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Jan 1

From Text to Actionable Intelligence: Automating STIX Entity and Relationship Extraction

Sharing methods of attack and their effectiveness is a cornerstone of building robust defensive systems. Threat analysis reports, produced by various individuals and organizations, play a critical role in supporting security operations and combating emerging threats. To enhance the timeliness and automation of threat intelligence sharing, several standards have been established, with the Structured Threat Information Expression (STIX) framework emerging as one of the most widely adopted. However, generating STIX-compatible data from unstructured security text remains a largely manual, expert-driven process. To address this challenge, we introduce AZERG, a tool designed to assist security analysts in automatically generating structured STIX representations. To achieve this, we adapt general-purpose large language models for the specific task of extracting STIX-formatted threat data. To manage the complexity, the task is divided into four subtasks: entity detection (T1), entity type identification (T2), related pair detection (T3), and relationship type identification (T4). We apply task-specific fine-tuning to accurately extract relevant entities and infer their relationships in accordance with the STIX specification. To address the lack of training data, we compiled a comprehensive dataset with 4,011 entities and 2,075 relationships extracted from 141 full threat analysis reports, all annotated in alignment with the STIX standard. Our models achieved F1-scores of 84.43% for T1, 88.49% for T2, 95.47% for T3, and 84.60% for T4 in real-world scenarios. We validated their performance against a range of open- and closed-parameter models, as well as state-of-the-art methods, demonstrating improvements of 2-25% across tasks.

Named Clinical Entity Recognition Benchmark

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.

  • 9 authors
·
Oct 7, 2024 3

DepNeCTI: Dependency-based Nested Compound Type Identification for Sanskrit

Multi-component compounding is a prevalent phenomenon in Sanskrit, and understanding the implicit structure of a compound's components is crucial for deciphering its meaning. Earlier approaches in Sanskrit have focused on binary compounds and neglected the multi-component compound setting. This work introduces the novel task of nested compound type identification (NeCTI), which aims to identify nested spans of a multi-component compound and decode the implicit semantic relations between them. To the best of our knowledge, this is the first attempt in the field of lexical semantics to propose this task. We present 2 newly annotated datasets including an out-of-domain dataset for this task. We also benchmark these datasets by exploring the efficacy of the standard problem formulations such as nested named entity recognition, constituency parsing and seq2seq, etc. We present a novel framework named DepNeCTI: Dependency-based Nested Compound Type Identifier that surpasses the performance of the best baseline with an average absolute improvement of 13.1 points F1-score in terms of Labeled Span Score (LSS) and a 5-fold enhancement in inference efficiency. In line with the previous findings in the binary Sanskrit compound identification task, context provides benefits for the NeCTI task. The codebase and datasets are publicly available at: https://github.com/yaswanth-iitkgp/DepNeCTI

  • 7 authors
·
Oct 14, 2023

EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical Text

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

  • 11 authors
·
Apr 16, 2023

CIFAKE: Image Classification and Explainable Identification of AI-Generated Synthetic Images

Recent technological advances in synthetic data have enabled the generation of images with such high quality that human beings cannot tell the difference between real-life photographs and Artificial Intelligence (AI) generated images. Given the critical necessity of data reliability and authentication, this article proposes to enhance our ability to recognise AI-generated images through computer vision. Initially, a synthetic dataset is generated that mirrors the ten classes of the already available CIFAR-10 dataset with latent diffusion which provides a contrasting set of images for comparison to real photographs. The model is capable of generating complex visual attributes, such as photorealistic reflections in water. The two sets of data present as a binary classification problem with regard to whether the photograph is real or generated by AI. This study then proposes the use of a Convolutional Neural Network (CNN) to classify the images into two categories; Real or Fake. Following hyperparameter tuning and the training of 36 individual network topologies, the optimal approach could correctly classify the images with 92.98% accuracy. Finally, this study implements explainable AI via Gradient Class Activation Mapping to explore which features within the images are useful for classification. Interpretation reveals interesting concepts within the image, in particular, noting that the actual entity itself does not hold useful information for classification; instead, the model focuses on small visual imperfections in the background of the images. The complete dataset engineered for this study, referred to as the CIFAKE dataset, is made publicly available to the research community for future work.

  • 2 authors
·
Mar 24, 2023

LLMs-in-the-Loop Part 2: Expert Small AI Models for Anonymization and De-identification of PHI Across Multiple Languages

The rise of chronic diseases and pandemics like COVID-19 has emphasized the need for effective patient data processing while ensuring privacy through anonymization and de-identification of protected health information (PHI). Anonymized data facilitates research without compromising patient confidentiality. This paper introduces expert small AI models developed using the LLM-in-the-loop methodology to meet the demand for domain-specific de-identification NER models. These models overcome the privacy risks associated with large language models (LLMs) used via APIs by eliminating the need to transmit or store sensitive data. More importantly, they consistently outperform LLMs in de-identification tasks, offering superior performance and reliability. Our de-identification NER models, developed in eight languages (English, German, Italian, French, Romanian, Turkish, Spanish, and Arabic) achieved f1-micro score averages of 0.966, 0.975, 0.976, 0.970, 0.964, 0.974, 0.978, and 0.953 respectively. These results establish them as the most accurate healthcare anonymization solutions, surpassing existing small models and even general-purpose LLMs such as GPT-4o. While Part-1 of this series introduced the LLM-in-the-loop methodology for bio-medical document translation, this second paper showcases its success in developing cost-effective expert small NER models in de-identification tasks. Our findings lay the groundwork for future healthcare AI innovations, including biomedical entity and relation extraction, demonstrating the value of specialized models for domain-specific challenges.

  • 3 authors
·
Dec 14, 2024

DeID-GPT: Zero-shot Medical Text De-Identification by GPT-4

The digitization of healthcare has facilitated the sharing and re-using of medical data but has also raised concerns about confidentiality and privacy. HIPAA (Health Insurance Portability and Accountability Act) mandates removing re-identifying information before the dissemination of medical records. Thus, effective and efficient solutions for de-identifying medical data, especially those in free-text forms, are highly needed. While various computer-assisted de-identification methods, including both rule-based and learning-based, have been developed and used in prior practice, such solutions still lack generalizability or need to be fine-tuned according to different scenarios, significantly imposing restrictions in wider use. The advancement of large language models (LLM), such as ChatGPT and GPT-4, have shown great potential in processing text data in the medical domain with zero-shot in-context learning, especially in the task of privacy protection, as these models can identify confidential information by their powerful named entity recognition (NER) capability. In this work, we developed a novel GPT4-enabled de-identification framework (``DeID-GPT") to automatically identify and remove the identifying information. Compared to existing commonly used medical text data de-identification methods, our developed DeID-GPT showed the highest accuracy and remarkable reliability in masking private information from the unstructured medical text while preserving the original structure and meaning of the text. This study is one of the earliest to utilize ChatGPT and GPT-4 for medical text data processing and de-identification, which provides insights for further research and solution development on the use of LLMs such as ChatGPT/GPT-4 in healthcare. Codes and benchmarking data information are available at https://github.com/yhydhx/ChatGPT-API.

  • 18 authors
·
Mar 20, 2023

ReLiK: Retrieve and LinK, Fast and Accurate Entity Linking and Relation Extraction on an Academic Budget

Entity Linking (EL) and Relation Extraction (RE) are fundamental tasks in Natural Language Processing, serving as critical components in a wide range of applications. In this paper, we propose ReLiK, a Retriever-Reader architecture for both EL and RE, where, given an input text, the Retriever module undertakes the identification of candidate entities or relations that could potentially appear within the text. Subsequently, the Reader module is tasked to discern the pertinent retrieved entities or relations and establish their alignment with the corresponding textual spans. Notably, we put forward an innovative input representation that incorporates the candidate entities or relations alongside the text, making it possible to link entities or extract relations in a single forward pass and to fully leverage pre-trained language models contextualization capabilities, in contrast with previous Retriever-Reader-based methods, which require a forward pass for each candidate. Our formulation of EL and RE achieves state-of-the-art performance in both in-domain and out-of-domain benchmarks while using academic budget training and with up to 40x inference speed compared to competitors. Finally, we show how our architecture can be used seamlessly for Information Extraction (cIE), i.e. EL + RE, and setting a new state of the art by employing a shared Reader that simultaneously extracts entities and relations.

  • 4 authors
·
Jul 31, 2024 2

Event Extraction in Basque: Typologically motivated Cross-Lingual Transfer-Learning Analysis

Cross-lingual transfer-learning is widely used in Event Extraction for low-resource languages and involves a Multilingual Language Model that is trained in a source language and applied to the target language. This paper studies whether the typological similarity between source and target languages impacts the performance of cross-lingual transfer, an under-explored topic. We first focus on Basque as the target language, which is an ideal target language because it is typologically different from surrounding languages. Our experiments on three Event Extraction tasks show that the shared linguistic characteristic between source and target languages does have an impact on transfer quality. Further analysis of 72 language pairs reveals that for tasks that involve token classification such as entity and event trigger identification, common writing script and morphological features produce higher quality cross-lingual transfer. In contrast, for tasks involving structural prediction like argument extraction, common word order is the most relevant feature. In addition, we show that when increasing the training size, not all the languages scale in the same way in the cross-lingual setting. To perform the experiments we introduce EusIE, an event extraction dataset for Basque, which follows the Multilingual Event Extraction dataset (MEE). The dataset and code are publicly available.

  • 5 authors
·
Apr 9, 2024

Distilling the Knowledge of Romanian BERTs Using Multiple Teachers

Running large-scale pre-trained language models in computationally constrained environments remains a challenging problem yet to be addressed, while transfer learning from these models has become prevalent in Natural Language Processing tasks. Several solutions, including knowledge distillation, network quantization, or network pruning have been previously proposed; however, these approaches focus mostly on the English language, thus widening the gap when considering low-resource languages. In this work, we introduce three light and fast versions of distilled BERT models for the Romanian language: Distil-BERT-base-ro, Distil-RoBERT-base, and DistilMulti-BERT-base-ro. The first two models resulted from the individual distillation of knowledge from two base versions of Romanian BERTs available in literature, while the last one was obtained by distilling their ensemble. To our knowledge, this is the first attempt to create publicly available Romanian distilled BERT models, which were thoroughly evaluated on five tasks: part-of-speech tagging, named entity recognition, sentiment analysis, semantic textual similarity, and dialect identification. Our experimental results argue that the three distilled models offer performance comparable to their teachers, while being twice as fast on a GPU and ~35% smaller. In addition, we further test the similarity between the predictions of our students versus their teachers by measuring their label and probability loyalty, together with regression loyalty - a new metric introduced in this work.

  • 7 authors
·
Dec 23, 2021

Dice Loss for Data-imbalanced NLP Tasks

Many NLP tasks such as tagging and machine reading comprehension are faced with the severe data imbalance issue: negative examples significantly outnumber positive examples, and the huge number of background examples (or easy-negative examples) overwhelms the training. The most commonly used cross entropy (CE) criteria is actually an accuracy-oriented objective, and thus creates a discrepancy between training and test: at training time, each training instance contributes equally to the objective function, while at test time F1 score concerns more about positive examples. In this paper, we propose to use dice loss in replacement of the standard cross-entropy objective for data-imbalanced NLP tasks. Dice loss is based on the Sorensen-Dice coefficient or Tversky index, which attaches similar importance to false positives and false negatives, and is more immune to the data-imbalance issue. To further alleviate the dominating influence from easy-negative examples in training, we propose to associate training examples with dynamically adjusted weights to deemphasize easy-negative examples.Theoretical analysis shows that this strategy narrows down the gap between the F1 score in evaluation and the dice loss in training. With the proposed training objective, we observe significant performance boost on a wide range of data imbalanced NLP tasks. Notably, we are able to achieve SOTA results on CTB5, CTB6 and UD1.4 for the part of speech tagging task; SOTA results on CoNLL03, OntoNotes5.0, MSRA and OntoNotes4.0 for the named entity recognition task; along with competitive results on the tasks of machine reading comprehension and paraphrase identification.

  • 6 authors
·
Nov 7, 2019