nlp-clinical-ner-indo
Query: named entity recognition clinical Indonesian
Results: 50
Date: 2026-07-07T18:52:57.082Z
1. BanglaCoNER: Towards Robust Bangla Complex Named Entity Recognition
Authors: HAZ Sameen Shahgir, Ramisa Alam, Md. Zarif Ul Alam
Categories: cs.CL, cs.AI
Published: 2023-03-16
arXiv: 2303.09306v2
Abstract:
Named Entity Recognition (NER) is a fundamental task in natural language processing that involves identifying and classifying named entities in text. But much work hasn’t been done for complex named entity recognition in Bangla, despite being the seventh most spoken language globally. CNER is a more challenging task than traditional NER as it involves identifying and classifying complex and compound entities, which are not common in Bangla language. In this paper, we present the winning solution of Bangla Complex Named Entity Recognition Challenge - addressing the CNER task on BanglaCoNER dataset using two different approaches, namely Conditional Random Fields (CRF) and finetuning transformer based Deep Learning models such as BanglaBERT. The dataset consisted of 15300 sentences for training and 800 sentences for validation, in the .conll format. Exploratory Data Analysis (EDA) on the dataset revealed that the dataset had 7 different NER tags, with notable presence of English words, suggesting that the dataset is synthetic and likely a product of translation. We experimented with a variety of feature combinations including Part of Speech (POS) tags, word suffixes, Gazetteers, and cluster information from embeddings, while also finetuning the BanglaBERT (large) model for NER. We found that not all linguistic patterns are immediately apparent or even intuitive to humans, which is why Deep Learning based models has proved to be the more effective model in NLP, including CNER task. Our fine tuned BanglaBERT (large) model achieves an F1 Score of 0.79 on the validation set. Overall, our study highlights the importance of Bangla Complex Named Entity Recognition, particularly in the context of synthetic datasets. Our findings also demonstrate the efficacy of Deep Learning models such as BanglaBERT for NER in Bangla language.
2. A Morpho-Syntactically Informed LSTM-CRF Model for Named Entity Recognition
Authors: Lilia Simeonova, Kiril Simov, Petya Osenova, Preslav Nakov
Categories: cs.CL
Published: 2019-08-27
arXiv: 1908.10261v1
Abstract:
We propose a morphologically informed model for named entity recognition, which is based on LSTM-CRF architecture and combines word embeddings, Bi-LSTM character embeddings, part-of-speech (POS) tags, and morphological information. While previous work has focused on learning from raw word input, using word and character embeddings only, we show that for morphologically rich languages, such as Bulgarian, access to POS information contributes more to the performance gains than the detailed morphological information. Thus, we show that named entity recognition needs only coarse-grained POS tags, but at the same time it can benefit from simultaneously using some POS information of different granularity. Our evaluation results over a standard dataset show sizable improvements over the state-of-the-art for Bulgarian NER.
3. Query-Based Named Entity Recognition
Authors: Yuxian Meng, Xiaoya Li, Zijun Sun, Jiwei Li
Categories: cs.CL
Published: 2019-08-24
arXiv: 1908.09138v2
Abstract:
In this paper, we propose a new strategy for the task of named entity recognition (NER). We cast the task as a query-based machine reading comprehension task: e.g., the task of extracting entities with PER is formalized as answering the question of “which person is mentioned in the text ?”. Such a strategy comes with the advantage that it solves the long-standing issue of handling overlapping or nested entities (the same token that participates in more than one entity categories) with sequence-labeling techniques for NER. Additionally, since the query encodes informative prior knowledge, this strategy facilitates the process of entity extraction, leading to better performances. We experiment the proposed model on five widely used NER datasets on English and Chinese, including MSRA, Resume, OntoNotes, ACE04 and ACE05. The proposed model sets new SOTA results on all of these datasets.
4. CMNEROne at SemEval-2022 Task 11: Code-Mixed Named Entity Recognition by leveraging multilingual data
Authors: Suman Dowlagar, Radhika Mamidi
Categories: cs.CL
Published: 2022-06-15
arXiv: 2206.07318v1
Abstract:
Identifying named entities is, in general, a practical and challenging task in the field of Natural Language Processing. Named Entity Recognition on the code-mixed text is further challenging due to the linguistic complexity resulting from the nature of the mixing. This paper addresses the submission of team CMNEROne to the SEMEVAL 2022 shared task 11 MultiCoNER. The Code-mixed NER task aimed to identify named entities on the code-mixed dataset. Our work consists of Named Entity Recognition (NER) on the code-mixed dataset by leveraging the multilingual data. We achieved a weighted average F1 score of 0.7044, i.e., 6% greater than the baseline.
5. Feature-Rich Named Entity Recognition for Bulgarian Using Conditional Random Fields
Authors: Georgi Georgiev, Preslav Nakov, Kuzman Ganchev, Petya Osenova, Kiril Ivanov Simov
Categories: cs.CL, cs.AI, cs.LG
Published: 2021-09-26
arXiv: 2109.15121v1
Abstract:
The paper presents a feature-rich approach to the automatic recognition and categorization of named entities (persons, organizations, locations, and miscellaneous) in news text for Bulgarian. We combine well-established features used for other languages with language-specific lexical, syntactic and morphological information. In particular, we make use of the rich tagset annotation of the BulTreeBank (680 morpho-syntactic tags), from which we derive suitable task-specific tagsets (local and nonlocal). We further add domain-specific gazetteers and additional unlabeled data, achieving F1=89.4%, which is comparable to the state-of-the-art results for English.
6. On Fusing ChatGPT and Ensemble Learning in Discon-tinuous Named Entity Recognition in Health Corpora
Authors: Tzu-Chieh Chen, Wen-Yang Lin
Categories: cs.CL, cs.AI
Published: 2024-12-22
arXiv: 2412.16976v3
Abstract:
Named Entity Recognition has traditionally been a key task in natural language processing, aiming to identify and extract important terms from unstructured text data. However, a notable challenge for contemporary deep-learning NER models has been identifying discontinuous entities, which are often fragmented within the text. To date, methods to address Discontinuous Named Entity Recognition have not been explored using ensemble learning to the best of our knowledge. Furthermore, the rise of large language models, such as ChatGPT in recent years, has shown significant effectiveness across many NLP tasks. Most existing approaches, however, have primarily utilized ChatGPT as a problem-solving tool rather than exploring its potential as an integrative element within ensemble learning algorithms. In this study, we investigated the integration of ChatGPT as an arbitrator within an ensemble method, aiming to enhance performance on DNER tasks. Our method combines five state-of-the-art NER models with ChatGPT using custom prompt engineering to assess the robustness and generalization capabilities of the ensemble algorithm. We conducted experiments on three benchmark medical datasets, comparing our method against the five SOTA models, individual applications of GPT-3.5 and GPT-4, and a voting ensemble method. The results indicate that our proposed fusion of ChatGPT with the ensemble learning algorithm outperforms the SOTA results in the CADEC, ShARe13, and ShARe14 datasets, showcasing its potential to enhance NLP applications in the healthcare domain.
7. An HMM Based Named Entity Recognition System for Indian Languages: The JU System at ICON 2013
Authors: Vivekananda Gayen, Kamal Sarkar
Categories: cs.CL
Published: 2014-05-28
arXiv: 1405.7397v1
Abstract:
This paper reports about our work in the ICON 2013 NLP TOOLS CONTEST on Named Entity Recognition. We submitted runs for Bengali, English, Hindi, Marathi, Punjabi, Tamil and Telugu. A statistical HMM (Hidden Markov Models) based model has been used to implement our system. The system has been trained and tested on the NLP TOOLS CONTEST: ICON 2013 datasets. Our system obtains F-measures of 0.8599, 0.7704, 0.7520, 0.4289, 0.5455, 0.4466, and 0.4003 for Bengali, English, Hindi, Marathi, Punjabi, Tamil and Telugu respectively.
8. SlugNERDS: A Named Entity Recognition Tool for Open Domain Dialogue Systems
Authors: Kevin K. Bowden, Jiaqi Wu, Shereen Oraby, Amita Misra, Marilyn Walker
Categories: cs.CL
Published: 2018-05-10
arXiv: 1805.03784v1
Abstract:
In dialogue systems, the tasks of named entity recognition (NER) and named entity linking (NEL) are vital preprocessing steps for understanding user intent, especially in open domain interaction where we cannot rely on domain-specific inference. UCSC’s effort as one of the funded teams in the 2017 Amazon Alexa Prize Contest has yielded Slugbot, an open domain social bot, aimed at casual conversation. We discovered several challenges specifically associated with both NER and NEL when building Slugbot, such as that the NE labels are too coarse-grained or the entity types are not linked to a useful ontology. Moreover, we have discovered that traditional approaches do not perform well in our context: even systems designed to operate on tweets or other social media data do not work well in dialogue systems. In this paper, we introduce Slugbot’s Named Entity Recognition for dialogue Systems (SlugNERDS), a NER and NEL tool which is optimized to address these issues. We describe two new resources that we are building as part of this work: SlugEntityDB and SchemaActuator. We believe these resources will be useful for the research community.
9. A Neural Model for Text Localization, Transcription and Named Entity Recognition in Full Pages
Authors: Manuel Carbonell, Alicia Fornés, Mauricio Villegas, Josep Lladós
Categories: cs.CV
Published: 2019-12-20
arXiv: 1912.10016v2
Abstract:
In the last years, the consolidation of deep neural network architectures for information extraction in document images has brought big improvements in the performance of each of the tasks involved in this process, consisting of text localization, transcription, and named entity recognition. However, this process is traditionally performed with separate methods for each task. In this work we propose an end-to-end model that combines a one stage object detection network with branches for the recognition of text and named entities respectively in a way that shared features can be learned simultaneously from the training error of each of the tasks. By doing so the model jointly performs handwritten text detection, transcription, and named entity recognition at page level with a single feed forward step. We exhaustively evaluate our approach on different datasets, discussing its advantages and limitations compared to sequential approaches. The results show that the model is capable of benefiting from shared features for simultaneously solving interdependent tasks.
10. Boundary identification of events in clinical named entity recognition
Authors: Azad Dehghan
Categories: cs.CL
Published: 2013-08-05
arXiv: 1308.1004v3
Abstract:
The problem of named entity recognition in the medical/clinical domain has gained increasing attention do to its vital role in a wide range of clinical decision support applications. The identification of complete and correct term span is vital for further knowledge synthesis (e.g., coding/mapping concepts thesauruses and classification standards). This paper investigates boundary adjustment by sequence labeling representations models and post-processing techniques in the problem of clinical named entity recognition (recognition of clinical events). Using current state-of-the-art sequence labeling algorithm (conditional random fields), we show experimentally that sequence labeling representation and post-processing can be significantly helpful in strict boundary identification of clinical events.
11. Named Clinical Entity Recognition Benchmark
Authors: Wadood M Abdul, Marco AF Pimentel, Muhammad Umar Salman, Tathagata Raha, Clément Christophe, Praveen K Kanithi, Nasir Hayat, Ronnie Rajan, Shadab Khan
Categories: cs.CL, cs.AI
Published: 2024-10-07
arXiv: 2410.05046v1
Abstract:
This technical report introduces a Named Clinical Entity Recognition Benchmark for evaluating language models in healthcare, addressing the crucial natural language processing (NLP) task of extracting structured information from clinical narratives to support applications like automated coding, clinical trial cohort identification, and clinical decision support. The leaderboard provides a standardized platform for assessing diverse language models, including encoder and decoder architectures, on their ability to identify and classify clinical entities across multiple medical domains. A curated collection of openly available clinical datasets is utilized, encompassing entities such as diseases, symptoms, medications, procedures, and laboratory measurements. Importantly, these entities are standardized according to the Observational Medical Outcomes Partnership (OMOP) Common Data Model, ensuring consistency and interoperability across different healthcare systems and datasets, and a comprehensive evaluation of model performance. Performance of models is primarily assessed using the F1-score, and it is complemented by various assessment modes to provide comprehensive insights into model performance. The report also includes a brief analysis of models evaluated to date, highlighting observed trends and limitations. By establishing this benchmarking framework, the leaderboard aims to promote transparency, facilitate comparative analyses, and drive innovation in clinical entity recognition tasks, addressing the need for robust evaluation methods in healthcare NLP.
12. Entity Decomposition with Filtering: A Zero-Shot Clinical Named Entity Recognition Framework
Authors: Reza Averly, Xia Ning
Categories: cs.CL, cs.AI
Published: 2024-07-05
arXiv: 2407.04629v2
Abstract:
Clinical named entity recognition (NER) aims to retrieve important entities within clinical narratives. Recent works have demonstrated that large language models (LLMs) can achieve strong performance in this task. While previous works focus on proprietary LLMs, we investigate how open NER LLMs, trained specifically for entity recognition, perform in clinical NER. Our initial experiment reveals significant contrast in performance for some clinical entities and how a simple exploitment on entity types can alleviate this issue. In this paper, we introduce a novel framework, entity decomposition with filtering, or EDF. Our key idea is to decompose the entity recognition task into several retrievals of entity sub-types and then filter them. Our experimental results demonstrate the efficacies of our framework and the improvements across all metrics, models, datasets, and entity types. Our analysis also reveals substantial improvement in recognizing previously missed entities using entity decomposition. We further provide a comprehensive evaluation of our framework and an in-depth error analysis to pave future works.
13. Lightweight Transformers for Clinical Natural Language Processing
Authors: Omid Rohanian, Mohammadmahdi Nouriborji, Hannah Jauncey, Samaneh Kouchaki, ISARIC Clinical Characterisation Group, Lei Clifton, Laura Merson, David A. Clifton
Categories: cs.CL, cs.AI, cs.LG
Published: 2023-02-09
arXiv: 2302.04725v1
Abstract:
Specialised pre-trained language models are becoming more frequent in NLP since they can potentially outperform models trained on generic texts. BioBERT and BioClinicalBERT are two examples of such models that have shown promise in medical NLP tasks. Many of these models are overparametrised and resource-intensive, but thanks to techniques like Knowledge Distillation (KD), it is possible to create smaller versions that perform almost as well as their larger counterparts. In this work, we specifically focus on development of compact language models for processing clinical texts (i.e. progress notes, discharge summaries etc). We developed a number of efficient lightweight clinical transformers using knowledge distillation and continual learning, with the number of parameters ranging from 15 million to 65 million. These models performed comparably to larger models such as BioBERT and ClinicalBioBERT and significantly outperformed other compact models trained on general or biomedical data. Our extensive evaluation was done across several standard datasets and covered a wide range of clinical text-mining tasks, including Natural Language Inference, Relation Extraction, Named Entity Recognition, and Sequence Classification. To our knowledge, this is the first comprehensive study specifically focused on creating efficient and compact transformers for clinical NLP tasks. The models and code used in this study can be found on our Huggingface profile at https://huggingface.co/nlpie and Github page at https://github.com/nlpie-research/Lightweight-Clinical-Transformers, respectively, promoting reproducibility of our results.
14. Exploring the Value of Pre-trained Language Models for Clinical Named Entity Recognition
Authors: Samuel Belkadi, Lifeng Han, Yuping Wu, Goran Nenadic
Categories: cs.CL, cs.AI, cs.LG
Published: 2022-10-23
arXiv: 2210.12770v4
Abstract:
The practice of fine-tuning Pre-trained Language Models (PLMs) from general or domain-specific data to a specific task with limited resources, has gained popularity within the field of natural language processing (NLP). In this work, we re-visit this assumption and carry out an investigation in clinical NLP, specifically Named Entity Recognition on drugs and their related attributes. We compare Transformer models that are trained from scratch to fine-tuned BERT-based LLMs namely BERT, BioBERT, and ClinicalBERT. Furthermore, we examine the impact of an additional CRF layer on such models to encourage contextual learning. We use n2c2-2018 shared task data for model development and evaluations. The experimental outcomes show that 1) CRF layers improved all language models; 2) referring to BIO-strict span level evaluation using macro-average F1 score, although the fine-tuned LLMs achieved 0.83+ scores, the TransformerCRF model trained from scratch achieved 0.78+, demonstrating comparable performances with much lower cost - e.g. with 39.80% less training parameters; 3) referring to BIO-strict span-level evaluation using weighted-average F1 score, ClinicalBERT-CRF, BERT-CRF, and TransformerCRF exhibited lower score differences, with 97.59%/97.44%/96.84% respectively. 4) applying efficient training by down-sampling for better data distribution further reduced the training cost and need for data, while maintaining similar scores - i.e. around 0.02 points lower compared to using the full dataset. Our models will be hosted at \url{https://github.com/HECTA-UoM/TransformerCRF}
15. Transformer-Based Approach for Joint Handwriting and Named Entity Recognition in Historical documents
Authors: Ahmed Cheikh Rouhoua, Marwa Dhiaf, Yousri Kessentini, Sinda Ben Salem
Categories: cs.CV, cs.CL
Published: 2021-12-08
arXiv: 2112.04189v1
Abstract:
The extraction of relevant information carried out by named entities in handwriting documents is still a challenging task. Unlike traditional information extraction approaches that usually face text transcription and named entity recognition as separate subsequent tasks, we propose in this paper an end-to-end transformer-based approach to jointly perform these two tasks. The proposed approach operates at the paragraph level, which brings two main benefits. First, it allows the model to avoid unrecoverable early errors due to line segmentation. Second, it allows the model to exploit larger bi-dimensional context information to identify the semantic categories, reaching a higher final prediction accuracy. We also explore different training scenarios to show their effect on the performance and we demonstrate that a two-stage learning strategy can make the model reach a higher final prediction accuracy. As far as we know, this work presents the first approach that adopts the transformer networks for named entity recognition in handwritten documents. We achieve the new state-of-the-art performance in the ICDAR 2017 Information Extraction competition using the Esposalles database, for the complete task, even though the proposed technique does not use any dictionaries, language modeling, or post-processing.
16. A Benchmark Evaluation of Clinical Named Entity Recognition in French
Authors: Nesrine Bannour, Christophe Servan, Aurélie Névéol, Xavier Tannier
Categories: cs.CL, cs.AI, q-bio.QM
Published: 2024-03-28
arXiv: 2403.19726v1
Abstract:
Background: Transformer-based language models have shown strong performance on many Natural LanguageProcessing (NLP) tasks. Masked Language Models (MLMs) attract sustained interest because they can be adaptedto different languages and sub-domains through training or fine-tuning on specific corpora while remaining lighterthan modern Large Language Models (LLMs). Recently, several MLMs have been released for the biomedicaldomain in French, and experiments suggest that they outperform standard French counterparts. However, nosystematic evaluation comparing all models on the same corpora is available. Objective: This paper presentsan evaluation of masked language models for biomedical French on the task of clinical named entity recognition.Material and methods: We evaluate biomedical models CamemBERT-bio and DrBERT and compare them tostandard French models CamemBERT, FlauBERT and FrALBERT as well as multilingual mBERT using three publicallyavailable corpora for clinical named entity recognition in French. The evaluation set-up relies on gold-standardcorpora as released by the corpus developers. Results: Results suggest that CamemBERT-bio outperformsDrBERT consistently while FlauBERT offers competitive performance and FrAlBERT achieves the lowest carbonfootprint. Conclusion: This is the first benchmark evaluation of biomedical masked language models for Frenchclinical entity recognition that compares model performance consistently on nested entity recognition using metricscovering performance and environmental impact.
17. Software Mention Recognition with a Three-Stage Framework Based on BERTology Models at SOMD 2024
Authors: Thuy Nguyen Thi, Anh Nguyen Viet, Thin Dang Van, Ngan Nguyen Luu Thuy
Categories: cs.SE, cs.AI, cs.CL
Published: 2024-04-23
arXiv: 2405.01575v1
Abstract:
This paper describes our systems for the sub-task I in the Software Mention Detection in Scholarly Publications shared-task. We propose three approaches leveraging different pre-trained language models (BERT, SciBERT, and XLM-R) to tackle this challenge. Our bestperforming system addresses the named entity recognition (NER) problem through a three-stage framework. (1) Entity Sentence Classification - classifies sentences containing potential software mentions; (2) Entity Extraction - detects mentions within classified sentences; (3) Entity Type Classification - categorizes detected mentions into specific software types. Experiments on the official dataset demonstrate that our three-stage framework achieves competitive performance, surpassing both other participating teams and our alternative approaches. As a result, our framework based on the XLM-R-based model achieves a weighted F1-score of 67.80%, delivering our team the 3rd rank in Sub-task I for the Software Mention Recognition task.
18. Pretrained language model transfer on neural named entity recognition in Indonesian conversational texts
Authors: Rezka Leonandya, Fariz Ikhwantri
Categories: cs.CL
Published: 2019-02-21
arXiv: 1902.07938v1
Abstract:
Named entity recognition (NER) is an important task in NLP, which is all the more challenging in conversational domain with their noisy facets. Moreover, conversational texts are often available in limited amount, making supervised tasks infeasible. To learn from small data, strong inductive biases are required. Previous work relied on hand-crafted features to encode these biases until transfer learning emerges. Here, we explore a transfer learning method, namely language model pretraining, on NER task in Indonesian conversational texts. We utilize large unlabeled data (generic domain) to be transferred to conversational texts, enabling supervised training on limited in-domain data. We report two transfer learning variants, namely supervised model fine-tuning and unsupervised pretrained LM fine-tuning. Our experiments show that both variants outperform baseline neural models when trained on small data (100 sentences), yielding an absolute improvement of 32 points of test F1 score. Furthermore, we find that the pretrained LM encodes part-of-speech information which is a strong predictor for NER.
19. NEAR: Named Entity and Attribute Recognition of clinical concepts
Authors: Namrata Nath, Sang-Heon Lee, Ivan Lee
Categories: cs.CL
Published: 2022-08-30
arXiv: 2208.13949v1
Abstract:
Named Entity Recognition (NER) or the extraction of concepts from clinical text is the task of identifying entities in text and slotting them into categories such as problems, treatments, tests, clinical departments, occurrences (such as admission and discharge) and others. NER forms a critical component of processing and leveraging unstructured data from Electronic Health Records (EHR). While identifying the spans and categories of concepts is itself a challenging task, these entities could also have attributes such as negation that pivot their meanings implied to the consumers of the named entities. There has been little research dedicated to identifying the entities and their qualifying attributes together. This research hopes to contribute to the area of detecting entities and their corresponding attributes by modelling the NER task as a supervised, multi-label tagging problem with each of the attributes assigned tagging sequence labels. In this paper, we propose 3 architectures to achieve this multi-label entity tagging: BiLSTM n-CRF, BiLSTM-CRF-Smax-TF and BiLSTM n-CRF-TF. We evaluate these methods on the 2010 i2b2/VA and the i2b2 2012 shared task datasets. Our different models obtain best NER F1 scores of 0. 894 and 0.808 on the i2b2 2010/VA and i2b2 2012 respectively. The highest span based micro-averaged F1 polarity scores obtained were 0.832 and 0.836 on the i2b2 2010/VA and i2b2 2012 datasets respectively, and the highest macro-averaged F1 polarity scores obtained were 0.924 and 0.888 respectively. The modality studies conducted on i2b2 2012 dataset revealed high scores of 0.818 and 0.501 for span based micro-averaged F1 and macro-averaged F1 respectively.
20. HistNERo: Historical Named Entity Recognition for the Romanian Language
Authors: Andrei-Marius Avram, Andreea Iuga, George-Vlad Manolache, Vlad-Cristian Matei, Răzvan-Gabriel Micliuş, Vlad-Andrei Muntean, Manuel-Petru Sorlescu, Dragoş-Andrei Şerban, Adrian-Dinu Urse, Vasile Păiş, Dumitru-Clementin Cercel
Categories: cs.CL
Published: 2024-04-30
arXiv: 2405.00155v1
Abstract:
This work introduces HistNERo, the first Romanian corpus for Named Entity Recognition (NER) in historical newspapers. The dataset contains 323k tokens of text, covering more than half of the 19th century (i.e., 1817) until the late part of the 20th century (i.e., 1990). Eight native Romanian speakers annotated the dataset with five named entities. The samples belong to one of the following four historical regions of Romania, namely Bessarabia, Moldavia, Transylvania, and Wallachia. We employed this proposed dataset to perform several experiments for NER using Romanian pre-trained language models. Our results show that the best model achieved a strict F1-score of 55.69%. Also, by reducing the discrepancies between regions through a novel domain adaption technique, we improved the performance on this corpus to a strict F1-score of 66.80%, representing an absolute gain of more than 10%.
21. Leveraging Semantic Type Dependencies for Clinical Named Entity Recognition
Authors: Linh Le, Guido Zuccon, Gianluca Demartini, Genghong Zhao, Xia Zhang
Categories: cs.CL
Published: 2025-03-07
arXiv: 2503.05373v1
Abstract:
Previous work on clinical relation extraction from free-text sentences leveraged information about semantic types from clinical knowledge bases as a part of entity representations. In this paper, we exploit additional evidence by also making use of domain-specific semantic type dependencies. We encode the relation between a span of tokens matching a Unified Medical Language System (UMLS) concept and other tokens in the sentence. We implement our method and compare against different named entity recognition (NER) architectures (i.e., BiLSTM-CRF and BiLSTM-GCN-CRF) using different pre-trained clinical embeddings (i.e., BERT, BioBERT, UMLSBert). Our experimental results on clinical datasets show that in some cases NER effectiveness can be significantly improved by making use of domain-specific semantic type dependencies. Our work is also the first study generating a matrix encoding to make use of more than three dependencies in one pass for the NER task.
22. Incorporating Dictionaries into Deep Neural Networks for the Chinese Clinical Named Entity Recognition
Authors: Qi Wang, Yuhang Xia, Yangming Zhou, Tong Ruan, Daqi Gao, Ping He
Categories: cs.CL
Published: 2018-04-13
arXiv: 1804.05017v1
Abstract:
Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other Natural Language Processing (NLP) tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we address the problem by incorporating dictionaries into deep neural networks for the Chinese CNER task. Two different architectures that extend the Bi-directional Long Short-Term Memory (Bi-LSTM) neural network and five different feature representation schemes are proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.
23. Connecting Distant Entities with Induction through Conditional Random Fields for Named Entity Recognition: Precursor-Induced CRF
Authors: Wangjin Lee, Jinwook Choi
Categories: cs.CL
Published: 2018-05-26
arXiv: 1805.10414v1
Abstract:
This paper presents a method of designing specific high-order dependency factor on the linear chain conditional random fields (CRFs) for named entity recognition (NER). Named entities tend to be separated from each other by multiple outside tokens in a text, and thus the first-order CRF, as well as the second-order CRF, may innately lose transition information between distant named entities. The proposed design uses outside label in NER as a transmission medium of precedent entity information on the CRF. Then, empirical results apparently demonstrate that it is possible to exploit long-distance label dependency in the original first-order linear chain CRF structure upon NER while reducing computational loss rather than in the second-order CRF.
24. Terminologies augmented recurrent neural network model for clinical named entity recognition
Authors: Ivan Lerner, Nicolas Paris, Xavier Tannier
Categories: cs.CL
Published: 2019-04-25
arXiv: 1904.11473v2
Abstract:
We aimed to enhance the performance of a supervised model for clinical named-entity recognition (NER) using medical terminologies. In order to evaluate our system in French, we built a corpus for 5 types of clinical entities. We used a terminology-based system as baseline, built upon UMLS and SNOMED. Then, we evaluated a biGRU-CRF, and an hybrid system using the prediction of the terminology-based system as feature for the biGRU-CRF. In English, we evaluated the NER systems on the i2b2-2009 Medication Challenge for Drug name recognition, which contained 8,573 entities for 268 documents. In French, we built APcNER, a corpus of 147 documents annotated for 5 entities (drug name, sign or symptom, disease or disorder, diagnostic procedure or lab test and therapeutic procedure). We evaluated each NER systems using exact and partial match definition of F-measure for NER. The APcNER contains 4,837 entities which took 28 hours to annotate, the inter-annotator agreement was acceptable for Drug name in exact match (85%) and acceptable for other entity types in non-exact match (>70%). For drug name recognition on both i2b2-2009 and APcNER, the biGRU-CRF performed better that the terminology-based system, with an exact-match F-measure of 91.1% versus 73% and 81.9% versus 75% respectively. Moreover, the hybrid system outperformed the biGRU-CRF, with an exact-match F-measure of 92.2% versus 91.1% (i2b2-2009) and 88.4% versus 81.9% (APcNER). On APcNER corpus, the micro-average F-measure of the hybrid system on the 5 entities was 69.5% in exact match, and 84.1% in non-exact match. APcNER is a French corpus for clinical-NER of five type of entities which covers a large variety of document types. Extending supervised model with terminology allowed for an easy performance gain, especially in low regimes of entities, and established near state of the art results on the i2b2-2009 corpus.
25. Biomedical Named Entity Recognition at Scale
Authors: Veysel Kocaman, David Talby
Categories: cs.CL, cs.AI, cs.LG
Published: 2020-11-12
arXiv: 2011.06315v1
Abstract:
Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting meaningful chunks from clinical notes and reports, which are then fed to downstream tasks like assertion status detection, entity resolution, relation extraction, and de-identification. Reimplementing a Bi-LSTM-CNN-Char deep learning architecture on top of Apache Spark, we present a single trainable NER model that obtains new state-of-the-art results on seven public biomedical benchmarks without using heavy contextual embeddings like BERT. This includes improving BC4CHEMD to 93.72% (4.1% gain), Species800 to 80.91% (4.6% gain), and JNLPBA to 81.29% (5.2% gain). In addition, this model is freely available within a production-grade code base as part of the open-source Spark NLP library; can scale up for training and inference in any Spark cluster; has GPU support and libraries for popular programming languages such as Python, R, Scala and Java; and can be extended to support other human languages with no code changes.
26. An Emergency Medical Services Clinical Audit System driven by Named Entity Recognition from Deep Learning
Authors: Wang Han, Wesley Yeung, Angeline Tung, Joey Tay Ai Meng, Davin Ryanputera, Feng Mengling, Shalini Arulanadam
Categories: cs.CL, cs.CY, cs.LG
Published: 2020-07-07
arXiv: 2007.03596v1
Abstract:
Clinical performance audits are routinely performed in Emergency Medical Services (EMS) to ensure adherence to treatment protocols, to identify individual areas of weakness for remediation, and to discover systemic deficiencies to guide the development of the training syllabus. At present, these audits are performed by manual chart review which is time-consuming and laborious. In this paper, we present an automatic audit system based on both the structured and unstructured ambulance case records and clinical notes with a deep neural network-based named entities recognition model. The dataset used in this study contained 58,898 unlabelled ambulance incidents encountered by the Singapore Civil Defence Force from 1st April 2019 to 30th June 2019. A weakly-supervised training approach was adopted to label the sentences. Later on, we trained three different models to perform the NER task. All three models achieve F1 scores of around 0.981 under entity type matching evaluation and around 0.976 under strict evaluation, while the BiLSTM-CRF model is 1~2 orders of magnitude lighter and faster than our BERT-based models. Overall, our approach yielded a named entity recognition model that could reliably identify clinical entities from unstructured paramedic free-text reports. Our proposed system may improve the efficiency of clinical performance audits and can also help with EMS database research.
27. Suryakala-Nusantara: Documenting Indonesian Sundials
Authors: Rhorom Priyatikanto
Categories: physics.pop-ph, astro-ph.IM
Published: 2013-12-10
arXiv: 1312.2742v1
Abstract:
Sundial is the ancient or classic timekeeper device, especially prior to the invention of mechanical clock. In the classical Islamic civilization, the daily movement of the Sun becomes main indicator of praying time, which can be deduced using sundial. This kind of device probably permeated to Indonesia during the Islamic acculturation. Since then, the development of astronomical knowledge, technology, art and architectural in classical Indonesia are partially reflected into sundial. These historical attractions of sundial demand comprehensive documentation and investigation of Indonesian sundial which are rarely found in the current literatures. The required spatial and temporal information regarding Indonesian sundial can be collected by general public through citizen science scheme. This concept may answer scientific curiosity of a research and also educate the people, expose them with science. In this article, general scheme of citizen science are discussed, its application for sundial study in Indonesia is proposed as Suryakala-Nusantara program.
28. Clinical Named Entity Recognition using Contextualized Token Representations
Authors: Yichao Zhou, Chelsea Ju, J. Harry Caufield, Kevin Shih, Calvin Chen, Yizhou Sun, Kai-Wei Chang, Peipei Ping, Wei Wang
Categories: cs.CL, q-bio.QM
Published: 2021-06-23
arXiv: 2106.12608v1
Abstract:
The clinical named entity recognition (CNER) task seeks to locate and classify clinical terminologies into predefined categories, such as diagnostic procedure, disease disorder, severity, medication, medication dosage, and sign symptom. CNER facilitates the study of side-effect on medications including identification of novel phenomena and human-focused information extraction. Existing approaches in extracting the entities of interests focus on using static word embeddings to represent each word. However, one word can have different interpretations that depend on the context of the sentences. Evidently, static word embeddings are insufficient to integrate the diverse interpretation of a word. To overcome this challenge, the technique of contextualized word embedding has been introduced to better capture the semantic meaning of each word based on its context. Two of these language models, ELMo and Flair, have been widely used in the field of Natural Language Processing to generate the contextualized word embeddings on domain-generic documents. However, these embeddings are usually too general to capture the proximity among vocabularies of specific domains. To facilitate various downstream applications using clinical case reports (CCRs), we pre-train two deep contextualized language models, Clinical Embeddings from Language Model (C-ELMo) and Clinical Contextual String Embeddings (C-Flair) using the clinical-related corpus from the PubMed Central. Explicit experiments show that our models gain dramatic improvements compared to both static word embeddings and domain-generic language models.
29. Entity-Switched Datasets: An Approach to Auditing the In-Domain Robustness of Named Entity Recognition Models
Authors: Oshin Agarwal, Yinfei Yang, Byron C. Wallace, Ani Nenkova
Categories: cs.CL
Published: 2020-04-08
arXiv: 2004.04123v2
Abstract:
Named entity recognition systems perform well on standard datasets comprising English news. But given the paucity of data, it is difficult to draw conclusions about the robustness of systems with respect to recognizing a diverse set of entities. We propose a method for auditing the in-domain robustness of systems, focusing specifically on differences in performance due to the national origin of entities. We create entity-switched datasets, in which named entities in the original texts are replaced by plausible named entities of the same type but of different national origin. We find that state-of-the-art systems’ performance vary widely even in-domain: In the same context, entities from certain origins are more reliably recognized than entities from elsewhere. Systems perform best on American and Indian entities, and worst on Vietnamese and Indonesian entities. This auditing approach can facilitate the development of more robust named entity recognition systems, and will allow research in this area to consider fairness criteria that have received heightened attention in other predictive technology work.
30. Semantic-Aware Scene Recognition
Authors: Alejandro López-Cifuentes, Marcos Escudero-Viñolo, Jesús Bescós, Álvaro García-Martín
Categories: cs.CV
Published: 2019-09-05
arXiv: 1909.02410v3
Abstract:
Scene recognition is currently one of the top-challenging research fields in computer vision. This may be due to the ambiguity between classes: images of several scene classes may share similar objects, which causes confusion among them. The problem is aggravated when images of a particular scene class are notably different. Convolutional Neural Networks (CNNs) have significantly boosted performance in scene recognition, albeit it is still far below from other recognition tasks (e.g., object or image recognition). In this paper, we describe a novel approach for scene recognition based on an end-to-end multi-modal CNN that combines image and context information by means of an attention module. Context information, in the shape of semantic segmentation, is used to gate features extracted from the RGB image by leveraging on information encoded in the semantic representation: the set of scene objects and stuff, and their relative locations. This gating process reinforces the learning of indicative scene content and enhances scene disambiguation by refocusing the receptive fields of the CNN towards them. Experimental results on four publicly available datasets show that the proposed approach outperforms every other state-of-the-art method while significantly reducing the number of network parameters. All the code and data used along this paper is available at https://github.com/vpulab/Semantic-Aware-Scene-Recognition
31. Domain Adaptation of the Pyannote Diarization Pipeline for Conversational Indonesian Audio
Authors: Muhammad Daffa’i Rafi Prasetyo, Ramadhan Andika Putra, Zaidan Naufal Ilmi, Kurniawati Azizah
Categories: cs.SD
Published: 2026-01-07
arXiv: 2601.03684v1
Abstract:
This study presents a domain adaptation approach for speaker diarization targeting conversational Indonesian audio. We address the challenge of adapting an English-centric diarization pipeline to a low-resource language by employing synthetic data generation using neural Text-to-Speech technology. Experiments were conducted with varying training configurations, a small dataset (171 samples) and a large dataset containing 25 hours of synthetic speech. Results demonstrate that the baseline \texttt{pyannote/segmentation-3.0} model, trained on the AMI Corpus, achieves a Diarization Error Rate (DER) of 53.47% when applied zero-shot to Indonesian. Domain adaptation significantly improves performance, with the small dataset models reducing DER to 34.31% (1 epoch) and 34.81% (2 epochs). The model trained on the 25-hour dataset achieves the best performance with a DER of 29.24%, representing a 13.68% absolute improvement over the baseline while maintaining 99.06% Recall and 87.14% F1-Score.
32. Exploring Text Specific and Blackbox Fairness Algorithms in Multimodal Clinical NLP
Authors: John Chen, Ian Berlot-Attwell, Safwan Hossain, Xindi Wang, Frank Rudzicz
Categories: cs.CL, cs.AI
Published: 2020-11-19
arXiv: 2011.09625v2
Abstract:
Clinical machine learning is increasingly multimodal, collected in both structured tabular formats and unstructured forms such as freetext. We propose a novel task of exploring fairness on a multimodal clinical dataset, adopting equalized odds for the downstream medical prediction tasks. To this end, we investigate a modality-agnostic fairness algorithm - equalized odds post processing - and compare it to a text-specific fairness algorithm: debiased clinical word embeddings. Despite the fact that debiased word embeddings do not explicitly address equalized odds of protected groups, we show that a text-specific approach to fairness may simultaneously achieve a good balance of performance and classical notions of fairness. We hope that our paper inspires future contributions at the critical intersection of clinical NLP and fairness. The full source code is available here: https://github.com/johntiger1/multimodal_fairness
33. Saliency for Fine-grained Object Recognition in Domains with Scarce Training Data
Authors: Carola Figueroa Flores, Abel Gonzalez-García, Joost van de Weijer, Bogdan Raducanu
Categories: cs.CV
Published: 2018-08-01
arXiv: 1808.00262v3
Abstract:
This paper investigates the role of saliency to improve the classification accuracy of a Convolutional Neural Network (CNN) for the case when scarce training data is available. Our approach consists in adding a saliency branch to an existing CNN architecture which is used to modulate the standard bottom-up visual features from the original image input, acting as an attentional mechanism that guides the feature extraction process. The main aim of the proposed approach is to enable the effective training of a fine-grained recognition model with limited training samples and to improve the performance on the task, thereby alleviating the need to annotate large dataset. % The vast majority of saliency methods are evaluated on their ability to generate saliency maps, and not on their functionality in a complete vision pipeline. Our proposed pipeline allows to evaluate saliency methods for the high-level task of object recognition. We perform extensive experiments on various fine-grained datasets (Flowers, Birds, Cars, and Dogs) under different conditions and show that saliency can considerably improve the network’s performance, especially for the case of scarce training data. Furthermore, our experiments show that saliency methods that obtain improved saliency maps (as measured by traditional saliency benchmarks) also translate to saliency methods that yield improved performance gains when applied in an object recognition pipeline.
34. A Biomedical Pipeline to Detect Clinical and Non-Clinical Named Entities
Authors: Shaina Raza, Brian Schwartz
Categories: cs.CL, cs.IR
Published: 2022-07-02
arXiv: 2207.00876v1
Abstract:
There are a few challenges related to the task of biomedical named entity recognition, which are: the existing methods consider a fewer number of biomedical entities (e.g., disease, symptom, proteins, genes); and these methods do not consider the social determinants of health (age, gender, employment, race), which are the non-medical factors related to patients’ health. We propose a machine learning pipeline that improves on previous efforts in the following ways: first, it recognizes many biomedical entity types other than the standard ones; second, it considers non-clinical factors related to patient’s health. This pipeline also consists of stages, such as preprocessing, tokenization, mapping embedding lookup and named entity recognition task to extract biomedical named entities from the free texts. We present a new dataset that we prepare by curating the COVID-19 case reports. The proposed approach outperforms the baseline methods on five benchmark datasets with macro-and micro-average F1 scores around 90, as well as our dataset with a macro-and micro-average F1 score of 95.25 and 93.18 respectively.
35. HMM-based Indic Handwritten Word Recognition using Zone Segmentation
Authors: Partha Pratim Roy, Ayan Kumar Bhunia, Ayan Das, Prasenjit Dey, Umapada Pal
Categories: cs.CV
Published: 2017-08-01
arXiv: 1708.00227v1
Abstract:
This paper presents a novel approach towards Indic handwritten word recognition using zone-wise information. Because of complex nature due to compound characters, modifiers, overlapping and touching, etc., character segmentation and recognition is a tedious job in Indic scripts (e.g. Devanagari, Bangla, Gurumukhi, and other similar scripts). To avoid character segmentation in such scripts, HMM-based sequence modeling has been used earlier in holistic way. This paper proposes an efficient word recognition framework by segmenting the handwritten word images horizontally into three zones (upper, middle and lower) and recognize the corresponding zones. The main aim of this zone segmentation approach is to reduce the number of distinct component classes compared to the total number of classes in Indic scripts. As a result, use of this zone segmentation approach enhances the recognition performance of the system. The components in middle zone where characters are mostly touching are recognized using HMM. After the recognition of middle zone, HMM based Viterbi forced alignment is applied to mark the left and right boundaries of the characters. Next, the residue components, if any, in upper and lower zones in their respective boundary are combined to achieve the final word level recognition. Water reservoir feature has been integrated in this framework to improve the zone segmentation and character alignment defects while segmentation. A novel sliding window-based feature, called Pyramid Histogram of Oriented Gradient (PHOG) is proposed for middle zone recognition. An exhaustive experiment is performed on two Indic scripts namely, Bangla and Devanagari for the performance evaluation. From the experiment, it has been noted that proposed zone-wise recognition improves accuracy with respect to the traditional way of Indic word recognition.
36. Investigating Bi-LSTM and CRF with POS Tag Embedding for Indonesian Named Entity Tagger
Authors: Devin Hoesen, Ayu Purwarianti
Categories: cs.CL, cs.AI
Published: 2020-09-11
arXiv: 2009.05687v1
Abstract:
Researches on Indonesian named entity (NE) tagger have been conducted since years ago. However, most did not use deep learning and instead employed traditional machine learning algorithms such as association rule, support vector machine, random forest, naïve bayes, etc. In those researches, word lists as gazetteers or clue words were provided to enhance the accuracy. Here, we attempt to employ deep learning in our Indonesian NE tagger. We use long short-term memory (LSTM) as the topology since it is the state-of-the-art of NE tagger. By using LSTM, we do not need a word list in order to enhance the accuracy. Basically, there are two main things that we investigate. The first is the output layer of the network: Softmax vs conditional random field (CRF). The second is the usage of part of speech (POS) tag embedding input layer. Using 8400 sentences as the training data and 97 sentences as the evaluation data, we find that using POS tag embedding as additional input improves the performance of our Indonesian NE tagger. As for the comparison between Softmax and CRF, we find that both architectures have a weakness in classifying an NE tag.
37. Dynamic Named Entity Recognition
Authors: Tristan Luiggi, Laure Soulier, Vincent Guigue, Siwar Jendoubi, Aurélien Baelde
Categories: cs.CL, cs.AI
Published: 2023-02-16
arXiv: 2302.10314v1
Abstract:
Named Entity Recognition (NER) is a challenging and widely studied task that involves detecting and typing entities in text. So far,NER still approaches entity typing as a task of classification into universal classes (e.g. date, person, or location). Recent advances innatural language processing focus on architectures of increasing complexity that may lead to overfitting and memorization, and thus, underuse of context. Our work targets situations where the type of entities depends on the context and cannot be solved solely by memorization. We hence introduce a new task: Dynamic Named Entity Recognition (DNER), providing a framework to better evaluate the ability of algorithms to extract entities by exploiting the context. The DNER benchmark is based on two datasets, DNER-RotoWire and DNER-IMDb. We evaluate baseline models and present experiments reflecting issues and research axes related to this novel task.
38. Named Entity Recognition with Extremely Limited Data
Authors: John Foley, Sheikh Muhammad Sarwar, James Allan
Categories: cs.IR
Published: 2018-06-12
arXiv: 1806.04411v2
Abstract:
Traditional information retrieval treats named entity recognition as a pre-indexing corpus annotation task, allowing entity tags to be indexed and used during search. Named entity taggers themselves are typically trained on thousands or tens of thousands of examples labeled by humans. However, there is a long tail of named entities classes, and for these cases, labeled data may be impossible to find or justify financially. We propose exploring named entity recognition as a search task, where the named entity class of interest is a query, and entities of that class are the relevant “documents”. What should that query look like? Can we even perform NER-style labeling with tens of labels? This study presents an exploration of CRF-based NER models with handcrafted features and of how we might transform them into search queries.
39. Preserving Empirical Probabilities in BERT for Small-sample Clinical Entity Recognition
Authors: Abdul Rehman, Jian Jun Zhang, Xiaosong Yang
Categories: cs.CL, cs.LG
Published: 2024-09-05
arXiv: 2409.03238v1
Abstract:
Named Entity Recognition (NER) encounters the challenge of unbalanced labels, where certain entity types are overrepresented while others are underrepresented in real-world datasets. This imbalance can lead to biased models that perform poorly on minority entity classes, impeding accurate and equitable entity recognition. This paper explores the effects of unbalanced entity labels of the BERT-based pre-trained model. We analyze the different mechanisms of loss calculation and loss propagation for the task of token classification on randomized datasets. Then we propose ways to improve the token classification for the highly imbalanced task of clinical entity recognition.
40. Using Bottleneck Adapters to Identify Cancer in Clinical Notes under Low-Resource Constraints
Authors: Omid Rohanian, Hannah Jauncey, Mohammadmahdi Nouriborji, Vinod Kumar Chauhan, Bronner P. Gonçalves, Christiana Kartsonaki, ISARIC Clinical Characterisation Group, Laura Merson, David Clifton
Categories: cs.CL, cs.AI
Published: 2022-10-17
arXiv: 2210.09440v2
Abstract:
Processing information locked within clinical health records is a challenging task that remains an active area of research in biomedical NLP. In this work, we evaluate a broad set of machine learning techniques ranging from simple RNNs to specialised transformers such as BioBERT on a dataset containing clinical notes along with a set of annotations indicating whether a sample is cancer-related or not. Furthermore, we specifically employ efficient fine-tuning methods from NLP, namely, bottleneck adapters and prompt tuning, to adapt the models to our specialised task. Our evaluations suggest that fine-tuning a frozen BERT model pre-trained on natural language and with bottleneck adapters outperforms all other strategies, including full fine-tuning of the specialised BioBERT model. Based on our findings, we suggest that using bottleneck adapters in low-resource situations with limited access to labelled data or processing capacity could be a viable strategy in biomedical text mining. The code used in the experiments are going to be made available at https://github.com/omidrohanian/bottleneck-adapters.
41. Soft Gazetteers for Low-Resource Named Entity Recognition
Authors: Shruti Rijhwani, Shuyan Zhou, Graham Neubig, Jaime Carbonell
Categories: cs.CL
Published: 2020-05-04
arXiv: 2005.01866v1
Abstract:
Traditional named entity recognition models use gazetteers (lists of entities) as features to improve performance. Although modern neural network models do not require such hand-crafted features for strong performance, recent work has demonstrated their utility for named entity recognition on English data. However, designing such features for low-resource languages is challenging, because exhaustive entity gazetteers do not exist in these languages. To address this problem, we propose a method of “soft gazetteers” that incorporates ubiquitously available information from English knowledge bases, such as Wikipedia, into neural named entity recognition models through cross-lingual entity linking. Our experiments on four low-resource languages show an average improvement of 4 points in F1 score. Code and data are available at https://github.com/neulab/soft-gazetteers.
42. Named Entity Recognition in COVID-19 tweets with Entity Knowledge Augmentation
Authors: Xuankang Zhang, Jiangming Liu
Categories: cs.CL, cs.AI
Published: 2025-10-05
arXiv: 2510.04001v1
Abstract:
The COVID-19 pandemic causes severe social and economic disruption around the world, raising various subjects that are discussed over social media. Identifying pandemic-related named entities as expressed on social media is fundamental and important to understand the discussions about the pandemic. However, there is limited work on named entity recognition on this topic due to the following challenges: 1) COVID-19 texts in social media are informal and their annotations are rare and insufficient to train a robust recognition model, and 2) named entity recognition in COVID-19 requires extensive domain-specific knowledge. To address these issues, we propose a novel entity knowledge augmentation approach for COVID-19, which can also be applied in general biomedical named entity recognition in both informal text format and formal text format. Experiments carried out on the COVID-19 tweets dataset and PubMed dataset show that our proposed entity knowledge augmentation improves NER performance in both fully-supervised and few-shot settings. Our source code is publicly available: https://github.com/kkkenshi/LLM-EKA/tree/master
43. Cost-Quality Adaptive Active Learning for Chinese Clinical Named Entity Recognition
Authors: Tingting Cai, Yangming Zhou, Hong Zheng
Categories: cs.CL
Published: 2020-08-28
arXiv: 2008.12548v1
Abstract:
Clinical Named Entity Recognition (CNER) aims to automatically identity clinical terminologies in Electronic Health Records (EHRs), which is a fundamental and crucial step for clinical research. To train a high-performance model for CNER, it usually requires a large number of EHRs with high-quality labels. However, labeling EHRs, especially Chinese EHRs, is time-consuming and expensive. One effective solution to this is active learning, where a model asks labelers to annotate data which the model is uncertain of. Conventional active learning assumes a single labeler that always replies noiseless answers to queried labels. However, in real settings, multiple labelers provide diverse quality of annotation with varied costs and labelers with low overall annotation quality can still assign correct labels for some specific instances. In this paper, we propose a Cost-Quality Adaptive Active Learning (CQAAL) approach for CNER in Chinese EHRs, which maintains a balance between the annotation quality, labeling costs, and the informativeness of selected instances. Specifically, CQAAL selects cost-effective instance-labeler pairs to achieve better annotation quality with lower costs in an adaptive manner. Computational results on the CCKS-2017 Task 2 benchmark dataset demonstrate the superiority and effectiveness of the proposed CQAAL.
44. Zero- and Few-Shot Named-Entity Recognition: Case Study and Dataset in the Crime Domain (CrimeNER)
Authors: Miguel Lopez-Duran, Julian Fierrez, Aythami Morales, Daniel DeAlcala, Gonzalo Mancera, Javier Irigoyen, Ruben Tolosana, Oscar Delgado, Francisco Jurado, Alvaro Ortigosa
Categories: cs.CL, cs.AI, cs.DB
Published: 2026-03-02
arXiv: 2603.02150v1
Abstract:
The extraction of critical information from crime-related documents is a crucial task for law enforcement agencies. Named-Entity Recognition (NER) can perform this task in extracting information about the crime, the criminal, or law enforcement agencies involved. However, there is a considerable lack of adequately annotated data on general real-world crime scenarios. To address this issue, we present CrimeNER, a case-study of Crime-related zero- and Few-Shot NER, and a general Crime-related Named-Entity Recognition database (CrimeNERdb) consisting of more than 1.5k annotated documents for the NER task extracted from public reports on terrorist attacks and the U.S. Department of Justice’s press notes. We define 5 types of coarse crime entity and a total of 22 types of fine-grained entity. We address the quality of the case-study and the annotated data with experiments on Zero and Few-Shot settings with State-of-the-Art NER models as well as generalist and commonly used Large Language Models.
45. Named entity recognition in resumes
Authors: Ege Kesim, Aysu Deliahmetoglu
Categories: cs.CL
Published: 2023-06-22
arXiv: 2306.13062v1
Abstract:
Named entity recognition (NER) is used to extract information from various documents and texts such as names and dates. It is important to extract education and work experience information from resumes in order to filter them. Considering the fact that all information in a resume has to be entered to the companys system manually, automatizing this process will save time of the companies. In this study, a deep learning-based semi-automatic named entity recognition system has been implemented with a focus on resumes in the field of IT. Firstly, resumes of employees from five different IT related fields has been annotated. Six transformer based pre-trained models have been adapted to named entity recognition problem using the annotated data. These models have been selected among popular models in the natural language processing field. The obtained system can recognize eight different entity types which are city, date, degree, diploma major, job title, language, country and skill. Models used in the experiments are compared using micro, macro and weighted F1 scores and the performance of the methods was evaluated. Taking these scores into account for test set the best micro and weighted F1 score is obtained by RoBERTa and the best macro F1 score is obtained by Electra model.
46. Multilingual Clinical NER for Diseases and Medications Recognition in Cardiology Texts using BERT Embeddings
Authors: Manuela Daniela Danu, George Marica, Constantin Suciu, Lucian Mihai Itu, Oladimeji Farri
Categories: cs.CL
Published: 2025-10-20
arXiv: 2510.17437v1
Abstract:
The rapidly increasing volume of electronic health record (EHR) data underscores a pressing need to unlock biomedical knowledge from unstructured clinical texts to support advancements in data-driven clinical systems, including patient diagnosis, disease progression monitoring, treatment effects assessment, prediction of future clinical events, etc. While contextualized language models have demonstrated impressive performance improvements for named entity recognition (NER) systems in English corpora, there remains a scarcity of research focused on clinical texts in low-resource languages. To bridge this gap, our study aims to develop multiple deep contextual embedding models to enhance clinical NER in the cardiology domain, as part of the BioASQ MultiCardioNER shared task. We explore the effectiveness of different monolingual and multilingual BERT-based models, trained on general domain text, for extracting disease and medication mentions from clinical case reports written in English, Spanish, and Italian. We achieved an F1-score of 77.88% on Spanish Diseases Recognition (SDR), 92.09% on Spanish Medications Recognition (SMR), 91.74% on English Medications Recognition (EMR), and 88.9% on Italian Medications Recognition (IMR). These results outperform the mean and median F1 scores in the test leaderboard across all subtasks, with the mean/median values being: 69.61%/75.66% for SDR, 81.22%/90.18% for SMR, 89.2%/88.96% for EMR, and 82.8%/87.76% for IMR.
47. Large Language Models Struggle in Token-Level Clinical Named Entity Recognition
Authors: Qiuhao Lu, Rui Li, Andrew Wen, Jinlian Wang, Liwei Wang, Hongfang Liu
Categories: cs.CL, cs.AI, cs.LG
Published: 2024-06-30
arXiv: 2407.00731v2
Abstract:
Large Language Models (LLMs) have revolutionized various sectors, including healthcare where they are employed in diverse applications. Their utility is particularly significant in the context of rare diseases, where data scarcity, complexity, and specificity pose considerable challenges. In the clinical domain, Named Entity Recognition (NER) stands out as an essential task and it plays a crucial role in extracting relevant information from clinical texts. Despite the promise of LLMs, current research mostly concentrates on document-level NER, identifying entities in a more general context across entire documents, without extracting their precise location. Additionally, efforts have been directed towards adapting ChatGPT for token-level NER. However, there is a significant research gap when it comes to employing token-level NER for clinical texts, especially with the use of local open-source LLMs. This study aims to bridge this gap by investigating the effectiveness of both proprietary and local LLMs in token-level clinical NER. Essentially, we delve into the capabilities of these models through a series of experiments involving zero-shot prompting, few-shot prompting, retrieval-augmented generation (RAG), and instruction-fine-tuning. Our exploration reveals the inherent challenges LLMs face in token-level NER, particularly in the context of rare diseases, and suggests possible improvements for their application in healthcare. This research contributes to narrowing a significant gap in healthcare informatics and offers insights that could lead to a more refined application of LLMs in the healthcare sector.
48. Retrieval-Enhanced Named Entity Recognition
Authors: Enzo Shiraishi, Raphael Y. de Camargo, Henrique L. P. Silva, Ronaldo C. Prati
Categories: cs.CL, cs.IR
Published: 2024-10-17
arXiv: 2410.13118v1
Abstract:
When combined with In-Context Learning, a technique that enables models to adapt to new tasks by incorporating task-specific examples or demonstrations directly within the input prompt, autoregressive language models have achieved good performance in a wide range of tasks and applications. However, this combination has not been properly explored in the context of named entity recognition, where the structure of this task poses unique challenges. We propose RENER (Retrieval-Enhanced Named Entity Recognition), a technique for named entity recognition using autoregressive language models based on In-Context Learning and information retrieval techniques. When presented with an input text, RENER fetches similar examples from a dataset of training examples that are used to enhance a language model to recognize named entities from this input text. RENER is modular and independent of the underlying language model and information retrieval algorithms. Experimental results show that in the CrossNER collection we achieve state-of-the-art performance with the proposed technique and that information retrieval can increase the F-score by up to 11 percentage points.
49. Empirical Evaluation of Character-Based Model on Neural Named-Entity Recognition in Indonesian Conversational Texts
Authors: Kemal Kurniawan, Samuel Louvan
Categories: cs.CL
Published: 2018-05-31
arXiv: 1805.12291v3
Abstract:
Despite the long history of named-entity recognition (NER) task in the natural language processing community, previous work rarely studied the task on conversational texts. Such texts are challenging because they contain a lot of word variations which increase the number of out-of-vocabulary (OOV) words. The high number of OOV words poses a difficulty for word-based neural models. Meanwhile, there is plenty of evidence to the effectiveness of character-based neural models in mitigating this OOV problem. We report an empirical evaluation of neural sequence labeling models with character embedding to tackle NER task in Indonesian conversational texts. Our experiments show that (1) character models outperform word embedding-only models by up to 4 $F_1$ points, (2) character models perform better in OOV cases with an improvement of as high as 15 $F_1$ points, and (3) character models are robust against a very high OOV rate.
50. Fast and Accurate Recognition of Chinese Clinical Named Entities with Residual Dilated Convolutions
Authors: Jiahui Qiu, Qi Wang, Yangming Zhou, Tong Ruan, Ju Gao
Categories: cs.CL
Published: 2018-08-27
arXiv: 1808.08669v3
Abstract:
Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translation research. In recent years, deep learning methods have achieved significant success in CNER tasks. However, these methods depend greatly on Recurrent Neural Networks (RNNs), which maintain a vector of hidden activations that are propagated through time, thus causing too much time to train models. In this paper, we propose a Residual Dilated Convolutional Neural Network with Conditional Random Field (RD-CNN-CRF) to solve it. Specifically, Chinese characters and dictionary features are first projected into dense vector representations, then they are fed into the residual dilated convolutional neural network to capture contextual features. Finally, a conditional random field is employed to capture dependencies between neighboring tags. Computational results on the CCKS-2017 Task 2 benchmark dataset show that our proposed RD-CNN-CRF method competes favorably with state-of-the-art RNN-based methods both in terms of computational performance and training time.