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Sep 16

STP-BENCH: A Unified Systematic Benchmark for Virtual Spatial Transcriptomics from Histopathology Images

Spatial transcriptomics (ST) provides unprecedented insights into tumor heterogeneity by capturing spatially resolved gene expression, yet its high experimental cost hinders large-scale adoption. Consequently, computational approaches that predict spatial gene expression directly from hematoxylin and eosin slides, termed virtual ST, have rapidly emerged. Despite this progress, assessing advances in the field remains difficult due to insufficient benchmarking: prior studies rely on small, heterogeneous datasets, inconsistent training and inference pipelines, and limited evaluation of biological interpretability and model robustness. To address these gaps, we present STP-BENCH, a standardized benchmark for virtual ST models. STP-BENCH comprises six cancer types spanning two ST platforms (Visium and Xenium), with each training dataset containing more than 30,000 spots and at least 15 slides to ensure statistical reliability. We evaluate 21 predictive approaches, re-implemented with a unified pathology foundation model as the morphological encoder when architecturally applicable. Beyond conventional benchmarks that report average predictive accuracy on highly variable genes, we systematically examine which genes and gene sets are recoverable from histomorphology. We further evaluate the downstream biological utility of predicted profiles through cell-type deconvolution and spatial domain identification, and assess model reliability under domain shifts and data scaling. Notably, unified morphological encoding substantially re-orders model rankings established in prior studies, indicating that architectural innovations and image encoding have been conflated in previous evaluations. We publicly release STP-BENCH to support reproducibility and serve as a community benchmark at https://github.com/NEXGEM/STP-Bench.

  • 11 authors
·
Sep 4

Morpheus: A Morphology-Aware Neural Tokenizer and Word Embedder for Turkish

Turkish is agglutinative: meaning is carried by morphemes, yet the subword tokenizers that drive modern language models split words by corpus statistics, fragmenting semantically loaded suffixes and -- in the case of WordPiece and rule-based analyzers -- failing to decode their output back to the original text. This paper presents Morpheus, a neural morpheme-boundary model for Turkish that is at once a lossless, morphology-aware tokenizer and a word-embedding producer. A differentiable Poisson-binomial dynamic program turns per-character boundary probabilities into soft morpheme memberships during training and exact segments at inference, with no string normalization, so decode(encode(w)) = w holds by construction. Because the model is neural, the same forward pass that tokenizes also emits a structured word embedding. Among reversible tokenizers -- the only ones valid for generation -- Morpheus attains the lowest bits-per-character (1.425), roughly doubles the gold morphological alignment of the subword family (MorphScore macro-F1 0.61 vs.\ {sim}0.32), and uses {sim}19% less GPU memory than 64K-vocabulary subword tokenizers. As an embedder, frozen Morpheus vectors lead on lexical retrieval (root-family MAP 0.85) and same-root verification (ROC-AUC 1.00), surpassing the multilingual retriever BGE-M3 and BERTurk; on context- and inflection-dependent tasks (NER, case/number probing) the heavier contextual encoders remain ahead -- a trade-off we attribute to Morpheus's root-centric geometry. Code: https://github.com/lonewolf-rd/TurkishMorpheus; model: https://huggingface.co/lonewolflab/Morpheus-TR-50K; interactive demo: https://huggingface.co/spaces/lonewolflab/morpheus-tr-demo.

Neural Recovery of Historical Lexical Structure in Bantu Languages from Modern Data

We investigate whether neural models trained exclusively on modern morphological data can recover cross-lingual lexical structure consistent with historical reconstruction. Using BantuMorph v7, a transformer over Bantu morphological paradigms, we analyze 14 Eastern and Southern Bantu languages, extract encoder embeddings for their noun and verb lemmas, and identify 728 noun and 1,525 verb cognate candidates shared across 5+ languages. Evaluating these candidates against established historical resources-the Bantu Lexical Reconstructions database (BLR3; 4,786 reconstructed Proto-Bantu forms) and the ASJP basic vocabulary-we confirm 10 of the top 11 noun candidates (90.9%) align with previously reconstructed Proto-Bantu forms, including *-ntU 'person' (8 languages), *gombe 'cow' (9 languages), and *mUn (9 languages). Extending to verbs, 12 verb cognates align with reconstructed Proto-Bantu roots, including *-bon- 'see' and *-jIm- 'stand', each attested across wide geographic ranges. Cross-model validation using an independent translation model (NLLB-600M) confirms these patterns: both models recover cognate clusters and phylogenetic groupings consistent with established Guthrie-zone classifications (p < 0.01). Cross-lingual noun class analysis reveals that all 13 productive classes maintain >0.83 cosine similarity across languages (within-class > between-class, p < 10^-9). Our dataset is restricted to Eastern and Southern Bantu, so we interpret these results as recovering shared Bantu lexical structure consistent with Proto-Bantu rather than definitively distinguishing Proto-Bantu retentions from later regional innovations.

thiomi Thiomi NLP
·
Apr 23

CellCLIP -- Learning Perturbation Effects in Cell Painting via Text-Guided Contrastive Learning

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

  • 4 authors
·
May 16, 2025

Unveiling and Bridging the Functional Perception Gap in MLLMs: Atomic Visual Alignment and Hierarchical Evaluation via PET-Bench

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in tasks such as abnormality detection and report generation for anatomical modalities, their capability in functional imaging remains largely unexplored. In this work, we identify and quantify a fundamental functional perception gap: the inability of current vision encoders to decode functional tracer biodistribution independent of morphological priors. Identifying Positron Emission Tomography (PET) as the quintessential modality to investigate this disconnect, we introduce PET-Bench, the first large-scale functional imaging benchmark comprising 52,308 hierarchical QA pairs from 9,732 multi-site, multi-tracer PET studies. Extensive evaluation of 19 state-of-the-art MLLMs reveals a critical safety hazard termed the Chain-of-Thought (CoT) hallucination trap. We observe that standard CoT prompting, widely considered to enhance reasoning, paradoxically decouples linguistic generation from visual evidence in PET, producing clinically fluent but factually ungrounded diagnoses. To resolve this, we propose Atomic Visual Alignment (AVA), a simple fine-tuning strategy that enforces the mastery of low-level functional perception prior to high-level diagnostic reasoning. Our results demonstrate that AVA effectively bridges the perception gap, transforming CoT from a source of hallucination into a robust inference tool and improving diagnostic accuracy by up to 14.83%. Code and data are available at https://github.com/yezanting/PET-Bench.

  • 17 authors
·
Jan 6

Rethinking Tokenization for Rich Morphology: The Dominance of Unigram over BPE and Morphological Alignment

The relationship between tokenizer algorithm (e.g., Byte-Pair Encoding (BPE), Unigram), morphological alignment, tokenization quality (e.g., compression efficiency), and downstream performance remains largely unclear, particularly for languages with complex morphology. In this paper, we conduct a comprehensive evaluation of tokenizers using small-sized BERT models -- from pre-training through fine-tuning -- for Telugu (agglutinative), along with preliminary evaluation in Hindi (primarily fusional with some agglutination) and English (fusional). To evaluate morphological alignment of tokenizers in Telugu, we create a dataset containing gold morpheme segmentations of 600 derivational and 7000 inflectional word forms. Our experiments reveal two key findings for Telugu. First, the choice of tokenizer algorithm is the most significant factor influencing performance, with Unigram-based tokenizers consistently outperforming BPE across most settings. Second, while better morphological alignment shows a moderate, positive correlation with performance on text classification and structure prediction tasks, its impact is secondary to the tokenizer algorithm. Notably, hybrid approaches that use morphological information for pre-segmentation significantly boost the performance of BPE, though not Unigram. Our results further showcase the need for comprehensive intrinsic evaluation metrics for tokenizers that could explain downstream performance trends consistently.

  • 4 authors
·
Nov 9, 2025

On the Role of Morphological Information for Contextual Lemmatization

Lemmatization is a natural language processing (NLP) task which consists of producing, from a given inflected word, its canonical form or lemma. Lemmatization is one of the basic tasks that facilitate downstream NLP applications, and is of particular importance for high-inflected languages. Given that the process to obtain a lemma from an inflected word can be explained by looking at its morphosyntactic category, including fine-grained morphosyntactic information to train contextual lemmatizers has become common practice, without considering whether that is the optimum in terms of downstream performance. In order to address this issue, in this paper we empirically investigate the role of morphological information to develop contextual lemmatizers in six languages within a varied spectrum of morphological complexity: Basque, Turkish, Russian, Czech, Spanish and English. Furthermore, and unlike the vast majority of previous work, we also evaluate lemmatizers in out-of-domain settings, which constitutes, after all, their most common application use. The results of our study are rather surprising. It turns out that providing lemmatizers with fine-grained morphological features during training is not that beneficial, not even for agglutinative languages. In fact, modern contextual word representations seem to implicitly encode enough morphological information to obtain competitive contextual lemmatizers without seeing any explicit morphological signal. Moreover, our experiments suggest that the best lemmatizers out-of-domain are those using simple UPOS tags or those trained without morphology and, finally, that current evaluation practices for lemmatization are not adequate to clearly discriminate between models.

  • 2 authors
·
Feb 1, 2023

Optimal Turkish Subword Strategies at Scale: Systematic Evaluation of Data, Vocabulary, Morphology Interplay

Tokenization is a pivotal design choice for neural language modeling in morphologically rich languages (MRLs) such as Turkish, where productive agglutination challenges both vocabulary efficiency and morphological fidelity. Prior studies have explored tokenizer families and vocabulary sizes but typically (i) vary vocabulary without systematically controlling the tokenizer's training corpus, (ii) provide limited intrinsic diagnostics, and (iii) evaluate a narrow slice of downstream tasks. We present the first comprehensive, principled study of Turkish subword tokenization; a "subwords manifest", that jointly varies vocabulary size and tokenizer training corpus size (data and vocabulary coupling), compares multiple tokenizer families under matched parameter budgets (WordPiece, morphology level, and character baselines), and evaluates across semantic (NLI, STS, sentiment analysis, NER), syntactic (POS, dependency parsing), and morphology-sensitive probes. To explain why tokenizers succeed or fail, we introduce a morphology-aware diagnostic toolkit that goes beyond coarse aggregates to boundary-level micro/macro F1, decoupled lemma atomicity vs. surface boundary hits, over/under-segmentation indices, character/word edit distances (CER/WER), continuation rates, and affix-type coverage and token-level atomicity. Our contributions are fourfold: (i) a systematic investigation of the vocabulary-corpus-success triad; (ii) a unified, morphology-aware evaluation framework linking intrinsic diagnostics to extrinsic outcomes; (iii) controlled comparisons identifying when character-level and morphology-level tokenization pay off; and (iv) an open-source release of evaluation code, tokenizer pipelines, and models. As the first work of its kind, this "subwords manifest" delivers actionable guidance for building effective tokenizers in MRLs and establishes a reproducible foundation for future research.

MorphTok: Morphologically Grounded Tokenization for Indian Languages

Tokenization is a crucial step in NLP, especially with the rise of large language models (LLMs), impacting downstream performance, computational cost, and efficiency. Existing LLMs rely on the classical Byte-pair Encoding (BPE) algorithm for subword tokenization that greedily merges frequent character bigrams, often leading to segmentation that does not align with linguistically meaningful units. To address this, we propose morphology-aware segmentation as a pre-tokenization step before applying BPE. To facilitate morphology-aware segmentation, we create a novel dataset for Hindi and Marathi, incorporating sandhi splitting to enhance the subword tokenization. Experiments on downstream tasks show that morphologically grounded tokenization improves machine translation and language modeling performance. Additionally, to handle the dependent vowels common in syllable-based writing systems used by Indic languages, we propose Constrained BPE (CBPE), an extension to the standard BPE algorithm incorporating script-specific constraints. In particular, CBPE handles dependent vowels to form a cohesive unit with other characters instead of occurring as a single unit. Our results show that CBPE achieves a 1.68\% reduction in fertility scores while maintaining comparable or improved downstream performance in machine translation and language modeling, offering a computationally efficient alternative to standard BPE. Moreover, to evaluate segmentation across different tokenization algorithms, we introduce a new human evaluation metric, EvalTok, enabling more human-grounded assessment.

  • 8 authors
·
Apr 14, 2025

ARC-Encoder: learning compressed text representations for large language models

Recent techniques such as retrieval-augmented generation or chain-of-thought reasoning have led to longer contexts and increased inference costs. Context compression techniques can reduce these costs, but the most effective approaches require fine-tuning the target model or even modifying its architecture. This can degrade its general abilities when not used for this specific purpose. Here we explore an alternative approach: an encoder that compresses the context into continuous representations which replace token embeddings in decoder LLMs. First, we perform a systematic study of training strategies and architecture choices for the encoder. Our findings led to the design of an Adaptable text Representations Compressor, named ARC-Encoder, which outputs x-times fewer continuous representations (typically x!in!{4,8}) than text tokens. We evaluate ARC-Encoder across a variety of LLM usage scenarios, ranging from in-context learning to context window extension, on both instruct and base decoders. Results show that ARC-Encoder achieves state-of-the-art performance on several benchmarks while improving computational efficiency at inference. Finally, we demonstrate that our models can be adapted to multiple decoders simultaneously, allowing a single encoder to generalize across different decoder LLMs. This makes ARC-Encoder a flexible and efficient solution for portable encoders that work seamlessly with multiple LLMs. We release a training code at https://github.com/kyutai-labs/ARC-Encoder , fine-tuning dataset and pretrained models are available at https://huggingface.co/collections/kyutai/arc-encoders-68ee18787301407d60a57047 .

kyutai Kyutai
·
Oct 23, 2025 1

IASC: Interactive Agentic System for ConLangs

We present a system that uses LLMs as a tool in the development of Constructed Languages. The system is modular in that one first creates a target phonology for the language using an agentic approach that refines its output at each step with commentary feedback on its previous attempt. Next, a set of sentences is 'translated' from their English original into a morphosyntactic markup that reflects the word order and morphosyntactic feature specifications of the desired target language, with affixes represented as morphosyntactic feature bundles. From this translated corpus, a lexicon is constructed using the phonological model and the set of morphemes (stems and affixes) extracted from the 'translated' sentences. The system is then instructed to provide an orthography for the language, using an existing script such as Latin or Cyrillic. Finally, the system writes a brief grammatical handbook of the language. The system can also translate further sentences into the target language. Our goal is twofold. First, we hope that these tools will be fun to use for creating artificially constructed languages. Second, we are interested in exploring what LLMs 'know' about language-not what they know about any particular language or linguistic phenomenon, but how much they know about and understand language and linguistic concepts. As we shall see, there is a fairly wide gulf in capabilities both among different LLMs and among different linguistic specifications, with it being notably easier for systems to deal with more common patterns than rarer ones. An additional avenue that we explore is the application of our approach to translating from high-resource into low-resource languages. While the results so far are mostly negative, we provide some evidence that an improved version of the present system could afford some real gains in such tasks. https://github.com/SakanaAI/IASC

  • 2 authors
·
Oct 20, 2025

Learn Your Tokens: Word-Pooled Tokenization for Language Modeling

Language models typically tokenize text into subwords, using a deterministic, hand-engineered heuristic of combining characters into longer surface-level strings such as 'ing' or whole words. Recent literature has repeatedly shown the limitations of such a tokenization strategy, particularly for documents not written in English and for representing numbers. On the other extreme, byte/character-level language models are much less restricted but suffer from increased sequence description lengths and a subsequent quadratic expansion in self-attention computation. Recent attempts to compress and limit these context lengths with fixed size convolutions is helpful but completely ignores the word boundary. This paper considers an alternative 'learn your tokens' scheme which utilizes the word boundary to pool bytes/characters into word representations, which are fed to the primary language model, before again decoding individual characters/bytes per word in parallel. We find that our moderately expressive and moderately fast end-to-end tokenizer outperform by over 300% both subwords and byte/character models over the intrinsic language modeling metric of next-word prediction across datasets. It particularly outshines on rare words, outperforming by a factor of 30! We extensively study the language modeling setup for all three categories of tokenizers and theoretically analyze how our end-to-end models can also be a strong trade-off in efficiency and robustness.

  • 4 authors
·
Oct 17, 2023

Tokens with Meaning: A Hybrid Tokenization Approach for NLP

Tokenization plays a pivotal role in natural language processing (NLP), shaping how text is segmented and interpreted by language models. While subword methods such as Byte Pair Encoding (BPE) and WordPiece have been effective, they often struggle with morphologically rich and agglutinative languages because they rely on frequency rather than linguistic structure. We introduce a hybrid tokenization framework that combines rule-based morphological analysis with statistical subword segmentation. The method uses phonological normalization, root-affix dictionaries, and a novel algorithm that balances morpheme preservation with vocabulary efficiency. It assigns shared identifiers to phonologically variant affixes (e.g., -ler and -lar) and altered root forms (e.g., kitap vs. kitab{\i}), reducing redundancy while maintaining semantic integrity. Special tokens are added for whitespace and case, including an UPPERCASE marker to avoid vocabulary inflation from capitalization. BPE is integrated for out-of-vocabulary coverage without harming morphological coherence. On the TR-MMLU benchmark, the tokenizer achieves the highest Turkish Token Percentage (90.29\%) and Pure Token Percentage (85.8\%). Comparisons with tokenizers from LLaMA, Gemma, and GPT show more linguistically meaningful and coherent tokens. Although demonstrated on Turkish, the approach is language-independent and adaptable to other languages, offering a practical path toward more interpretable and effective multilingual NLP systems.

  • 7 authors
·
Aug 19, 2025 2

A Probabilistic Generative Grammar for Semantic Parsing

Domain-general semantic parsing is a long-standing goal in natural language processing, where the semantic parser is capable of robustly parsing sentences from domains outside of which it was trained. Current approaches largely rely on additional supervision from new domains in order to generalize to those domains. We present a generative model of natural language utterances and logical forms and demonstrate its application to semantic parsing. Our approach relies on domain-independent supervision to generalize to new domains. We derive and implement efficient algorithms for training, parsing, and sentence generation. The work relies on a novel application of hierarchical Dirichlet processes (HDPs) for structured prediction, which we also present in this manuscript. This manuscript is an excerpt of chapter 4 from the Ph.D. thesis of Saparov (2022), where the model plays a central role in a larger natural language understanding system. This manuscript provides a new simplified and more complete presentation of the work first introduced in Saparov, Saraswat, and Mitchell (2017). The description and proofs of correctness of the training algorithm, parsing algorithm, and sentence generation algorithm are much simplified in this new presentation. We also describe the novel application of hierarchical Dirichlet processes for structured prediction. In addition, we extend the earlier work with a new model of word morphology, which utilizes the comprehensive morphological data from Wiktionary.

  • 1 authors
·
Jun 20, 2016

Exploring Large Language Models for Classical Philology

Recent advances in NLP have led to the creation of powerful language models for many languages including Ancient Greek and Latin. While prior work on Classical languages unanimously uses BERT, in this work we create four language models for Ancient Greek that vary along two dimensions to study their versatility for tasks of interest for Classical languages: we explore (i) encoder-only and encoder-decoder architectures using RoBERTa and T5 as strong model types, and create for each of them (ii) a monolingual Ancient Greek and a multilingual instance that includes Latin and English. We evaluate all models on morphological and syntactic tasks, including lemmatization, which demonstrates the added value of T5's decoding abilities. We further define two probing tasks to investigate the knowledge acquired by models pre-trained on Classical texts. Our experiments provide the first benchmarking analysis of existing models of Ancient Greek. Results show that our models provide significant improvements over the SoTA. The systematic analysis of model types can inform future research in designing language models for Classical languages, including the development of novel generative tasks. We make all our models available as community resources, along with a large curated pre-training corpus for Ancient Greek, to support the creation of a larger, comparable model zoo for Classical Philology. Our models and resources are available at https://github.com/Heidelberg-NLP/ancient-language-models.

  • 2 authors
·
May 23, 2023

Machine Translation by Projecting Text into the Same Phonetic-Orthographic Space Using a Common Encoding

The use of subword embedding has proved to be a major innovation in Neural Machine Translation (NMT). It helps NMT to learn better context vectors for Low Resource Languages (LRLs) so as to predict the target words by better modelling the morphologies of the two languages and also the morphosyntax transfer. Even so, their performance for translation in Indian language to Indian language scenario is still not as good as for resource-rich languages. One reason for this is the relative morphological richness of Indian languages, while another is that most of them fall into the extremely low resource or zero-shot categories. Since most major Indian languages use Indic or Brahmi origin scripts, the text written in them is highly phonetic in nature and phonetically similar in terms of abstract letters and their arrangements. We use these characteristics of Indian languages and their scripts to propose an approach based on common multilingual Latin-based encodings (WX notation) that take advantage of language similarity while addressing the morphological complexity issue in NMT. These multilingual Latin-based encodings in NMT, together with Byte Pair Embedding (BPE) allow us to better exploit their phonetic and orthographic as well as lexical similarities to improve the translation quality by projecting different but similar languages on the same orthographic-phonetic character space. We verify the proposed approach by demonstrating experiments on similar language pairs (Gujarati-Hindi, Marathi-Hindi, Nepali-Hindi, Maithili-Hindi, Punjabi-Hindi, and Urdu-Hindi) under low resource conditions. The proposed approach shows an improvement in a majority of cases, in one case as much as ~10 BLEU points compared to baseline techniques for similar language pairs. We also get up to ~1 BLEU points improvement on distant and zero-shot language pairs.

  • 4 authors
·
May 21, 2023

Seq vs Seq: An Open Suite of Paired Encoders and Decoders

The large language model (LLM) community focuses almost exclusively on decoder-only language models, since they are easier to use for text generation. However, a large subset of the community still uses encoder-only models for tasks such as classification or retrieval. Previous work has attempted to compare these architectures, but is forced to make comparisons with models that have different numbers of parameters, training techniques, and datasets. We introduce the SOTA open-data Ettin suite of models: paired encoder-only and decoder-only models ranging from 17 million parameters to 1 billion, trained on up to 2 trillion tokens. Using the same recipe for both encoder-only and decoder-only models produces SOTA recipes in both categories for their respective sizes, beating ModernBERT as an encoder and Llama 3.2 and SmolLM2 as decoders. Like previous work, we find that encoder-only models excel at classification and retrieval tasks while decoders excel at generative tasks. However, we show that adapting a decoder model to encoder tasks (and vice versa) through continued training is subpar compared to using only the reverse objective (i.e. a 400M encoder outperforms a 1B decoder on MNLI, and vice versa for generative tasks). We open-source all artifacts of this study including training data, training order segmented by checkpoint, and 200+ checkpoints to allow future work to analyze or extend all aspects of training.

  • 6 authors
·
Jul 15, 2025 7

MrT5: Dynamic Token Merging for Efficient Byte-level Language Models

Models that rely on subword tokenization have significant drawbacks, such as sensitivity to character-level noise like spelling errors and inconsistent compression rates across different languages and scripts. While character- or byte-level models like ByT5 attempt to address these concerns, they have not gained widespread adoption -- processing raw byte streams without tokenization results in significantly longer sequence lengths, making training and inference inefficient. This work introduces MrT5 (MergeT5), a more efficient variant of ByT5 that integrates a token deletion mechanism in its encoder to dynamically shorten the input sequence length. After processing through a fixed number of encoder layers, a learnt delete gate determines which tokens are to be removed and which are to be retained for subsequent layers. MrT5 effectively ``merges'' critical information from deleted tokens into a more compact sequence, leveraging contextual information from the remaining tokens. In continued pre-training experiments, we find that MrT5 can achieve significant gains in inference runtime with minimal effect on performance. When trained on English text, MrT5 demonstrates the capability to transfer its deletion feature zero-shot across several languages, with significant additional improvements following multilingual training. Furthermore, MrT5 shows comparable accuracy to ByT5 on downstream evaluations such as XNLI and character-level tasks while reducing sequence lengths by up to 80%. Our approach presents a solution to the practical limitations of existing byte-level models.

  • 5 authors
·
Oct 28, 2024 1

Kronecker Embeddings: Byte-Level Structured Token Representations for Parameter-Efficient Language Models

Large language models route every input through a learned embedding table of shape |V| x d_model, consuming hundreds of millions to billions of trainable parameters at frontier scale. We introduce Kronecker Embeddings, a deterministic byte-level character-position factorization that replaces this table with a fixed encoder and a single learned projection, compatible with standard BPE tokenizers, eliminating 91--94% of input-side trainable parameters at frontier scale. We provide five contributions. First, a cross-model probe across six LMs (135M-671B parameters) shows trained input embeddings cluster typographic variants of the probe word far more than morphological relatives; Kronecker escapes this clustering at the embedding layer. Second, a controlled three-seed comparison on nanoGPT GPT-2 124M over 2.5B tokens of FineWeb-Edu shows Kronecker reaching 2.5 +- 0.2% lower validation loss than the BPE-tied baseline (gap 0.083 +- 0.007 nats, ~9% lower perplexity), needing ~1.43x fewer steps to reach BPE's converged loss. Third, a spelling-robustness probe over 110 clean/typo pairs shows Kronecker preserves the top-1 prediction on 55.5% of pairs vs. 47.3% for BPE (+8.2 pp) and lowers KL by 7.6%, winning or tying in 10 of 11 categories; a generation probe shows Kronecker echoes byte-novel strings and typos through generation where BPE forgets them. Fourth, BPE embedding norm drifts during training while Kronecker projection norm stays near 1.0, consistent with a stable representational target. Fifth, an on-the-fly runtime variant reconstructs embeddings from a 4.5 MB byte buffer rather than a 2.15 GB table at vocabulary 131,072, with 0.01--0.24% step-time overhead. Byte-level locality has a tradeoff: byte-similar but semantically distant pairs (compute/commute, nation/notion) cluster together, shifting disambiguation to early attention layers.

  • 1 authors
·
May 27

Leveraging Morphology for Historical Script Metrological Analysis

Advances in handwritten text recognition have enabled large-scale transcription of historical documents, but still provide limited access to interpretable visual measurements for paleography, the study of historical scripts. In this paper, our main insight is that morphological script analysis, in particular the capacity to learn character prototypes from line-level transcriptions, enables the definition of scalable, meaningful, and stable paleographic measurements. More precisely, we leverage a transformer-based detection architecture together with a prototype-based line reconstruction module to learn prototypical characters and their occurrence, deformation, and positioning. Our contributions are twofold. First, we introduce a deep architecture and learning methodology that enables efficient character modeling with only line-level transcription supervision, significantly improving over the Learnable Typewriter baseline and enabling accurate character bounding box prediction, unlocking its potential for paleographic measurements. Second, we introduce and demonstrate the paleographical relevance of automatic measurements enabled by our architecture for characters, bi-grams, and spaces between graphical units. For this demonstration, we extend the annotations of the codex Paris, BnF, fr. 2813, commissioned in the late fourteenth century by Charles V and copied by four hands, to 160 pages. We visualize our measurements over these pages, showing how they enable us not only to differentiate graphical profiles, but also to discover and analyze subtle variations. This case study outlines the scalability of our approach and its frugality in terms of required training data, since a single column of text is sufficient to compute our measurements on each of the 160 pages. Data and code are publicly available at: https://malamatenia.github.io/morphology4metrology-analysis.

Automatic Annotation of Ancient Greek Vowel Length

Prior work in Ancient Greek NLP relies on corpora that do not disambiguate the phonemic vowel length of alpha, iota, and ypsilon, together known as the dichrona. Depending on lexeme, morphology, sandhi, syntax, and conventions of period, genre, and verse form, each of these letters can represent either a long or a short vowel. Deciding and marking the correct length is known as "macronizing", a long-tail problem given the sheer mass of word forms and the context dependency of individual instances. No macronized corpus of Ancient Greek is publicly available at scale, so a stand-alone macronizer is needed. While previous work has shown how to build a static, corpus-bespoke vowel-length dictionary, the present paper constructs the first general-purpose macronizer for arbitrary Ancient Greek input. Given input carrying lemma, part-of-speech, and morphological annotation in the standard CoNLL-U format, a set of recursive modules lets less common word forms inherit markup from more common forms of the same lexical word. The macronizer's chief application is generating training data for machine learning: we show that a small character-level transformer trained on the macronizer's own output learns to generalize past the cases the rule-based system leaves unmarked, matching or exceeding its accuracy on a gold-standard, manually annotated benchmark of verse and prose. We also show that macronization can improve downstream prosodical NLP tasks like verse scansion.

  • 2 authors
·
Aug 2

Hierarchical Autoregressive Transformers: Combining Byte-~and Word-Level Processing for Robust, Adaptable Language Models

Tokenization is a fundamental step in natural language processing, breaking text into units that computational models can process. While learned subword tokenizers have become the de-facto standard, they present challenges such as large vocabularies, limited adaptability to new domains or languages, and sensitivity to spelling errors and variations. To overcome these limitations, we investigate a hierarchical architecture for autoregressive language modelling that combines character-level and word-level processing. It employs a lightweight character-level encoder to convert character sequences into word embeddings, which are then processed by a word-level backbone model and decoded back into characters via a compact character-level decoder. This method retains the sequence compression benefits of word-level tokenization without relying on a rigid, predefined vocabulary. We demonstrate, at scales up to 7 billion parameters, that hierarchical transformers match the downstream task performance of subword-tokenizer-based models while exhibiting significantly greater robustness to input perturbations. Additionally, during continued pretraining on an out-of-domain language, our model trains almost twice as fast, achieves superior performance on the target language, and retains more of its previously learned knowledge. Hierarchical transformers pave the way for NLP systems that are more robust, flexible, and generalizable across languages and domains.

  • 4 authors
·
Jan 17, 2025 4

Length-MAX Tokenizer for Language Models

We introduce a new tokenizer for language models that minimizes the average tokens per character, thereby reducing the number of tokens needed to represent text during training and to generate text during inference. Our method, which we refer to as the Length-MAX tokenizer, obtains its vocabulary by casting a length-weighted objective maximization as a graph partitioning problem and developing a greedy approximation algorithm. On FineWeb and diverse domains, it yields 14--18\% fewer tokens than Byte Pair Encoding (BPE) across vocabulary sizes from 10K to 50K, and the reduction is 13.0\% when the size is 64K. Training GPT-2 models at 124M, 355M, and 1.3B parameters from scratch with five runs each shows 18.5\%, 17.2\%, and 18.5\% fewer steps, respectively, to reach a fixed validation loss, and 13.7\%, 12.7\%, and 13.7\% lower inference latency, together with a 16\% throughput gain at 124M, while consistently improving on downstream tasks including reducing LAMBADA perplexity by 11.7\% and enhancing HellaSwag accuracy by 4.3\%. Moreover, the Length-MAX tokenizer achieves 99.62\% vocabulary coverage and the out-of-vocabulary rate remains low at 0.12\% on test sets. These results demonstrate that optimizing for average token length, rather than frequency alone, offers an effective approach to more efficient language modeling without sacrificing -- and often improving -- downstream performance. The tokenizer is compatible with production systems and reduces embedding and KV-cache memory by 18\% at inference.

  • 2 authors
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Aug 7

Tokenization Standards for Linguistic Integrity: Turkish as a Benchmark

Tokenization is a fundamental preprocessing step in NLP, directly impacting large language models' (LLMs) ability to capture syntactic, morphosyntactic, and semantic structures. This paper introduces a novel framework for systematically evaluating tokenization strategies, addressing challenges in morphologically rich and low-resource languages. Using a Turkish dataset of 6,200 multiple-choice questions from the Massive Multitask Language Understanding (MMLU) benchmark, the framework assesses tokenizers across five key metrics: vocabulary size, token count, processing time, language-specific token percentages (\%TR), and token purity. These metrics provide a structured approach to evaluating how well tokenizers preserve linguistic structures. While \%TR measures the proportion of valid words in the target language, \%Pure assesses the alignment of tokens with meaningful linguistic units, such as roots and valid morphemes, minimizing semantic fragmentation. The findings reveal that \%TR, introduced as a critical metric, exhibits a stronger correlation with downstream performance (e.g., MMLU scores) than token purity, emphasizing its role in improving model accuracy. Additionally, larger model parameters do not necessarily yield better tokenization quality or enhanced results, highlighting the importance of tailored tokenization strategies that prioritize linguistic alignment. This framework sets a new standard for developing robust tokenization methods optimized for morphologically complex and low-resource languages. Future work will refine morphological analysis, explore domain-specific customizations, and conduct cross-linguistic evaluations to further enhance tokenization practices.

  • 6 authors
·
Feb 10, 2025

Zero-Shot Tokenizer Transfer

Language models (LMs) are bound to their tokenizer, which maps raw text to a sequence of vocabulary items (tokens). This restricts their flexibility: for example, LMs trained primarily on English may still perform well in other natural and programming languages, but have vastly decreased efficiency due to their English-centric tokenizer. To mitigate this, we should be able to swap the original LM tokenizer with an arbitrary one, on the fly, without degrading performance. Hence, in this work we define a new problem: Zero-Shot Tokenizer Transfer (ZeTT). The challenge at the core of ZeTT is finding embeddings for the tokens in the vocabulary of the new tokenizer. Since prior heuristics for initializing embeddings often perform at chance level in a ZeTT setting, we propose a new solution: we train a hypernetwork taking a tokenizer as input and predicting the corresponding embeddings. We empirically demonstrate that the hypernetwork generalizes to new tokenizers both with encoder (e.g., XLM-R) and decoder LLMs (e.g., Mistral-7B). Our method comes close to the original models' performance in cross-lingual and coding tasks while markedly reducing the length of the tokenized sequence. We also find that the remaining gap can be quickly closed by continued training on less than 1B tokens. Finally, we show that a ZeTT hypernetwork trained for a base (L)LM can also be applied to fine-tuned variants without extra training. Overall, our results make substantial strides toward detaching LMs from their tokenizer.

  • 3 authors
·
May 13, 2024 3

End-to-End Context Compression at Scale

Long-context language model inference is bottlenecked by memory, as the KV cache grows with context length. Recent techniques to compress the KV cache fall short: they either degrade model quality substantially or require considerable time and compute to compress a single long prompt. Furthermore, many methods require the input to fit within the target model's context window, and are generally incompatible with modern production inference engines. Encoder-decoder compressors, which map a long token sequence to a shorter sequence of latent embeddings consumed by a decoder, are an appealing alternative in principle. However, existing approaches are not competitive with KV cache compression on the accuracy-efficiency frontier. In this work, we revisit encoder-decoder compression and close this gap. We first perform an architecture search, pre-training many variants from scratch to determine how best to design and train encoder-decoder compressors. Guided by our findings, we continually pre-train a family of 0.6B-encoder, 4B-decoder models on over 350B tokens each, at compression ratios of 1:4, 1:8, and 1:16. We introduce Latent Context Language Models (LCLMs), a family of compressors that improve the Pareto frontier across general-task performance, compression speed, and peak memory usage. We demonstrate that LCLMs serve as efficient backbones for long-horizon agents, letting the agent skim through a compressed long context and adaptively expand relevant segments on demand.

  • 15 authors
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Jun 7 2

GECTurk: Grammatical Error Correction and Detection Dataset for Turkish

Grammatical Error Detection and Correction (GEC) tools have proven useful for native speakers and second language learners. Developing such tools requires a large amount of parallel, annotated data, which is unavailable for most languages. Synthetic data generation is a common practice to overcome the scarcity of such data. However, it is not straightforward for morphologically rich languages like Turkish due to complex writing rules that require phonological, morphological, and syntactic information. In this work, we present a flexible and extensible synthetic data generation pipeline for Turkish covering more than 20 expert-curated grammar and spelling rules (a.k.a., writing rules) implemented through complex transformation functions. Using this pipeline, we derive 130,000 high-quality parallel sentences from professionally edited articles. Additionally, we create a more realistic test set by manually annotating a set of movie reviews. We implement three baselines formulating the task as i) neural machine translation, ii) sequence tagging, and iii) prefix tuning with a pretrained decoder-only model, achieving strong results. Furthermore, we perform exhaustive experiments on out-of-domain datasets to gain insights on the transferability and robustness of the proposed approaches. Our results suggest that our corpus, GECTurk, is high-quality and allows knowledge transfer for the out-of-domain setting. To encourage further research on Turkish GEC, we release our datasets, baseline models, and the synthetic data generation pipeline at https://github.com/GGLAB-KU/gecturk.

  • 4 authors
·
Sep 20, 2023 1

RankGen: Improving Text Generation with Large Ranking Models

Given an input sequence (or prefix), modern language models often assign high probabilities to output sequences that are repetitive, incoherent, or irrelevant to the prefix; as such, model-generated text also contains such artifacts. To address these issues we present RankGen, a 1.2B parameter encoder model for English that scores model generations given a prefix. RankGen can be flexibly incorporated as a scoring function in beam search and used to decode from any pretrained language model. We train RankGen using large-scale contrastive learning to map a prefix close to the ground-truth sequence that follows it and far away from two types of negatives: (1) random sequences from the same document as the prefix, and (2) sequences generated from a large language model conditioned on the prefix. Experiments across four different language models (345M-11B parameters) and two domains show that RankGen significantly outperforms decoding algorithms like nucleus, top-k, and typical sampling, as well as contrastive decoding and search, on both automatic metrics (85.0 vs 77.3 MAUVE over nucleus) as well as human evaluations with English writers (74.5% human preference over nucleus sampling). Analysis reveals that RankGen outputs are more relevant to the prefix and improve continuity and coherence compared to baselines. We release our model checkpoints, code, and human preference data with explanations to facilitate future research.

  • 4 authors
·
May 19, 2022

SindBERT, the Sailor: Charting the Seas of Turkish NLP

Transformer models have revolutionized NLP, yet many morphologically rich languages remain underrepresented in large-scale pre-training efforts. With SindBERT, we set out to chart the seas of Turkish NLP, providing the first large-scale RoBERTa-based encoder for Turkish. Trained from scratch on 312 GB of Turkish text (mC4, OSCAR23, Wikipedia), SindBERT is released in both base and large configurations, representing the first large-scale encoder-only language model available for Turkish. We evaluate SindBERT on part-of-speech tagging, named entity recognition, offensive language detection, and the TurBLiMP linguistic acceptability benchmark. Our results show that SindBERT performs competitively with existing Turkish and multilingual models, with the large variant achieving the best scores in two of four tasks but showing no consistent scaling advantage overall. This flat scaling trend, also observed for XLM-R and EuroBERT, suggests that current Turkish benchmarks may already be saturated. At the same time, comparisons with smaller but more curated models such as BERTurk highlight that corpus quality and diversity can outweigh sheer data volume. Taken together, SindBERT contributes both as an openly released resource for Turkish NLP and as an empirical case study on the limits of scaling and the central role of corpus composition in morphologically rich languages. The SindBERT models are released under the MIT license and made available in both fairseq and Huggingface formats.

SindBERT SindBERT
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Oct 24, 2025

Learning to Collocate Neural Modules for Image Captioning

We do not speak word by word from scratch; our brain quickly structures a pattern like sth do sth at someplace and then fill in the detailed descriptions. To render existing encoder-decoder image captioners such human-like reasoning, we propose a novel framework: learning to Collocate Neural Modules (CNM), to generate the `inner pattern' connecting visual encoder and language decoder. Unlike the widely-used neural module networks in visual Q\&A, where the language (ie, question) is fully observable, CNM for captioning is more challenging as the language is being generated and thus is partially observable. To this end, we make the following technical contributions for CNM training: 1) compact module design --- one for function words and three for visual content words (eg, noun, adjective, and verb), 2) soft module fusion and multi-step module execution, robustifying the visual reasoning in partial observation, 3) a linguistic loss for module controller being faithful to part-of-speech collocations (eg, adjective is before noun). Extensive experiments on the challenging MS-COCO image captioning benchmark validate the effectiveness of our CNM image captioner. In particular, CNM achieves a new state-of-the-art 127.9 CIDEr-D on Karpathy split and a single-model 126.0 c40 on the official server. CNM is also robust to few training samples, eg, by training only one sentence per image, CNM can halve the performance loss compared to a strong baseline.

  • 3 authors
·
Apr 18, 2019

A Family of LLMs Liberated from Static Vocabularies

Tokenization is a central component of natural language processing in current large language models (LLMs), enabling models to convert raw text into processable units. Although learned tokenizers are widely adopted, they exhibit notable limitations, including their large, fixed vocabulary sizes and poor adaptability to new domains or languages. We present a family of models with up to 70 billion parameters based on the hierarchical autoregressive transformer (HAT) architecture. In HAT, an encoder transformer aggregates bytes into word embeddings and then feeds them to the backbone, a classical autoregressive transformer. The outputs of the backbone are then cross-attended by the decoder and converted back into bytes. We show that we can reuse available pre-trained models by converting the Llama 3.1 8B and 70B models into the HAT architecture: Llama-3.1-8B-TFree-HAT and Llama-3.1-70B-TFree-HAT are byte-level models whose encoder and decoder are trained from scratch, but where we adapt the pre-trained Llama backbone, i.e., the transformer blocks with the embedding matrix and head removed, to handle word embeddings instead of the original tokens. We also provide a 7B HAT model, Llama-TFree-HAT-Pretrained, trained entirely from scratch on nearly 4 trillion words. The HAT architecture improves text compression by reducing the number of required sequence positions and enhances robustness to intra-word variations, e.g., spelling differences. Through pre-training, as well as subsequent supervised fine-tuning and direct preference optimization in English and German, we show strong proficiency in both languages, improving on the original Llama 3.1 in most benchmarks. We release our models (including 200 pre-training checkpoints) on Hugging Face.

  • 37 authors
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Mar 16

Vocab Diet: Reshaping the Vocabulary of LLMs via Vector Arithmetic

Large language models (LLMs) often encode word-form variation (e.g., walk vs. walked) as linear directions in the embedding space. However, standard tokenization algorithms treat such variants as distinct words with different vocabulary entries, quickly filling the size-capped token vocabulary with surface-form variation (e.g., walk, walking, Walk) at the expense of diversity and multilingual coverage. We show that many of these variations can be captured by transformation vectors: additive offsets that yield the appropriate word representation when applied to a base form embedding, in both the input and output spaces. Building on this, we propose a compact reshaping of the vocabulary: instead of assigning unique tokens to each surface form, we compose them from shared base form and transformation vectors (e.g., walked is walk+past tense). Our approach is lightweight, keeping the pretrained backbone frozen and only training small adaptation modules. We apply it across five languages and multiple LLMs in both pretraining and post-hoc adaptation, freeing 10-40% of vocabulary slots to be reallocated where tokenization is inefficient. Importantly, we do so while also expanding vocabulary coverage to out-of-vocabulary words, and with minimal impact on downstream performance. Our findings motivate a rethinking of vocabulary design, towards a representation that better matches the underlying structure of language and the practical needs of multilingual coverage.

  • 3 authors
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Apr 19