isa Marin, Panagiotis Antoniadis, Dionysia Danai Brilli, Andreas Bjerregaard, Rachael DeVries, Yan Li, Ole Winther, Wouter Boomsma
arXiv Computation and Language
Sep 21

Beyond Atomic Tokens: Factorizing Syllables for Language Model Pretraining

arXiv:2609. 21362v1 Announce Type: new Abstract: Conventional tokenizers represent text as characters or statistically derived subwords, overlooking the internal phonological structure of syllables and often requiring large vocabularies.

By Nghia Hieu Nguyen, Thai Bao Huynh, Binh-An Dinh-Le, Phu Gia Hoang, Dat Tien Nguyen, Kiet Van Nguyen, Ngan Luu-Thuy Nguyen
arXiv Computation and Language
Aug 31

Phoneme- and Word-Level Metrics Using Self-Supervised Speech Representations for Forced Alignment Evaluation

The paper introduces two new corpus‑level, reference‑free metrics—Phoneme‑Cluster Mutual Information (PCMI) and Word Acoustic Consistency Score (WACS)—that use self‑supervised speech representations to evaluate forced alignment quality. PCMI quantifies how well aligned phoneme labels agree with clusters derived from SSL representations, while WACS assesses consistency across repeated word realizations via dynamic time warping of word representation sequences. Experiments on 85 languages from FLEURS and 45 languages in DoReCo show that both metrics degrade predictably under alignment perturbations, effectively distinguish high‑ from low‑quality alignments, and correlate strongly with traditional timestamp‑based measures, enabling scalable, multilingual alignment evaluation without manual annotations.

By V. S. D. S. Mahesh Akavarapu, Michael Daniel, Gerhard J\"ager
arXiv Computation and Language
Sep 2

CWoMP: Morpheme Representation Learning for Interlinear Glossing

CWoMP (Contrastive Word‑Morpheme Pretraining) is a new approach for generating interlinear glossed text that treats morphemes as atomic form‑meaning units with learned representations. It uses a contrastively trained encoder to align words in context with their constituent morphemes in a shared embedding space, and an autoregressive decoder that retrieves morpheme sequences from a mutable lexicon of these embeddings. The method yields interpretable predictions grounded in lexicon entries and allows users to improve results at inference time by expanding the lexicon without retraining, achieving superior performance and efficiency on diverse low‑resource languages, especially in extremely low‑resource settings.

By Morris Alper, Enora Rice, Bhargav Shandilya, Alexis Palmer, Lori Levin
arXiv Machine Learning
Oct 23

Escaping the Phylogenetic Trap: Persistent Homology Enables Cross-Species Ion Channel Classification via Multimodal Graph Neural Networks

The paper investigates how phylogenetic leakage can inflate performance estimates for protein classifiers, particularly in venom ion‑channel target prediction. By treating cross‑species prediction as a structured distribution shift, the authors compare five structural inductive biases using a multimodal graph neural network that fuses ESM‑2 embeddings with a disulfide‑aware attention mechanism. Persistent‑homology representations, which capture backbone geometry through topological descriptors, outperform other biases under a leave‑one‑taxon‑out protocol, achieving 63.4% accuracy versus 54‑55% for other geometric priors and 30% for a sequence‑only baseline.

By Arezoo Bybordi, Favour Achimba, Mariam Gelashvili, Jessy Ramirez, Weigang Qiu, Mand\"e Holford, Anita Raja
arXiv Computation and Language
Sep 16

PunGraph: Retrieval-Enhanced Phonetic-Semantic Graph Reasoning for Pun Understanding

PunGraph is a retrieval‑enhanced knowledge‑graph framework designed to improve pun understanding by combining phonetic and semantic information. It builds a phonetic‑semantic lexical graph using the Unisyn phonetic dictionary, IPA and G2P representations, and WordNet definitions, and uses this graph to retrieve candidate words or senses that constrain large language model reasoning. The authors also introduce WebPun, a new dataset of 5,730 annotated heterographic and homographic puns, and demonstrate that PunGraph consistently boosts the performance of small‑scale LLMs on SemEval‑2017 and WebPun, achieving results competitive with strong proprietary models.

By Yuchen Su, Zijian Huang, Yaotian Shi, Shaoxin Zhong, Ruofan Wang, Mengze Li, Yonghua Zhu, Diana Benavides-Prado, Michael Witbrock
arXiv Computation and Language
Sep 21

TatBLiMP: A Benchmark of Linguistic Minimal Pairs for Tatar

TatBLiMP is the first benchmark of linguistic minimal pairs for the Tatar language, covering 16 morphosyntactic phenomena across 1,248 sentence pairs that differ by a single morpheme. Each pair contains one grammatical and one ungrammatical sentence, with the ungrammatical version generated by a deterministic perturbation and ratified by a native speaker. The benchmark evaluates models by comparing their assigned probabilities, allowing assessment without text generation or parsing, and tracks performance across from-scratch, cross‑lingual, and multilingual large language models.

By Ilshat Saetov, Dmitry Gaynullin