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Nov 5

Hierarchical Spatial Algorithms for High-Resolution Image Quantization and Feature Extraction

This study introduces a modular framework for spatial image processing, integrating grayscale quantization, color and brightness enhancement, image sharpening, bidirectional transformation pipelines, and geometric feature extraction. A stepwise intensity transformation quantizes grayscale images into eight discrete levels, producing a posterization effect that simplifies representation while preserving structural detail. Color enhancement is achieved via histogram equalization in both RGB and YCrCb color spaces, with the latter improving contrast while maintaining chrominance fidelity. Brightness adjustment is implemented through HSV value-channel manipulation, and image sharpening is performed using a 3 * 3 convolution kernel to enhance high-frequency details. A bidirectional transformation pipeline that integrates unsharp masking, gamma correction, and noise amplification achieved accuracy levels of 76.10% and 74.80% for the forward and reverse processes, respectively. Geometric feature extraction employed Canny edge detection, Hough-based line estimation (e.g., 51.50{\deg} for billiard cue alignment), Harris corner detection, and morphological window localization. Cue isolation further yielded 81.87\% similarity against ground truth images. Experimental evaluation across diverse datasets demonstrates robust and deterministic performance, highlighting its potential for real-time image analysis and computer vision.

  • 1 authors
·
Oct 9

A Large-scale Multi Domain Leukemia Dataset for the White Blood Cells Detection with Morphological Attributes for Explainability

Earlier diagnosis of Leukemia can save thousands of lives annually. The prognosis of leukemia is challenging without the morphological information of White Blood Cells (WBC) and relies on the accessibility of expensive microscopes and the availability of hematologists to analyze Peripheral Blood Samples (PBS). Deep Learning based methods can be employed to assist hematologists. However, these algorithms require a large amount of labeled data, which is not readily available. To overcome this limitation, we have acquired a realistic, generalized, and large dataset. To collect this comprehensive dataset for real-world applications, two microscopes from two different cost spectrums (high-cost HCM and low-cost LCM) are used for dataset capturing at three magnifications (100x, 40x, 10x) through different sensors (high-end camera for HCM, middle-level camera for LCM and mobile-phone camera for both). The high-sensor camera is 47 times more expensive than the middle-level camera and HCM is 17 times more expensive than LCM. In this collection, using HCM at high resolution (100x), experienced hematologists annotated 10.3k WBC types (14) and artifacts, having 55k morphological labels (Cell Size, Nuclear Chromatin, Nuclear Shape, etc.) from 2.4k images of several PBS leukemia patients. Later on, these annotations are transferred to other 2 magnifications of HCM, and 3 magnifications of LCM, and on each camera captured images. Along with the LeukemiaAttri dataset, we provide baselines over multiple object detectors and Unsupervised Domain Adaptation (UDA) strategies, along with morphological information-based attribute prediction. The dataset will be publicly available after publication to facilitate the research in this direction.

  • 6 authors
·
May 17, 2024

A skeletonization algorithm for gradient-based optimization

The skeleton of a digital image is a compact representation of its topology, geometry, and scale. It has utility in many computer vision applications, such as image description, segmentation, and registration. However, skeletonization has only seen limited use in contemporary deep learning solutions. Most existing skeletonization algorithms are not differentiable, making it impossible to integrate them with gradient-based optimization. Compatible algorithms based on morphological operations and neural networks have been proposed, but their results often deviate from the geometry and topology of the true medial axis. This work introduces the first three-dimensional skeletonization algorithm that is both compatible with gradient-based optimization and preserves an object's topology. Our method is exclusively based on matrix additions and multiplications, convolutional operations, basic non-linear functions, and sampling from a uniform probability distribution, allowing it to be easily implemented in any major deep learning library. In benchmarking experiments, we prove the advantages of our skeletonization algorithm compared to non-differentiable, morphological, and neural-network-based baselines. Finally, we demonstrate the utility of our algorithm by integrating it with two medical image processing applications that use gradient-based optimization: deep-learning-based blood vessel segmentation, and multimodal registration of the mandible in computed tomography and magnetic resonance images.

  • 9 authors
·
Sep 5, 2023

hist2RNA: An efficient deep learning architecture to predict gene expression from breast cancer histopathology images

Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC). However, in the clinic, molecular profiling is primarily used for ER+ breast cancer, which is costly, tissue destructive, requires specialized platforms and takes several weeks to obtain a result. Deep learning algorithms can effectively extract morphological patterns in digital histopathology images to predict molecular phenotypes quickly and cost-effectively. We propose a new, computationally efficient approach called hist2RNA inspired by bulk RNA-sequencing techniques to predict the expression of 138 genes (incorporated from six commercially available molecular profiling tests), including luminal PAM50 subtype, from hematoxylin and eosin (H&E) stained whole slide images (WSIs). The training phase involves the aggregation of extracted features for each patient from a pretrained model to predict gene expression at the patient level using annotated H&E images from The Cancer Genome Atlas (TCGA, n=335). We demonstrate successful gene prediction on a held-out test set (n = 160, corr = 0.82 across patients, corr = 0.29 across genes) and perform exploratory analysis on an external tissue microarray (TMA) dataset (n = 498) with known IHC and survival information. Our model is able to predict gene expression and luminal PAM50 subtype (Luminal A versus Luminal B) on the TMA dataset with prognostic significance for overall survival in univariate analysis (c-index = 0.56, hazard ratio = 2.16 (95% CI 1.12-3.06), p < 5 x 10-3), and independent significance in multivariate analysis incorporating standard clinicopathological variables (c-index = 0.65, hazard ratio = 1.85 (95% CI 1.30-2.68), p < 5 x 10-3).

  • 6 authors
·
Apr 10, 2023

Modeling with the Crowd: Optimizing the Human-Machine Partnership with Zooniverse

LSST and Euclid must address the daunting challenge of analyzing the unprecedented volumes of imaging and spectroscopic data that these next-generation instruments will generate. A promising approach to overcoming this challenge involves rapid, automatic image processing using appropriately trained Deep Learning (DL) algorithms. However, reliable application of DL requires large, accurately labeled samples of training data. Galaxy Zoo Express (GZX) is a recent experiment that simulated using Bayesian inference to dynamically aggregate binary responses provided by citizen scientists via the Zooniverse crowd-sourcing platform in real time. The GZX approach enables collaboration between human and machine classifiers and provides rapidly generated, reliably labeled datasets, thereby enabling online training of accurate machine classifiers. We present selected results from GZX and show how the Bayesian aggregation engine it uses can be extended to efficiently provide object-localization and bounding-box annotations of two-dimensional data with quantified reliability. DL algorithms that are trained using these annotations will facilitate numerous panchromatic data modeling tasks including morphological classification and substructure detection in direct imaging, as well as decontamination and emission line identification for slitless spectroscopy. Effectively combining the speed of modern computational analyses with the human capacity to extrapolate from few examples will be critical if the potential of forthcoming large-scale surveys is to be realized.

  • 5 authors
·
Mar 18, 2019

SoftZoo: A Soft Robot Co-design Benchmark For Locomotion In Diverse Environments

While significant research progress has been made in robot learning for control, unique challenges arise when simultaneously co-optimizing morphology. Existing work has typically been tailored for particular environments or representations. In order to more fully understand inherent design and performance tradeoffs and accelerate the development of new breeds of soft robots, a comprehensive virtual platform with well-established tasks, environments, and evaluation metrics is needed. In this work, we introduce SoftZoo, a soft robot co-design platform for locomotion in diverse environments. SoftZoo supports an extensive, naturally-inspired material set, including the ability to simulate environments such as flat ground, desert, wetland, clay, ice, snow, shallow water, and ocean. Further, it provides a variety of tasks relevant for soft robotics, including fast locomotion, agile turning, and path following, as well as differentiable design representations for morphology and control. Combined, these elements form a feature-rich platform for analysis and development of soft robot co-design algorithms. We benchmark prevalent representations and co-design algorithms, and shed light on 1) the interplay between environment, morphology, and behavior; 2) the importance of design space representations; 3) the ambiguity in muscle formation and controller synthesis; and 4) the value of differentiable physics. We envision that SoftZoo will serve as a standard platform and template an approach toward the development of novel representations and algorithms for co-designing soft robots' behavioral and morphological intelligence.

  • 8 authors
·
Mar 16, 2023

Probabilistic road classification in historical maps using synthetic data and deep learning

Historical maps are invaluable for analyzing long-term changes in transportation and spatial development, offering a rich source of data for evolutionary studies. However, digitizing and classifying road networks from these maps is often expensive and time-consuming, limiting their widespread use. Recent advancements in deep learning have made automatic road extraction from historical maps feasible, yet these methods typically require large amounts of labeled training data. To address this challenge, we introduce a novel framework that integrates deep learning with geoinformation, computer-based painting, and image processing methodologies. This framework enables the extraction and classification of roads from historical maps using only road geometries without needing road class labels for training. The process begins with training of a binary segmentation model to extract road geometries, followed by morphological operations, skeletonization, vectorization, and filtering algorithms. Synthetic training data is then generated by a painting function that artificially re-paints road segments using predefined symbology for road classes. Using this synthetic data, a deep ensemble is trained to generate pixel-wise probabilities for road classes to mitigate distribution shift. These predictions are then discretized along the extracted road geometries. Subsequently, further processing is employed to classify entire roads, enabling the identification of potential changes in road classes and resulting in a labeled road class dataset. Our method achieved completeness and correctness scores of over 94% and 92%, respectively, for road class 2, the most prevalent class in the two Siegfried Map sheets from Switzerland used for testing. This research offers a powerful tool for urban planning and transportation decision-making by efficiently extracting and classifying roads from historical maps.

  • 6 authors
·
Oct 3, 2024

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

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

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 2

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

Rotation-invariant convolutional neural networks for galaxy morphology prediction

Measuring the morphological parameters of galaxies is a key requirement for studying their formation and evolution. Surveys such as the Sloan Digital Sky Survey (SDSS) have resulted in the availability of very large collections of images, which have permitted population-wide analyses of galaxy morphology. Morphological analysis has traditionally been carried out mostly via visual inspection by trained experts, which is time-consuming and does not scale to large (gtrsim10^4) numbers of images. Although attempts have been made to build automated classification systems, these have not been able to achieve the desired level of accuracy. The Galaxy Zoo project successfully applied a crowdsourcing strategy, inviting online users to classify images by answering a series of questions. Unfortunately, even this approach does not scale well enough to keep up with the increasing availability of galaxy images. We present a deep neural network model for galaxy morphology classification which exploits translational and rotational symmetry. It was developed in the context of the Galaxy Challenge, an international competition to build the best model for morphology classification based on annotated images from the Galaxy Zoo project. For images with high agreement among the Galaxy Zoo participants, our model is able to reproduce their consensus with near-perfect accuracy (> 99%) for most questions. Confident model predictions are highly accurate, which makes the model suitable for filtering large collections of images and forwarding challenging images to experts for manual annotation. This approach greatly reduces the experts' workload without affecting accuracy. The application of these algorithms to larger sets of training data will be critical for analysing results from future surveys such as the LSST.

  • 3 authors
·
Mar 24, 2015

Deep Learning Applied to Image and Text Matching

The ability to describe images with natural language sentences is the hallmark for image and language understanding. Such a system has wide ranging applications such as annotating images and using natural sentences to search for images.In this project we focus on the task of bidirectional image retrieval: such asystem is capable of retrieving an image based on a sentence (image search) andretrieve sentence based on an image query (image annotation). We present asystem based on a global ranking objective function which uses a combinationof convolutional neural networks (CNN) and multi layer perceptrons (MLP).It takes a pair of image and sentence and processes them in different channels,finally embedding it into a common multimodal vector space. These embeddingsencode abstract semantic information about the two inputs and can be comparedusing traditional information retrieval approaches. For each such pair, the modelreturns a score which is interpretted as a similarity metric. If this score is high,the image and sentence are likely to convey similar meaning, and if the score is low then they are likely not to. The visual input is modeled via deep convolutional neural network. On theother hand we explore three models for the textual module. The first one isbag of words with an MLP. The second one uses n-grams (bigram, trigrams,and a combination of trigram & skip-grams) with an MLP. The third is morespecialized deep network specific for modeling variable length sequences (SSE).We report comparable performance to recent work in the field, even though ouroverall model is simpler. We also show that the training time choice of how wecan generate our negative samples has a significant impact on performance, and can be used to specialize the bi-directional system in one particular task.

  • 1 authors
·
Sep 14, 2015

BEIR-PL: Zero Shot Information Retrieval Benchmark for the Polish Language

The BEIR dataset is a large, heterogeneous benchmark for Information Retrieval (IR) in zero-shot settings, garnering considerable attention within the research community. However, BEIR and analogous datasets are predominantly restricted to the English language. Our objective is to establish extensive large-scale resources for IR in the Polish language, thereby advancing the research in this NLP area. In this work, inspired by mMARCO and Mr.~TyDi datasets, we translated all accessible open IR datasets into Polish, and we introduced the BEIR-PL benchmark -- a new benchmark which comprises 13 datasets, facilitating further development, training and evaluation of modern Polish language models for IR tasks. We executed an evaluation and comparison of numerous IR models on the newly introduced BEIR-PL benchmark. Furthermore, we publish pre-trained open IR models for Polish language,d marking a pioneering development in this field. Additionally, the evaluation revealed that BM25 achieved significantly lower scores for Polish than for English, which can be attributed to high inflection and intricate morphological structure of the Polish language. Finally, we trained various re-ranking models to enhance the BM25 retrieval, and we compared their performance to identify their unique characteristic features. To ensure accurate model comparisons, it is necessary to scrutinise individual results rather than to average across the entire benchmark. Thus, we thoroughly analysed the outcomes of IR models in relation to each individual data subset encompassed by the BEIR benchmark. The benchmark data is available at URL {\bf https://huggingface.co/clarin-knext}.

  • 5 authors
·
May 31, 2023

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

Extracting Mathematical Concepts with Large Language Models

We extract mathematical concepts from mathematical text using generative large language models (LLMs) like ChatGPT, contributing to the field of automatic term extraction (ATE) and mathematical text processing, and also to the study of LLMs themselves. Our work builds on that of others in that we aim for automatic extraction of terms (keywords) in one mathematical field, category theory, using as a corpus the 755 abstracts from a snapshot of the online journal "Theory and Applications of Categories", circa 2020. Where our study diverges from previous work is in (1) providing a more thorough analysis of what makes mathematical term extraction a difficult problem to begin with; (2) paying close attention to inter-annotator disagreements; (3) providing a set of guidelines which both human and machine annotators could use to standardize the extraction process; (4) introducing a new annotation tool to help humans with ATE, applicable to any mathematical field and even beyond mathematics; (5) using prompts to ChatGPT as part of the extraction process, and proposing best practices for such prompts; and (6) raising the question of whether ChatGPT could be used as an annotator on the same level as human experts. Our overall findings are that the matter of mathematical ATE is an interesting field which can benefit from participation by LLMs, but LLMs themselves cannot at this time surpass human performance on it.

  • 4 authors
·
Aug 29, 2023

Linguistic Structure Induction from Language Models

Linear sequences of words are implicitly represented in our brains by hierarchical structures that organize the composition of words in sentences. Linguists formalize different frameworks to model this hierarchy; two of the most common syntactic frameworks are Constituency and Dependency. Constituency represents sentences as nested groups of phrases, while dependency represents a sentence by assigning relations between its words. Recently, the pursuit of intelligent machines has produced Language Models (LMs) capable of solving many language tasks with a human-level performance. Many studies now question whether LMs implicitly represent syntactic hierarchies. This thesis focuses on producing constituency and dependency structures from LMs in an unsupervised setting. I review the critical methods in this field and highlight a line of work that utilizes a numerical representation for binary constituency trees (Syntactic Distance). I present a detailed study on StructFormer (SF) (Shen et al., 2021), which retrofits a transformer encoder architecture with a parser network to produce constituency and dependency structures. I present six experiments to analyze and address this field's challenges; experiments include investigating the effect of repositioning the parser network within the SF architecture, evaluating subword-based induced trees, and benchmarking the models developed in the thesis experiments on linguistic tasks. Models benchmarking is performed by participating in the BabyLM challenge, published at CoNLL 2023 (Momen et al., 2023). The results of this thesis encourage further development in the direction of retrofitting transformer-based models to induce syntactic structures, supported by the acceptable performance of SF in different experimental settings and the observed limitations that require innovative solutions to advance the state of syntactic structure induction.

  • 1 authors
·
Mar 11, 2024

U-DIADS-Bib: a full and few-shot pixel-precise dataset for document layout analysis of ancient manuscripts

Document Layout Analysis, which is the task of identifying different semantic regions inside of a document page, is a subject of great interest for both computer scientists and humanities scholars as it represents a fundamental step towards further analysis tasks for the former and a powerful tool to improve and facilitate the study of the documents for the latter. However, many of the works currently present in the literature, especially when it comes to the available datasets, fail to meet the needs of both worlds and, in particular, tend to lean towards the needs and common practices of the computer science side, leading to resources that are not representative of the humanities real needs. For this reason, the present paper introduces U-DIADS-Bib, a novel, pixel-precise, non-overlapping and noiseless document layout analysis dataset developed in close collaboration between specialists in the fields of computer vision and humanities. Furthermore, we propose a novel, computer-aided, segmentation pipeline in order to alleviate the burden represented by the time-consuming process of manual annotation, necessary for the generation of the ground truth segmentation maps. Finally, we present a standardized few-shot version of the dataset (U-DIADS-BibFS), with the aim of encouraging the development of models and solutions able to address this task with as few samples as possible, which would allow for more effective use in a real-world scenario, where collecting a large number of segmentations is not always feasible.

  • 6 authors
·
Jan 16, 2024

Leveraging Corpus Metadata to Detect Template-based Translation: An Exploratory Case Study of the Egyptian Arabic Wikipedia Edition

Wikipedia articles (content pages) are commonly used corpora in Natural Language Processing (NLP) research, especially in low-resource languages other than English. Yet, a few research studies have studied the three Arabic Wikipedia editions, Arabic Wikipedia (AR), Egyptian Arabic Wikipedia (ARZ), and Moroccan Arabic Wikipedia (ARY), and documented issues in the Egyptian Arabic Wikipedia edition regarding the massive automatic creation of its articles using template-based translation from English to Arabic without human involvement, overwhelming the Egyptian Arabic Wikipedia with articles that do not only have low-quality content but also with articles that do not represent the Egyptian people, their culture, and their dialect. In this paper, we aim to mitigate the problem of template translation that occurred in the Egyptian Arabic Wikipedia by identifying these template-translated articles and their characteristics through exploratory analysis and building automatic detection systems. We first explore the content of the three Arabic Wikipedia editions in terms of density, quality, and human contributions and utilize the resulting insights to build multivariate machine learning classifiers leveraging articles' metadata to detect the template-translated articles automatically. We then publicly deploy and host the best-performing classifier, XGBoost, as an online application called EGYPTIAN WIKIPEDIA SCANNER and release the extracted, filtered, and labeled datasets to the research community to benefit from our datasets and the online, web-based detection system.

  • 5 authors
·
Mar 31, 2024

A standardized Project Gutenberg corpus for statistical analysis of natural language and quantitative linguistics

The use of Project Gutenberg (PG) as a text corpus has been extremely popular in statistical analysis of language for more than 25 years. However, in contrast to other major linguistic datasets of similar importance, no consensual full version of PG exists to date. In fact, most PG studies so far either consider only a small number of manually selected books, leading to potential biased subsets, or employ vastly different pre-processing strategies (often specified in insufficient details), raising concerns regarding the reproducibility of published results. In order to address these shortcomings, here we present the Standardized Project Gutenberg Corpus (SPGC), an open science approach to a curated version of the complete PG data containing more than 50,000 books and more than 3 times 10^9 word-tokens. Using different sources of annotated metadata, we not only provide a broad characterization of the content of PG, but also show different examples highlighting the potential of SPGC for investigating language variability across time, subjects, and authors. We publish our methodology in detail, the code to download and process the data, as well as the obtained corpus itself on 3 different levels of granularity (raw text, timeseries of word tokens, and counts of words). In this way, we provide a reproducible, pre-processed, full-size version of Project Gutenberg as a new scientific resource for corpus linguistics, natural language processing, and information retrieval.

  • 2 authors
·
Dec 19, 2018

Syllabification of the Divine Comedy

We provide a syllabification algorithm for the Divine Comedy using techniques from probabilistic and constraint programming. We particularly focus on the synalephe, addressed in terms of the "propensity" of a word to take part in a synalephe with adjacent words. We jointly provide an online vocabulary containing, for each word, information about its syllabification, the location of the tonic accent, and the aforementioned synalephe propensity, on the left and right sides. The algorithm is intrinsically nondeterministic, producing different possible syllabifications for each verse, with different likelihoods; metric constraints relative to accents on the 10th, 4th and 6th syllables are used to further reduce the solution space. The most likely syllabification is hence returned as output. We believe that this work could be a major milestone for a lot of different investigations. From the point of view of digital humanities it opens new perspectives on computer assisted analysis of digital sources, comprising automated detection of anomalous and problematic cases, metric clustering of verses and their categorization, or more foundational investigations addressing e.g. the phonetic roles of consonants and vowels. From the point of view of text processing and deep learning, information about syllabification and the location of accents opens a wide range of exciting perspectives, from the possibility of automatic learning syllabification of words and verses, to the improvement of generative models, aware of metric issues, and more respectful of the expected musicality.

  • 2 authors
·
Oct 26, 2020

Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing

This paper surveys and organizes research works in a new paradigm in natural language processing, which we dub "prompt-based learning". Unlike traditional supervised learning, which trains a model to take in an input x and predict an output y as P(y|x), prompt-based learning is based on language models that model the probability of text directly. To use these models to perform prediction tasks, the original input x is modified using a template into a textual string prompt x' that has some unfilled slots, and then the language model is used to probabilistically fill the unfilled information to obtain a final string x, from which the final output y can be derived. This framework is powerful and attractive for a number of reasons: it allows the language model to be pre-trained on massive amounts of raw text, and by defining a new prompting function the model is able to perform few-shot or even zero-shot learning, adapting to new scenarios with few or no labeled data. In this paper we introduce the basics of this promising paradigm, describe a unified set of mathematical notations that can cover a wide variety of existing work, and organize existing work along several dimensions, e.g.the choice of pre-trained models, prompts, and tuning strategies. To make the field more accessible to interested beginners, we not only make a systematic review of existing works and a highly structured typology of prompt-based concepts, but also release other resources, e.g., a website http://pretrain.nlpedia.ai/ including constantly-updated survey, and paperlist.

  • 6 authors
·
Jul 28, 2021

Where's the Point? Self-Supervised Multilingual Punctuation-Agnostic Sentence Segmentation

Many NLP pipelines split text into sentences as one of the crucial preprocessing steps. Prior sentence segmentation tools either rely on punctuation or require a considerable amount of sentence-segmented training data: both central assumptions might fail when porting sentence segmenters to diverse languages on a massive scale. In this work, we thus introduce a multilingual punctuation-agnostic sentence segmentation method, currently covering 85 languages, trained in a self-supervised fashion on unsegmented text, by making use of newline characters which implicitly perform segmentation into paragraphs. We further propose an approach that adapts our method to the segmentation in a given corpus by using only a small number (64-256) of sentence-segmented examples. The main results indicate that our method outperforms all the prior best sentence-segmentation tools by an average of 6.1% F1 points. Furthermore, we demonstrate that proper sentence segmentation has a point: the use of a (powerful) sentence segmenter makes a considerable difference for a downstream application such as machine translation (MT). By using our method to match sentence segmentation to the segmentation used during training of MT models, we achieve an average improvement of 2.3 BLEU points over the best prior segmentation tool, as well as massive gains over a trivial segmenter that splits text into equally sized blocks.

  • 3 authors
·
May 30, 2023

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

Alloprof: a new French question-answer education dataset and its use in an information retrieval case study

Teachers and students are increasingly relying on online learning resources to supplement the ones provided in school. This increase in the breadth and depth of available resources is a great thing for students, but only provided they are able to find answers to their queries. Question-answering and information retrieval systems have benefited from public datasets to train and evaluate their algorithms, but most of these datasets have been in English text written by and for adults. We introduce a new public French question-answering dataset collected from Alloprof, a Quebec-based primary and high-school help website, containing 29 349 questions and their explanations in a variety of school subjects from 10 368 students, with more than half of the explanations containing links to other questions or some of the 2 596 reference pages on the website. We also present a case study of this dataset in an information retrieval task. This dataset was collected on the Alloprof public forum, with all questions verified for their appropriateness and the explanations verified both for their appropriateness and their relevance to the question. To predict relevant documents, architectures using pre-trained BERT models were fine-tuned and evaluated. This dataset will allow researchers to develop question-answering, information retrieval and other algorithms specifically for the French speaking education context. Furthermore, the range of language proficiency, images, mathematical symbols and spelling mistakes will necessitate algorithms based on a multimodal comprehension. The case study we present as a baseline shows an approach that relies on recent techniques provides an acceptable performance level, but more work is necessary before it can reliably be used and trusted in a production setting.

  • 3 authors
·
Feb 10, 2023

Precise Legal Sentence Boundary Detection for Retrieval at Scale: NUPunkt and CharBoundary

We present NUPunkt and CharBoundary, two sentence boundary detection libraries optimized for high-precision, high-throughput processing of legal text in large-scale applications such as due diligence, e-discovery, and legal research. These libraries address the critical challenges posed by legal documents containing specialized citations, abbreviations, and complex sentence structures that confound general-purpose sentence boundary detectors. Our experimental evaluation on five diverse legal datasets comprising over 25,000 documents and 197,000 annotated sentence boundaries demonstrates that NUPunkt achieves 91.1% precision while processing 10 million characters per second with modest memory requirements (432 MB). CharBoundary models offer balanced and adjustable precision-recall tradeoffs, with the large model achieving the highest F1 score (0.782) among all tested methods. Notably, NUPunkt provides a 29-32% precision improvement over general-purpose tools while maintaining exceptional throughput, processing multi-million document collections in minutes rather than hours. Both libraries run efficiently on standard CPU hardware without requiring specialized accelerators. NUPunkt is implemented in pure Python with zero external dependencies, while CharBoundary relies only on scikit-learn and optional ONNX runtime integration for optimized performance. Both libraries are available under the MIT license, can be installed via PyPI, and can be interactively tested at https://sentences.aleainstitute.ai/. These libraries address critical precision issues in retrieval-augmented generation systems by preserving coherent legal concepts across sentences, where each percentage improvement in precision yields exponentially greater reductions in context fragmentation, creating cascading benefits throughout retrieval pipelines and significantly enhancing downstream reasoning quality.

  • 3 authors
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Apr 5

NERetrieve: Dataset for Next Generation Named Entity Recognition and Retrieval

Recognizing entities in texts is a central need in many information-seeking scenarios, and indeed, Named Entity Recognition (NER) is arguably one of the most successful examples of a widely adopted NLP task and corresponding NLP technology. Recent advances in large language models (LLMs) appear to provide effective solutions (also) for NER tasks that were traditionally handled with dedicated models, often matching or surpassing the abilities of the dedicated models. Should NER be considered a solved problem? We argue to the contrary: the capabilities provided by LLMs are not the end of NER research, but rather an exciting beginning. They allow taking NER to the next level, tackling increasingly more useful, and increasingly more challenging, variants. We present three variants of the NER task, together with a dataset to support them. The first is a move towards more fine-grained -- and intersectional -- entity types. The second is a move towards zero-shot recognition and extraction of these fine-grained types based on entity-type labels. The third, and most challenging, is the move from the recognition setup to a novel retrieval setup, where the query is a zero-shot entity type, and the expected result is all the sentences from a large, pre-indexed corpus that contain entities of these types, and their corresponding spans. We show that all of these are far from being solved. We provide a large, silver-annotated corpus of 4 million paragraphs covering 500 entity types, to facilitate research towards all of these three goals.

  • 4 authors
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Oct 22, 2023 6

A Reliable Knowledge Processing Framework for Combustion Science using Foundation Models

This research explores the integration of large language models (LLMs) into scientific data assimilation, focusing on combustion science as a case study. Leveraging foundational models integrated with Retrieval-Augmented Generation (RAG) framework, the study introduces an approach to process diverse combustion research data, spanning experimental studies, simulations, and literature. The multifaceted nature of combustion research emphasizes the critical role of knowledge processing in navigating and extracting valuable information from a vast and diverse pool of sources. The developed approach minimizes computational and economic expenses while optimizing data privacy and accuracy. It incorporates prompt engineering and offline open-source LLMs, offering user autonomy in selecting base models. The study provides a thorough examination of text segmentation strategies, conducts comparative studies between LLMs, and explores various optimized prompts to demonstrate the effectiveness of the framework. By incorporating an external database, the framework outperforms a conventional LLM in generating accurate responses and constructing robust arguments. Additionally, the study delves into the investigation of optimized prompt templates for the purpose of efficient extraction of scientific literature. The research addresses concerns related to hallucinations and false research articles by introducing a custom workflow developed with a detection algorithm to filter out inaccuracies. Despite identified areas for improvement, the framework consistently delivers accurate domain-specific responses with minimal human oversight. The prompt-agnostic approach introduced holds promise for future deliberations. The study underscores the significance of integrating LLMs and knowledge processing techniques in scientific research, providing a foundation for advancements in data assimilation and utilization.

  • 2 authors
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Dec 31, 2023

MarkushGrapher: Joint Visual and Textual Recognition of Markush Structures

The automated analysis of chemical literature holds promise to accelerate discovery in fields such as material science and drug development. In particular, search capabilities for chemical structures and Markush structures (chemical structure templates) within patent documents are valuable, e.g., for prior-art search. Advancements have been made in the automatic extraction of chemical structures from text and images, yet the Markush structures remain largely unexplored due to their complex multi-modal nature. In this work, we present MarkushGrapher, a multi-modal approach for recognizing Markush structures in documents. Our method jointly encodes text, image, and layout information through a Vision-Text-Layout encoder and an Optical Chemical Structure Recognition vision encoder. These representations are merged and used to auto-regressively generate a sequential graph representation of the Markush structure along with a table defining its variable groups. To overcome the lack of real-world training data, we propose a synthetic data generation pipeline that produces a wide range of realistic Markush structures. Additionally, we present M2S, the first annotated benchmark of real-world Markush structures, to advance research on this challenging task. Extensive experiments demonstrate that our approach outperforms state-of-the-art chemistry-specific and general-purpose vision-language models in most evaluation settings. Code, models, and datasets will be available.

  • 7 authors
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Mar 20

Segment Any Text: A Universal Approach for Robust, Efficient and Adaptable Sentence Segmentation

Segmenting text into sentences plays an early and crucial role in many NLP systems. This is commonly achieved by using rule-based or statistical methods relying on lexical features such as punctuation. Although some recent works no longer exclusively rely on punctuation, we find that no prior method achieves all of (i) robustness to missing punctuation, (ii) effective adaptability to new domains, and (iii) high efficiency. We introduce a new model - Segment any Text (SaT) - to solve this problem. To enhance robustness, we propose a new pretraining scheme that ensures less reliance on punctuation. To address adaptability, we introduce an extra stage of parameter-efficient fine-tuning, establishing state-of-the-art performance in distinct domains such as verses from lyrics and legal documents. Along the way, we introduce architectural modifications that result in a threefold gain in speed over the previous state of the art and solve spurious reliance on context far in the future. Finally, we introduce a variant of our model with fine-tuning on a diverse, multilingual mixture of sentence-segmented data, acting as a drop-in replacement and enhancement for existing segmentation tools. Overall, our contributions provide a universal approach for segmenting any text. Our method outperforms all baselines - including strong LLMs - across 8 corpora spanning diverse domains and languages, especially in practically relevant situations where text is poorly formatted. Our models and code, including documentation, are available at https://huggingface.co/segment-any-text under the MIT license.

  • 5 authors
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Jun 24, 2024 3

Samanantar: The Largest Publicly Available Parallel Corpora Collection for 11 Indic Languages

We present Samanantar, the largest publicly available parallel corpora collection for Indic languages. The collection contains a total of 49.7 million sentence pairs between English and 11 Indic languages (from two language families). Specifically, we compile 12.4 million sentence pairs from existing, publicly-available parallel corpora, and additionally mine 37.4 million sentence pairs from the web, resulting in a 4x increase. We mine the parallel sentences from the web by combining many corpora, tools, and methods: (a) web-crawled monolingual corpora, (b) document OCR for extracting sentences from scanned documents, (c) multilingual representation models for aligning sentences, and (d) approximate nearest neighbor search for searching in a large collection of sentences. Human evaluation of samples from the newly mined corpora validate the high quality of the parallel sentences across 11 languages. Further, we extract 83.4 million sentence pairs between all 55 Indic language pairs from the English-centric parallel corpus using English as the pivot language. We trained multilingual NMT models spanning all these languages on Samanantar, which outperform existing models and baselines on publicly available benchmarks, such as FLORES, establishing the utility of Samanantar. Our data and models are available publicly at https://indicnlp.ai4bharat.org/samanantar/ and we hope they will help advance research in NMT and multilingual NLP for Indic languages.

  • 18 authors
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Apr 12, 2021

Machine Reading Comprehension: The Role of Contextualized Language Models and Beyond

Machine reading comprehension (MRC) aims to teach machines to read and comprehend human languages, which is a long-standing goal of natural language processing (NLP). With the burst of deep neural networks and the evolution of contextualized language models (CLMs), the research of MRC has experienced two significant breakthroughs. MRC and CLM, as a phenomenon, have a great impact on the NLP community. In this survey, we provide a comprehensive and comparative review on MRC covering overall research topics about 1) the origin and development of MRC and CLM, with a particular focus on the role of CLMs; 2) the impact of MRC and CLM to the NLP community; 3) the definition, datasets, and evaluation of MRC; 4) general MRC architecture and technical methods in the view of two-stage Encoder-Decoder solving architecture from the insights of the cognitive process of humans; 5) previous highlights, emerging topics, and our empirical analysis, among which we especially focus on what works in different periods of MRC researches. We propose a full-view categorization and new taxonomies on these topics. The primary views we have arrived at are that 1) MRC boosts the progress from language processing to understanding; 2) the rapid improvement of MRC systems greatly benefits from the development of CLMs; 3) the theme of MRC is gradually moving from shallow text matching to cognitive reasoning.

  • 3 authors
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May 13, 2020

ScanBank: A Benchmark Dataset for Figure Extraction from Scanned Electronic Theses and Dissertations

We focus on electronic theses and dissertations (ETDs), aiming to improve access and expand their utility, since more than 6 million are publicly available, and they constitute an important corpus to aid research and education across disciplines. The corpus is growing as new born-digital documents are included, and since millions of older theses and dissertations have been converted to digital form to be disseminated electronically in institutional repositories. In ETDs, as with other scholarly works, figures and tables can communicate a large amount of information in a concise way. Although methods have been proposed for extracting figures and tables from born-digital PDFs, they do not work well with scanned ETDs. Considering this problem, our assessment of state-of-the-art figure extraction systems is that the reason they do not function well on scanned PDFs is that they have only been trained on born-digital documents. To address this limitation, we present ScanBank, a new dataset containing 10 thousand scanned page images, manually labeled by humans as to the presence of the 3.3 thousand figures or tables found therein. We use this dataset to train a deep neural network model based on YOLOv5 to accurately extract figures and tables from scanned ETDs. We pose and answer important research questions aimed at finding better methods for figure extraction from scanned documents. One of those concerns the value for training, of data augmentation techniques applied to born-digital documents which are used to train models better suited for figure extraction from scanned documents. To the best of our knowledge, ScanBank is the first manually annotated dataset for figure and table extraction for scanned ETDs. A YOLOv5-based model, trained on ScanBank, outperforms existing comparable open-source and freely available baseline methods by a considerable margin.

  • 4 authors
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Jun 23, 2021

T2Ranking: A large-scale Chinese Benchmark for Passage Ranking

Passage ranking involves two stages: passage retrieval and passage re-ranking, which are important and challenging topics for both academics and industries in the area of Information Retrieval (IR). However, the commonly-used datasets for passage ranking usually focus on the English language. For non-English scenarios, such as Chinese, the existing datasets are limited in terms of data scale, fine-grained relevance annotation and false negative issues. To address this problem, we introduce T2Ranking, a large-scale Chinese benchmark for passage ranking. T2Ranking comprises more than 300K queries and over 2M unique passages from real-world search engines. Expert annotators are recruited to provide 4-level graded relevance scores (fine-grained) for query-passage pairs instead of binary relevance judgments (coarse-grained). To ease the false negative issues, more passages with higher diversities are considered when performing relevance annotations, especially in the test set, to ensure a more accurate evaluation. Apart from the textual query and passage data, other auxiliary resources are also provided, such as query types and XML files of documents which passages are generated from, to facilitate further studies. To evaluate the dataset, commonly used ranking models are implemented and tested on T2Ranking as baselines. The experimental results show that T2Ranking is challenging and there is still scope for improvement. The full data and all codes are available at https://github.com/THUIR/T2Ranking/

  • 11 authors
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Apr 7, 2023

Can LLMs Really Learn to Translate a Low-Resource Language from One Grammar Book?

Extremely low-resource (XLR) languages lack substantial corpora for training NLP models, motivating the use of all available resources such as dictionaries and grammar books. Machine Translation from One Book (Tanzer et al., 2024) suggests that prompting long-context LLMs with one grammar book enables English-Kalamang translation, an XLR language unseen by LLMs - a noteworthy case of linguistics helping an NLP task. We investigate the source of this translation ability, finding almost all improvements stem from the book's parallel examples rather than its grammatical explanations. We find similar results for Nepali and Guarani, seen low-resource languages, and we achieve performance comparable to an LLM with a grammar book by simply fine-tuning an encoder-decoder translation model. We then investigate where grammar books help by testing two linguistic tasks, grammaticality judgment and gloss prediction, and we explore what kind of grammatical knowledge helps by introducing a typological feature prompt that achieves leading results on these more relevant tasks. We thus emphasise the importance of task-appropriate data for XLR languages: parallel examples for translation, and grammatical data for linguistic tasks. As we find no evidence that long-context LLMs can make effective use of grammatical explanations for XLR translation, we conclude data collection for multilingual XLR tasks such as translation is best focused on parallel data over linguistic description.

  • 5 authors
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Sep 27, 2024

Multi-Type-TD-TSR -- Extracting Tables from Document Images using a Multi-stage Pipeline for Table Detection and Table Structure Recognition: from OCR to Structured Table Representations

As global trends are shifting towards data-driven industries, the demand for automated algorithms that can convert digital images of scanned documents into machine readable information is rapidly growing. Besides the opportunity of data digitization for the application of data analytic tools, there is also a massive improvement towards automation of processes, which previously would require manual inspection of the documents. Although the introduction of optical character recognition technologies mostly solved the task of converting human-readable characters from images into machine-readable characters, the task of extracting table semantics has been less focused on over the years. The recognition of tables consists of two main tasks, namely table detection and table structure recognition. Most prior work on this problem focuses on either task without offering an end-to-end solution or paying attention to real application conditions like rotated images or noise artefacts inside the document image. Recent work shows a clear trend towards deep learning approaches coupled with the use of transfer learning for the task of table structure recognition due to the lack of sufficiently large datasets. In this paper we present a multistage pipeline named Multi-Type-TD-TSR, which offers an end-to-end solution for the problem of table recognition. It utilizes state-of-the-art deep learning models for table detection and differentiates between 3 different types of tables based on the tables' borders. For the table structure recognition we use a deterministic non-data driven algorithm, which works on all table types. We additionally present two algorithms. One for unbordered tables and one for bordered tables, which are the base of the used table structure recognition algorithm. We evaluate Multi-Type-TD-TSR on the ICDAR 2019 table structure recognition dataset and achieve a new state-of-the-art.

  • 4 authors
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May 23, 2021

Knowledge-driven Subword Grammar Modeling for Automatic Speech Recognition in Tamil and Kannada

In this paper, we present specially designed automatic speech recognition (ASR) systems for the highly agglutinative and inflective languages of Tamil and Kannada that can recognize unlimited vocabulary of words. We use subwords as the basic lexical units for recognition and construct subword grammar weighted finite state transducer (SG-WFST) graphs for word segmentation that captures most of the complex word formation rules of the languages. We have identified the following category of words (i) verbs, (ii) nouns, (ii) pronouns, and (iv) numbers. The prefix, infix and suffix lists of subwords are created for each of these categories and are used to design the SG-WFST graphs. We also present a heuristic segmentation algorithm that can even segment exceptional words that do not follow the rules encapsulated in the SG-WFST graph. Most of the data-driven subword dictionary creation algorithms are computation driven, and hence do not guarantee morpheme-like units and so we have used the linguistic knowledge of the languages and manually created the subword dictionaries and the graphs. Finally, we train a deep neural network acoustic model and combine it with the pronunciation lexicon of the subword dictionary and the SG-WFST graph to build the subword-ASR systems. Since the subword-ASR produces subword sequences as output for a given test speech, we post-process its output to get the final word sequence, so that the actual number of words that can be recognized is much higher. Upon experimenting the subword-ASR system with the IISc-MILE Tamil and Kannada ASR corpora, we observe an absolute word error rate reduction of 12.39% and 13.56% over the baseline word-based ASR systems for Tamil and Kannada, respectively.

  • 3 authors
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Jul 27, 2022

Zero-Shot Document-Level Biomedical Relation Extraction via Scenario-based Prompt Design in Two-Stage with LLM

With the advent of artificial intelligence (AI), many researchers are attempting to extract structured information from document-level biomedical literature by fine-tuning large language models (LLMs). However, they face significant challenges such as the need for expensive hardware, like high-performance GPUs and the high labor costs associated with annotating training datasets, especially in biomedical realm. Recent research on LLMs, such as GPT-4 and Llama3, has shown promising performance in zero-shot settings, inspiring us to explore a novel approach to achieve the same results from unannotated full documents using general LLMs with lower hardware and labor costs. Our approach combines two major stages: named entity recognition (NER) and relation extraction (RE). NER identifies chemical, disease and gene entities from the document with synonym and hypernym extraction using an LLM with a crafted prompt. RE extracts relations between entities based on predefined relation schemas and prompts. To enhance the effectiveness of prompt, we propose a five-part template structure and a scenario-based prompt design principles, along with evaluation method to systematically assess the prompts. Finally, we evaluated our approach against fine-tuning and pre-trained models on two biomedical datasets: ChemDisGene and CDR. The experimental results indicate that our proposed method can achieve comparable accuracy levels to fine-tuning and pre-trained models but with reduced human and hardware expenses.

  • 3 authors
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May 2

Advancing Retrieval-Augmented Generation for Persian: Development of Language Models, Comprehensive Benchmarks, and Best Practices for Optimization

This paper examines the specific obstacles of constructing Retrieval-Augmented Generation(RAG) systems in low-resource languages, with a focus on Persian's complicated morphology and versatile syntax. The research aims to improve retrieval and generation accuracy by introducing Persian-specific models, namely MatinaRoberta(a masked language model) and MatinaSRoberta(a fine-tuned Sentence-BERT), along with a comprehensive benchmarking framework. Three datasets-general knowledge(PQuad), scientifically specialized texts, and organizational reports, were used to assess these models after they were trained on a varied corpus of 73.11 billion Persian tokens. The methodology involved extensive pretraining, fine-tuning with tailored loss functions, and systematic evaluations using both traditional metrics and the Retrieval-Augmented Generation Assessment framework. The results show that MatinaSRoberta outperformed previous embeddings, achieving superior contextual relevance and retrieval accuracy across datasets. Temperature tweaking, chunk size modifications, and document summary indexing were explored to enhance RAG setups. Larger models like Llama-3.1 (70B) consistently demonstrated the highest generation accuracy, while smaller models faced challenges with domain-specific and formal contexts. The findings underscore the potential for developing RAG systems in Persian through customized embeddings and retrieval-generation settings and highlight the enhancement of NLP applications such as search engines and legal document analysis in low-resource languages.

  • 5 authors
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Jan 8

Malaysian English News Decoded: A Linguistic Resource for Named Entity and Relation Extraction

Standard English and Malaysian English exhibit notable differences, posing challenges for natural language processing (NLP) tasks on Malaysian English. Unfortunately, most of the existing datasets are mainly based on standard English and therefore inadequate for improving NLP tasks in Malaysian English. An experiment using state-of-the-art Named Entity Recognition (NER) solutions on Malaysian English news articles highlights that they cannot handle morphosyntactic variations in Malaysian English. To the best of our knowledge, there is no annotated dataset available to improvise the model. To address these issues, we constructed a Malaysian English News (MEN) dataset, which contains 200 news articles that are manually annotated with entities and relations. We then fine-tuned the spaCy NER tool and validated that having a dataset tailor-made for Malaysian English could improve the performance of NER in Malaysian English significantly. This paper presents our effort in the data acquisition, annotation methodology, and thorough analysis of the annotated dataset. To validate the quality of the annotation, inter-annotator agreement was used, followed by adjudication of disagreements by a subject matter expert. Upon completion of these tasks, we managed to develop a dataset with 6,061 entities and 3,268 relation instances. Finally, we discuss on spaCy fine-tuning setup and analysis on the NER performance. This unique dataset will contribute significantly to the advancement of NLP research in Malaysian English, allowing researchers to accelerate their progress, particularly in NER and relation extraction. The dataset and annotation guideline has been published on Github.

  • 4 authors
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Feb 22, 2024

PDF-WuKong: A Large Multimodal Model for Efficient Long PDF Reading with End-to-End Sparse Sampling

Document understanding is a challenging task to process and comprehend large amounts of textual and visual information. Recent advances in Large Language Models (LLMs) have significantly improved the performance of this task. However, existing methods typically focus on either plain text or a limited number of document images, struggling to handle long PDF documents with interleaved text and images, especially in academic papers. In this paper, we introduce PDF-WuKong, a multimodal large language model (MLLM) which is designed to enhance multimodal question-answering (QA) for long PDF documents. PDF-WuKong incorporates a sparse sampler that operates on both text and image representations, significantly improving the efficiency and capability of the MLLM. The sparse sampler is integrated with the MLLM's image encoder and selects the paragraphs or diagrams most pertinent to user queries for processing by the language model. To effectively train and evaluate our model, we construct PaperPDF, a dataset consisting of a broad collection of academic papers sourced from arXiv, multiple strategies are proposed to generate automatically 1M QA pairs along with their corresponding evidence sources. Experimental results demonstrate the superiority and high efficiency of our approach over other models on the task of long multimodal PDF understanding, surpassing proprietary products by an average of 8.6% on F1. Our code and dataset will be released at https://github.com/yh-hust/PDF-Wukong.

  • 9 authors
·
Oct 8, 2024