Daily Papers

Named entity recognition (NER) models generally perform poorly when large training datasets are unavailable for low-resource domains. Recently, pre-training a large-scale language model has become a promising direction for coping with the data scarcity issue. However, the underlying discrepancies between the language modeling and NER task could limit the models' performance, and pre-training for the NER task has rarely been studied since the collected NER datasets are generally small or large but with low quality. In this paper, we construct a massive NER corpus with a relatively high quality, and we pre-train a NER-BERT model based on the created dataset. Experimental results show that our pre-trained model can significantly outperform BERT as well as other strong baselines in low-resource scenarios across nine diverse domains. Moreover, a visualization of entity representations further indicates the effectiveness of NER-BERT for categorizing a variety of entities.

The use of BERT, one of the most popular language models, has led to improvements in many Natural Language Processing (NLP) tasks. One such task is Named Entity Recognition (NER) i.e. automatic identification of named entities such as location, person, organization, etc. from a given text. It is also an important base step for many NLP tasks such as information extraction and argumentation mining. Even though there is much research done on NER using BERT and other popular language models, the same is not explored in detail when it comes to Legal NLP or Legal Tech. Legal NLP applies various NLP techniques such as sentence similarity or NER specifically on legal data. There are only a handful of models for NER tasks using BERT language models, however, none of these are aimed at legal documents in German. In this paper, we fine-tune a popular BERT language model trained on German data (German BERT) on a Legal Entity Recognition (LER) dataset. To make sure our model is not overfitting, we performed a stratified 10-fold cross-validation. The results we achieve by fine-tuning German BERT on the LER dataset outperform the BiLSTM-CRF+ model used by the authors of the same LER dataset. Finally, we make the model openly available via HuggingFace.

Clinical texts, represented in electronic medical records (EMRs), contain rich medical information and are essential for disease prediction, personalised information recommendation, clinical decision support, and medication pattern mining and measurement. Relation extractions between medication mentions and temporal information can further help clinicians better understand the patients' treatment history. To evaluate the performances of deep learning (DL) and large language models (LLMs) in medication extraction and temporal relations classification, we carry out an empirical investigation of MedTem project using several advanced learning structures including BiLSTM-CRF and CNN-BiLSTM for a clinical domain named entity recognition (NER), and BERT-CNN for temporal relation extraction (RE), in addition to the exploration of different word embedding techniques. Furthermore, we also designed a set of post-processing roles to generate structured output on medications and the temporal relation. Our experiments show that CNN-BiLSTM slightly wins the BiLSTM-CRF model on the i2b2-2009 clinical NER task yielding 75.67, 77.83, and 78.17 for precision, recall, and F1 scores using Macro Average. BERT-CNN model also produced reasonable evaluation scores 64.48, 67.17, and 65.03 for P/R/F1 using Macro Avg on the temporal relation extraction test set from i2b2-2012 challenges. Code and Tools from MedTem will be hosted at https://github.com/HECTA-UoM/MedTem

In this work, we represent Lex-BERT, which incorporates the lexicon information into Chinese BERT for named entity recognition (NER) tasks in a natural manner. Instead of using word embeddings and a newly designed transformer layer as in FLAT, we identify the boundary of words in the sentences using special tokens, and the modified sentence will be encoded directly by BERT. Our model does not introduce any new parameters and are more efficient than FLAT. In addition, we do not require any word embeddings accompanying the lexicon collection. Experiments on Ontonotes and ZhCrossNER show that our model outperforms FLAT and other baselines.

This work introduces the L3Cube-MahaSocialNER dataset, the first and largest social media dataset specifically designed for Named Entity Recognition (NER) in the Marathi language. The dataset comprises 18,000 manually labeled sentences covering eight entity classes, addressing challenges posed by social media data, including non-standard language and informal idioms. Deep learning models, including CNN, LSTM, BiLSTM, and Transformer models, are evaluated on the individual dataset with IOB and non-IOB notations. The results demonstrate the effectiveness of these models in accurately recognizing named entities in Marathi informal text. The L3Cube-MahaSocialNER dataset offers user-centric information extraction and supports real-time applications, providing a valuable resource for public opinion analysis, news, and marketing on social media platforms. We also show that the zero-shot results of the regular NER model are poor on the social NER test set thus highlighting the need for more social NER datasets. The datasets and models are publicly available at https://github.com/l3cube-pune/MarathiNLP

The introduction of the Transformer neural network, along with techniques like self-supervised pre-training and transfer learning, has paved the way for advanced models like BERT. Despite BERT's impressive performance, opportunities for further enhancement exist. To our knowledge, most efforts are focusing on improving BERT's performance in English and in general domains, with no study specifically addressing the legal Turkish domain. Our study is primarily dedicated to enhancing the BERT model within the legal Turkish domain through modifications in the pre-training phase. In this work, we introduce our innovative modified pre-training approach by combining diverse masking strategies. In the fine-tuning task, we focus on two essential downstream tasks in the legal domain: name entity recognition and multi-label text classification. To evaluate our modified pre-training approach, we fine-tuned all customized models alongside the original BERT models to compare their performance. Our modified approach demonstrated significant improvements in both NER and multi-label text classification tasks compared to the original BERT model. Finally, to showcase the impact of our proposed models, we trained our best models with different corpus sizes and compared them with BERTurk models. The experimental results demonstrate that our innovative approach, despite being pre-trained on a smaller corpus, competes with BERTurk.

We present HILGEN, a Hierarchically-Informed Data Generation approach that combines domain knowledge from the Unified Medical Language System (UMLS) with synthetic data generated by large language models (LLMs), specifically GPT-3.5. Our approach leverages UMLS's hierarchical structure to expand training data with related concepts, while incorporating contextual information from LLMs through targeted prompts aimed at automatically generating synthetic examples for sparsely occurring named entities. The performance of the HILGEN approach was evaluated across four biomedical NER datasets (MIMIC III, BC5CDR, NCBI-Disease, and Med-Mentions) using BERT-Large and DANN (Data Augmentation with Nearest Neighbor Classifier) models, applying various data generation strategies, including UMLS, GPT-3.5, and their best ensemble. For the BERT-Large model, incorporating UMLS led to an average F1 score improvement of 40.36%, while using GPT-3.5 resulted in a comparable average increase of 40.52%. The Best-Ensemble approach using BERT-Large achieved the highest improvement, with an average increase of 42.29%. DANN model's F1 score improved by 22.74% on average using the UMLS-only approach. The GPT-3.5-based method resulted in a 21.53% increase, and the Best-Ensemble DANN model showed a more notable improvement, with an average increase of 25.03%. Our proposed HILGEN approach improves NER performance in few-shot settings without requiring additional manually annotated data. Our experiments demonstrate that an effective strategy for optimizing biomedical NER is to combine biomedical knowledge curated in the past, such as the UMLS, and generative LLMs to create synthetic training instances. Our future research will focus on exploring additional innovative synthetic data generation strategies for further improving NER performance.

Named Entity Recognition (NER) is a basic NLP task and finds major applications in conversational and search systems. It helps us identify key entities in a sentence used for the downstream application. NER or similar slot filling systems for popular languages have been heavily used in commercial applications. In this work, we focus on Marathi, an Indian language, spoken prominently by the people of Maharashtra state. Marathi is a low resource language and still lacks useful NER resources. We present L3Cube-MahaNER, the first major gold standard named entity recognition dataset in Marathi. We also describe the manual annotation guidelines followed during the process. In the end, we benchmark the dataset on different CNN, LSTM, and Transformer based models like mBERT, XLM-RoBERTa, IndicBERT, MahaBERT, etc. The MahaBERT provides the best performance among all the models. The data and models are available at https://github.com/l3cube-pune/MarathiNLP .

Natural language processing (NLP) of clinical trial documents can be useful in new trial design. Here we identify entity types relevant to clinical trial design and propose a framework called CT-BERT for information extraction from clinical trial text. We trained named entity recognition (NER) models to extract eligibility criteria entities by fine-tuning a set of pre-trained BERT models. We then compared the performance of CT-BERT with recent baseline methods including attention-based BiLSTM and Criteria2Query. The results demonstrate the superiority of CT-BERT in clinical trial NLP.

Large pretrained masked language models have become state-of-the-art solutions for many NLP problems. The research has been mostly focused on English language, though. While massively multilingual models exist, studies have shown that monolingual models produce much better results. We train two trilingual BERT-like models, one for Finnish, Estonian, and English, the other for Croatian, Slovenian, and English. We evaluate their performance on several downstream tasks, NER, POS-tagging, and dependency parsing, using the multilingual BERT and XLM-R as baselines. The newly created FinEst BERT and CroSloEngual BERT improve the results on all tasks in most monolingual and cross-lingual situations

NLP research has been focused on NER extraction and how to efficiently extract them from a sentence. However, generating relevant context of entities from a sentence has remained under-explored. In this work we introduce the task Context-NER in which relevant context of an entity has to be generated. The extracted context may not be found exactly as a substring in the sentence. We also introduce the EDGAR10-Q dataset for the same, which is a corpus of 1,500 publicly traded companies. It is a manually created complex corpus and one of the largest in terms of number of sentences and entities (1 M and 2.8 M). We introduce a baseline approach that leverages phrase generation algorithms and uses the pre-trained BERT model to get 33% ROUGE-L score. We also do a one shot evaluation with GPT-3 and get 39% score, signifying the hardness and future scope of this task. We hope that addition of this dataset and our study will pave the way for further research in this domain.

In the last few years, three major topics received increased interest: deep learning, NLP and conversational agents. Bringing these three topics together to create an amazing digital customer experience and indeed deploy in production and solve real-world problems is something innovative and disruptive. We introduce a new Portuguese financial domain language representation model called BERTa\'u. BERTa\'u is an uncased BERT-base trained from scratch with data from the Ita\'u virtual assistant chatbot solution. Our novel contribution is that BERTa\'u pretrained language model requires less data, reached state-of-the-art performance in three NLP tasks, and generates a smaller and lighter model that makes the deployment feasible. We developed three tasks to validate our model: information retrieval with Frequently Asked Questions (FAQ) from Ita\'u bank, sentiment analysis from our virtual assistant data, and a NER solution. All proposed tasks are real-world solutions in production on our environment and the usage of a specialist model proved to be effective when compared to Google BERT multilingual and the DPRQuestionEncoder from Facebook, available at Hugging Face. The BERTa\'u improves the performance in 22% of FAQ Retrieval MRR metric, 2.1% in Sentiment Analysis F1 score, 4.4% in NER F1 score and can also represent the same sequence in up to 66% fewer tokens when compared to "shelf models".

Named Entity Recognition (NER) models play a crucial role in various NLP tasks, including information extraction (IE) and text understanding. In academic writing, references to machine learning models and datasets are fundamental components of various computer science publications and necessitate accurate models for identification. Despite the advancements in NER, existing ground truth datasets do not treat fine-grained types like ML model and model architecture as separate entity types, and consequently, baseline models cannot recognize them as such. In this paper, we release a corpus of 100 manually annotated full-text scientific publications and a first baseline model for 10 entity types centered around ML models and datasets. In order to provide a nuanced understanding of how ML models and datasets are mentioned and utilized, our dataset also contains annotations for informal mentions like "our BERT-based model" or "an image CNN". You can find the ground truth dataset and code to replicate model training at https://data.gesis.org/gsap/gsap-ner.

Pre-trained text encoders have rapidly advanced the state of the art on many NLP tasks. We focus on one such model, BERT, and aim to quantify where linguistic information is captured within the network. We find that the model represents the steps of the traditional NLP pipeline in an interpretable and localizable way, and that the regions responsible for each step appear in the expected sequence: POS tagging, parsing, NER, semantic roles, then coreference. Qualitative analysis reveals that the model can and often does adjust this pipeline dynamically, revising lower-level decisions on the basis of disambiguating information from higher-level representations.

Pre-trained transformer language models (LMs) have in recent years become the dominant paradigm in applied NLP. These models have achieved state-of-the-art performance on tasks such as information extraction, question answering, sentiment analysis, document classification and many others. In the biomedical domain, significant progress has been made in adapting this paradigm to NLP tasks that require the integration of domain-specific knowledge as well as statistical modelling of language. In particular, research in this area has focused on the question of how best to construct LMs that take into account not only the patterns of token distribution in medical text, but also the wealth of structured information contained in terminology resources such as the UMLS. This work contributes a data-centric paradigm for enriching the language representations of biomedical transformer-encoder LMs by extracting text sequences from the UMLS. This allows for graph-based learning objectives to be combined with masked-language pre-training. Preliminary results from experiments in the extension of pre-trained LMs as well as training from scratch show that this framework improves downstream performance on multiple biomedical and clinical Named Entity Recognition (NER) tasks.

This paper presents Wojood, a corpus for Arabic nested Named Entity Recognition (NER). Nested entities occur when one entity mention is embedded inside another entity mention. Wojood consists of about 550K Modern Standard Arabic (MSA) and dialect tokens that are manually annotated with 21 entity types including person, organization, location, event and date. More importantly, the corpus is annotated with nested entities instead of the more common flat annotations. The data contains about 75K entities and 22.5% of which are nested. The inter-annotator evaluation of the corpus demonstrated a strong agreement with Cohen's Kappa of 0.979 and an F1-score of 0.976. To validate our data, we used the corpus to train a nested NER model based on multi-task learning and AraBERT (Arabic BERT). The model achieved an overall micro F1-score of 0.884. Our corpus, the annotation guidelines, the source code and the pre-trained model are publicly available.

Recent advances in language representation using neural networks have made it viable to transfer the learned internal states of a trained model to downstream natural language processing tasks, such as named entity recognition (NER) and question answering. It has been shown that the leverage of pre-trained language models improves the overall performance on many tasks and is highly beneficial when labeled data is scarce. In this work, we train Portuguese BERT models and employ a BERT-CRF architecture to the NER task on the Portuguese language, combining the transfer capabilities of BERT with the structured predictions of CRF. We explore feature-based and fine-tuning training strategies for the BERT model. Our fine-tuning approach obtains new state-of-the-art results on the HAREM I dataset, improving the F1-score by 1 point on the selective scenario (5 NE classes) and by 4 points on the total scenario (10 NE classes).

We present BERTweet, the first public large-scale pre-trained language model for English Tweets. Our BERTweet, having the same architecture as BERT-base (Devlin et al., 2019), is trained using the RoBERTa pre-training procedure (Liu et al., 2019). Experiments show that BERTweet outperforms strong baselines RoBERTa-base and XLM-R-base (Conneau et al., 2020), producing better performance results than the previous state-of-the-art models on three Tweet NLP tasks: Part-of-speech tagging, Named-entity recognition and text classification. We release BERTweet under the MIT License to facilitate future research and applications on Tweet data. Our BERTweet is available at https://github.com/VinAIResearch/BERTweet

We introduce FaBERT, a Persian BERT-base model pre-trained on the HmBlogs corpus, encompassing both informal and formal Persian texts. FaBERT is designed to excel in traditional Natural Language Understanding (NLU) tasks, addressing the intricacies of diverse sentence structures and linguistic styles prevalent in the Persian language. In our comprehensive evaluation of FaBERT on 12 datasets in various downstream tasks, encompassing Sentiment Analysis (SA), Named Entity Recognition (NER), Natural Language Inference (NLI), Question Answering (QA), and Question Paraphrasing (QP), it consistently demonstrated improved performance, all achieved within a compact model size. The findings highlight the importance of utilizing diverse and cleaned corpora, such as HmBlogs, to enhance the performance of language models like BERT in Persian Natural Language Processing (NLP) applications. FaBERT is openly accessible at https://huggingface.co/sbunlp/fabert

Language-specific pre-trained models have proven to be more accurate than multilingual ones in a monolingual evaluation setting, Arabic is no exception. However, we found that previously released Arabic BERT models were significantly under-trained. In this technical report, we present JABER and SABER, Junior and Senior Arabic BERt respectively, our pre-trained language model prototypes dedicated for Arabic. We conduct an empirical study to systematically evaluate the performance of models across a diverse set of existing Arabic NLU tasks. Experimental results show that JABER and SABER achieve state-of-the-art performances on ALUE, a new benchmark for Arabic Language Understanding Evaluation, as well as on a well-established NER benchmark.

Code-switching occurs when more than one language is mixed in a given sentence or a conversation. This phenomenon is more prominent on social media platforms and its adoption is increasing over time. Therefore code-mixed NLP has been extensively studied in the literature. As pre-trained transformer-based architectures are gaining popularity, we observe that real code-mixing data are scarce to pre-train large language models. We present L3Cube-HingCorpus, the first large-scale real Hindi-English code mixed data in a Roman script. It consists of 52.93M sentences and 1.04B tokens, scraped from Twitter. We further present HingBERT, HingMBERT, HingRoBERTa, and HingGPT. The BERT models have been pre-trained on codemixed HingCorpus using masked language modelling objectives. We show the effectiveness of these BERT models on the subsequent downstream tasks like code-mixed sentiment analysis, POS tagging, NER, and LID from the GLUECoS benchmark. The HingGPT is a GPT2 based generative transformer model capable of generating full tweets. We also release L3Cube-HingLID Corpus, the largest code-mixed Hindi-English language identification(LID) dataset and HingBERT-LID, a production-quality LID model to facilitate capturing of more code-mixed data using the process outlined in this work. The dataset and models are available at https://github.com/l3cube-pune/code-mixed-nlp .

This paper introduces the Swedish BERT ("KB-BERT") developed by the KBLab for data-driven research at the National Library of Sweden (KB). Building on recent efforts to create transformer-based BERT models for languages other than English, we explain how we used KB's collections to create and train a new language-specific BERT model for Swedish. We also present the results of our model in comparison with existing models - chiefly that produced by the Swedish Public Employment Service, Arbetsf\"ormedlingen, and Google's multilingual M-BERT - where we demonstrate that KB-BERT outperforms these in a range of NLP tasks from named entity recognition (NER) to part-of-speech tagging (POS). Our discussion highlights the difficulties that continue to exist given the lack of training data and testbeds for smaller languages like Swedish. We release our model for further exploration and research here: https://github.com/Kungbib/swedish-bert-models .

We present a new pre-trained language model (PLM) for modern Hebrew, termed AlephBERTGimmel, which employs a much larger vocabulary (128K items) than standard Hebrew PLMs before. We perform a contrastive analysis of this model against all previous Hebrew PLMs (mBERT, heBERT, AlephBERT) and assess the effects of larger vocabularies on task performance. Our experiments show that larger vocabularies lead to fewer splits, and that reducing splits is better for model performance, across different tasks. All in all this new model achieves new SOTA on all available Hebrew benchmarks, including Morphological Segmentation, POS Tagging, Full Morphological Analysis, NER, and Sentiment Analysis. Subsequently we advocate for PLMs that are larger not only in terms of number of layers or training data, but also in terms of their vocabulary. We release the new model publicly for unrestricted use.

We present L3Cube-MahaCorpus a Marathi monolingual data set scraped from different internet sources. We expand the existing Marathi monolingual corpus with 24.8M sentences and 289M tokens. We further present, MahaBERT, MahaAlBERT, and MahaRoBerta all BERT-based masked language models, and MahaFT, the fast text word embeddings both trained on full Marathi corpus with 752M tokens. We show the effectiveness of these resources on downstream Marathi sentiment analysis, text classification, and named entity recognition (NER) tasks. We also release MahaGPT, a generative Marathi GPT model trained on Marathi corpus. Marathi is a popular language in India but still lacks these resources. This work is a step forward in building open resources for the Marathi language. The data and models are available at https://github.com/l3cube-pune/MarathiNLP .

Pretrained contextual representation models (Peters et al., 2018; Devlin et al., 2018) have pushed forward the state-of-the-art on many NLP tasks. A new release of BERT (Devlin, 2018) includes a model simultaneously pretrained on 104 languages with impressive performance for zero-shot cross-lingual transfer on a natural language inference task. This paper explores the broader cross-lingual potential of mBERT (multilingual) as a zero shot language transfer model on 5 NLP tasks covering a total of 39 languages from various language families: NLI, document classification, NER, POS tagging, and dependency parsing. We compare mBERT with the best-published methods for zero-shot cross-lingual transfer and find mBERT competitive on each task. Additionally, we investigate the most effective strategy for utilizing mBERT in this manner, determine to what extent mBERT generalizes away from language specific features, and measure factors that influence cross-lingual transfer.

This paper presents a comprehensive analysis of various static word embeddings for Hungarian, including traditional models such as Word2Vec, FastText, as well as static embeddings derived from BERT-based models using different extraction methods. We evaluate these embeddings on both intrinsic and extrinsic tasks to provide a holistic view of their performance. For intrinsic evaluation, we employ a word analogy task, which assesses the embeddings ability to capture semantic and syntactic relationships. Our results indicate that traditional static embeddings, particularly FastText, excel in this task, achieving high accuracy and mean reciprocal rank (MRR) scores. Among the BERT-based models, the X2Static method for extracting static embeddings demonstrates superior performance compared to decontextualized and aggregate methods, approaching the effectiveness of traditional static embeddings. For extrinsic evaluation, we utilize a bidirectional LSTM model to perform Named Entity Recognition (NER) and Part-of-Speech (POS) tagging tasks. The results reveal that embeddings derived from dynamic models, especially those extracted using the X2Static method, outperform purely static embeddings. Notably, ELMo embeddings achieve the highest accuracy in both NER and POS tagging tasks, underscoring the benefits of contextualized representations even when used in a static form. Our findings highlight the continued relevance of static word embeddings in NLP applications and the potential of advanced extraction methods to enhance the utility of BERT-based models. This piece of research contributes to the understanding of embedding performance in the Hungarian language and provides valuable insights for future developments in the field. The training scripts, evaluation codes, restricted vocabulary, and extracted embeddings will be made publicly available to support further research and reproducibility.

In this work we present the experiments which lead to the creation of our BERT and ELECTRA based German language models, GBERT and GELECTRA. By varying the input training data, model size, and the presence of Whole Word Masking (WWM) we were able to attain SoTA performance across a set of document classification and named entity recognition (NER) tasks for both models of base and large size. We adopt an evaluation driven approach in training these models and our results indicate that both adding more data and utilizing WWM improve model performance. By benchmarking against existing German models, we show that these models are the best German models to date. Our trained models will be made publicly available to the research community.

Cross-domain NER is a practical yet challenging problem since the data scarcity in the real-world scenario. A common practice is first to learn a NER model in a rich-resource general domain and then adapt the model to specific domains. Due to the mismatch problem between entity types across domains, the wide knowledge in the general domain can not effectively transfer to the target domain NER model. To this end, we model the label relationship as a probability distribution and construct label graphs in both source and target label spaces. To enhance the contextual representation with label structures, we fuse the label graph into the word embedding output by BERT. By representing label relationships as graphs, we formulate cross-domain NER as a graph matching problem. Furthermore, the proposed method has good applicability with pre-training methods and is potentially capable of other cross-domain prediction tasks. Empirical results on four datasets show that our method outperforms a series of transfer learning, multi-task learning, and few-shot learning methods.

The Russian Drug Reaction Corpus (RuDReC) is a new partially annotated corpus of consumer reviews in Russian about pharmaceutical products for the detection of health-related named entities and the effectiveness of pharmaceutical products. The corpus itself consists of two parts, the raw one and the labelled one. The raw part includes 1.4 million health-related user-generated texts collected from various Internet sources, including social media. The labelled part contains 500 consumer reviews about drug therapy with drug- and disease-related information. Labels for sentences include health-related issues or their absence. The sentences with one are additionally labelled at the expression level for identification of fine-grained subtypes such as drug classes and drug forms, drug indications, and drug reactions. Further, we present a baseline model for named entity recognition (NER) and multi-label sentence classification tasks on this corpus. The macro F1 score of 74.85% in the NER task was achieved by our RuDR-BERT model. For the sentence classification task, our model achieves the macro F1 score of 68.82% gaining 7.47% over the score of BERT model trained on Russian data. We make the RuDReC corpus and pretrained weights of domain-specific BERT models freely available at https://github.com/cimm-kzn/RuDReC

We pretrain RoBERTa on a Turkish corpora using BPE tokenizer. Our model outperforms BERTurk family models on the BOUN dataset for the POS task while resulting in underperformance on the IMST dataset for the same task and achieving competitive scores on the Turkish split of the XTREME dataset for the NER task - all while being pretrained on smaller data than its competitors. We release our pretrained model and tokenizer.

While recent pre-trained transformer-based models can perform named entity recognition (NER) with great accuracy, their limited range remains an issue when applied to long documents such as whole novels. To alleviate this issue, a solution is to retrieve relevant context at the document level. Unfortunately, the lack of supervision for such a task means one has to settle for unsupervised approaches. Instead, we propose to generate a synthetic context retrieval training dataset using Alpaca, an instructiontuned large language model (LLM). Using this dataset, we train a neural context retriever based on a BERT model that is able to find relevant context for NER. We show that our method outperforms several retrieval baselines for the NER task on an English literary dataset composed of the first chapter of 40 books.

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.

Substance use disorders (SUDs) are a growing concern globally, necessitating enhanced understanding of the problem and its trends through data-driven research. Social media are unique and important sources of information about SUDs, particularly since the data in such sources are often generated by people with lived experiences. In this paper, we introduce Reddit-Impacts, a challenging Named Entity Recognition (NER) dataset curated from subreddits dedicated to discussions on prescription and illicit opioids, as well as medications for opioid use disorder. The dataset specifically concentrates on the lesser-studied, yet critically important, aspects of substance use--its clinical and social impacts. We collected data from chosen subreddits using the publicly available Application Programming Interface for Reddit. We manually annotated text spans representing clinical and social impacts reported by people who also reported personal nonmedical use of substances including but not limited to opioids, stimulants and benzodiazepines. Our objective is to create a resource that can enable the development of systems that can automatically detect clinical and social impacts of substance use from text-based social media data. The successful development of such systems may enable us to better understand how nonmedical use of substances affects individual health and societal dynamics, aiding the development of effective public health strategies. In addition to creating the annotated data set, we applied several machine learning models to establish baseline performances. Specifically, we experimented with transformer models like BERT, and RoBERTa, one few-shot learning model DANN by leveraging the full training dataset, and GPT-3.5 by using one-shot learning, for automatic NER of clinical and social impacts. The dataset has been made available through the 2024 SMM4H shared tasks.

Lately, pre-trained language models advanced the field of natural language processing (NLP). The introduction of Bidirectional Encoders for Transformers (BERT) and its optimized version RoBERTa have had significant impact and increased the relevance of pre-trained models. First, research in this field mainly started on English data followed by models trained with multilingual text corpora. However, current research shows that multilingual models are inferior to monolingual models. Currently, no German single language RoBERTa model is yet published, which we introduce in this work (GottBERT). The German portion of the OSCAR data set was used as text corpus. In an evaluation we compare its performance on the two Named Entity Recognition (NER) tasks Conll 2003 and GermEval 2014 as well as on the text classification tasks GermEval 2018 (fine and coarse) and GNAD with existing German single language BERT models and two multilingual ones. GottBERT was pre-trained related to the original RoBERTa model using fairseq. All downstream tasks were trained using hyperparameter presets taken from the benchmark of German BERT. The experiments were setup utilizing FARM. Performance was measured by the F_{1} score. GottBERT was successfully pre-trained on a 256 core TPU pod using the RoBERTa BASE architecture. Even without extensive hyper-parameter optimization, in all NER and one text classification task, GottBERT already outperformed all other tested German and multilingual models. In order to support the German NLP field, we publish GottBERT under the AGPLv3 license.

We present a new approach for pretraining a bi-directional transformer model that provides significant performance gains across a variety of language understanding problems. Our model solves a cloze-style word reconstruction task, where each word is ablated and must be predicted given the rest of the text. Experiments demonstrate large performance gains on GLUE and new state of the art results on NER as well as constituency parsing benchmarks, consistent with the concurrently introduced BERT model. We also present a detailed analysis of a number of factors that contribute to effective pretraining, including data domain and size, model capacity, and variations on the cloze objective.

Natural language processing (NLP) practitioners are leveraging large language models (LLM) to create structured datasets from semi-structured and unstructured data sources such as patents, papers, and theses, without having domain-specific knowledge. At the same time, ecological experts are searching for a variety of means to preserve biodiversity. To contribute to these efforts, we focused on endangered species and through in-context learning, we distilled knowledge from GPT-4. In effect, we created datasets for both named entity recognition (NER) and relation extraction (RE) via a two-stage process: 1) we generated synthetic data from GPT-4 of four classes of endangered species, 2) humans verified the factual accuracy of the synthetic data, resulting in gold data. Eventually, our novel dataset contains a total of 3.6K sentences, evenly divided between 1.8K NER and 1.8K RE sentences. The constructed dataset was then used to fine-tune both general BERT and domain-specific BERT variants, completing the knowledge distillation process from GPT-4 to BERT, because GPT-4 is resource intensive. Experiments show that our knowledge transfer approach is effective at creating a NER model suitable for detecting endangered species from texts.

Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on relations of a single type (e.g., protein-protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine. In this work, we first review commonly used named entity recognition (NER) and RE datasets. Then we present BioRED, a first-of-its-kind biomedical RE corpus with multiple entity types (e.g., gene/protein, disease, chemical) and relation pairs (e.g., gene-disease; chemical-chemical) at the document level, on a set of 600 PubMed abstracts. Further, we label each relation as describing either a novel finding or previously known background knowledge, enabling automated algorithms to differentiate between novel and background information. We assess the utility of BioRED by benchmarking several existing state-of-the-art methods, including BERT-based models, on the NER and RE tasks. Our results show that while existing approaches can reach high performance on the NER task (F-score of 89.3%), there is much room for improvement for the RE task, especially when extracting novel relations (F-score of 47.7%). Our experiments also demonstrate that such a rich dataset can successfully facilitate the development of more accurate, efficient, and robust RE systems for biomedicine. The BioRED dataset and annotation guideline are freely available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/.

Recent advancements in language models (LMs) have led to the emergence of powerful models such as Small LMs (e.g., T5) and Large LMs (e.g., GPT-4). These models have demonstrated exceptional capabilities across a wide range of tasks, such as name entity recognition (NER) in the general domain. (We define SLMs as pre-trained models with fewer parameters compared to models like GPT-3/3.5/4, such as T5, BERT, and others.) Nevertheless, their efficacy in the medical section remains uncertain and the performance of medical NER always needs high accuracy because of the particularity of the field. This paper aims to provide a thorough investigation to compare the performance of LMs in medical few-shot NER and answer How far is LMs from 100\% Few-shot NER in Medical Domain, and moreover to explore an effective entity recognizer to help improve the NER performance. Based on our extensive experiments conducted on 16 NER models spanning from 2018 to 2023, our findings clearly indicate that LLMs outperform SLMs in few-shot medical NER tasks, given the presence of suitable examples and appropriate logical frameworks. Despite the overall superiority of LLMs in few-shot medical NER tasks, it is important to note that they still encounter some challenges, such as misidentification, wrong template prediction, etc. Building on previous findings, we introduce a simple and effective method called RT (Retrieving and Thinking), which serves as retrievers, finding relevant examples, and as thinkers, employing a step-by-step reasoning process. Experimental results show that our proposed RT framework significantly outperforms the strong open baselines on the two open medical benchmark datasets

The integration of Large Language Models (LLMs) like GPT-4 into traditional Natural Language Processing (NLP) tasks has opened new avenues for enhancing model performance while reducing the reliance on extensive human annotations. This paper presents a novel approach that leverages the Chain of Thought (CoT) prompting technique to distill knowledge from GPT-4, subsequently applying it to improve the efficiency and effectiveness of a smaller model, BERT, on Named Entity Recognition (NER) tasks. Our method involves a two-phase training process: initially employing GPT-4 annotated data for pre-training and then refining the model with a combination of distilled and original human-annotated data. The results demonstrate that our mixed-training strategy significantly outperforms models trained solely on human annotations, achieving superior F1-scores and showcasing a cost-effective solution for resource-limited or closed-network settings. The study also discusses the challenges encountered, such as LLM output variability and the tendency towards hallucinations, proposing future work directions to enhance prompt design and annotation selection. Our findings indicate a promising synergy between LLM insights and traditional NLP techniques, paving the way for more accessible and robust NLP applications.

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. In this paper, we challenge this assumption by showing that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language models. To facilitate this investigation, we compile a comprehensive biomedical NLP benchmark from publicly-available datasets. Our experiments show that domain-specific pretraining serves as a solid foundation for a wide range of biomedical NLP tasks, leading to new state-of-the-art results across the board. Further, in conducting a thorough evaluation of modeling choices, both for pretraining and task-specific fine-tuning, we discover that some common practices are unnecessary with BERT models, such as using complex tagging schemes in named entity recognition (NER). To help accelerate research in biomedical NLP, we have released our state-of-the-art pretrained and task-specific models for the community, and created a leaderboard featuring our BLURB benchmark (short for Biomedical Language Understanding & Reasoning Benchmark) at https://aka.ms/BLURB.