Oladimeji Farri

Sanjeev Kumar Karn, Ning Liu, Hinrich Schuetze et al.

The IMPRESSIONS section of a radiology report about an imaging study is a summary of the radiologist's reasoning and conclusions, and it also aids the referring physician in confirming or excluding certain diagnoses. A cascade of tasks are required to automatically generate an abstractive summary of the typical information-rich radiology report. These tasks include acquisition of salient content from the report and generation of a concise, easily consumable IMPRESSIONS section. Prior research on radiology report summarization has focused on single-step end-to-end models -- which subsume the task of salient content acquisition. To fully explore the cascade structure and explainability of radiology report summarization, we introduce two innovations. First, we design a two-step approach: extractive summarization followed by abstractive summarization. Second, we additionally break down the extractive part into two independent tasks: extraction of salient (1) sentences and (2) keywords. Experiments on English radiology reports from two clinical sites show our novel approach leads to a more precise summary compared to single-step and to two-step-with-single-extractive-process baselines with an overall improvement in F1 score Of 3-4%.

Manuela Daniela Danu, George Marica, Sanjeev Kumar Karn et al.

Among all the sub-sections in a typical radiology report, the Clinical Indications, Findings, and Impression often reflect important details about the health status of a patient. The information included in Impression is also often covered in Findings. While Findings and Impression can be deduced by inspecting the image, Clinical Indications often require additional context. The cognitive task of interpreting medical images remains the most critical and often time-consuming step in the radiology workflow. Instead of generating an end-to-end radiology report, in this paper, we focus on generating the Findings from automated interpretation of medical images, specifically chest X-rays (CXRs). Thus, this work focuses on reducing the workload of radiologists who spend most of their time either writing or narrating the Findings. Unlike past research, which addresses radiology report generation as a single-step image captioning task, we have further taken into consideration the complexity of interpreting CXR images and propose a two-step approach: (a) detecting the regions with abnormalities in the image, and (b) generating relevant text for regions with abnormalities by employing a generative large language model (LLM). This two-step approach introduces a layer of interpretability and aligns the framework with the systematic reasoning that radiologists use when reviewing a CXR.

Ali H. Dhanaliwala, Rikhiya Ghosh, Sanjeev Kumar Karn et al.

Radiologists produce unstructured data that can be valuable for clinical care when consumed by information systems. However, variability in style limits usage. Study compares system using domain-adapted language model (RadLing) and general-purpose LLM (GPT-4) in extracting relevant features from chest radiology reports and standardizing them to common data elements (CDEs). Three radiologists annotated a retrospective dataset of 1399 chest XR reports (900 training, 499 test) and mapped to 44 pre-selected relevant CDEs. GPT-4 system was prompted with report, feature set, value set, and dynamic few-shots to extract values and map to CDEs. Output key:value pairs were compared to reference standard at both stages and an identical match was considered TP. F1 score for extraction was 97% for RadLing-based system and 78% for GPT-4 system. F1 score for mapping was 98% for RadLing and 94% for GPT-4; difference was statistically significant (P<.001). RadLing's domain-adapted embeddings were better in feature extraction and its light-weight mapper had better f1 score in CDE assignment. RadLing system also demonstrated higher capabilities in differentiating between absent (99% vs 64%) and unspecified (99% vs 89%). RadLing system's domain-adapted embeddings helped improve performance of GPT-4 system to 92% by giving more relevant few-shot prompts. RadLing system offers operational advantages including local deployment and reduced runtime costs.

Sanjeev Kumar Karn, Rikhiya Ghosh, Kusuma P et al.

Instruction-tuned generative Large language models (LLMs) like ChatGPT and Bloomz possess excellent generalization abilities, but they face limitations in understanding radiology reports, particularly in the task of generating the IMPRESSIONS section from the FINDINGS section. They tend to generate either verbose or incomplete IMPRESSIONS, mainly due to insufficient exposure to medical text data during training. We present a system which leverages large-scale medical text data for domain-adaptive pre-training of instruction-tuned LLMs to enhance its medical knowledge and performance on specific medical tasks. We show that this system performs better in a zero-shot setting than a number of pretrain-and-finetune adaptation methods on the IMPRESSIONS generation task, and ranks 1st among participating systems in Task 1B: Radiology Report Summarization at the BioNLP 2023 workshop.

Rikhiya Ghosh, Sanjeev Kumar Karn, Manuela Daniela Danu et al.

Most natural language tasks in the radiology domain use language models pre-trained on biomedical corpus. There are few pretrained language models trained specifically for radiology, and fewer still that have been trained in a low data setting and gone on to produce comparable results in fine-tuning tasks. We present RadLing, a continuously pretrained language model using Electra-small (Clark et al., 2020) architecture, trained using over 500K radiology reports, that can compete with state-of-the-art results for fine tuning tasks in radiology domain. Our main contribution in this paper is knowledge-aware masking which is a taxonomic knowledge-assisted pretraining task that dynamically masks tokens to inject knowledge during pretraining. In addition, we also introduce an knowledge base-aided vocabulary extension to adapt the general tokenization vocabulary to radiology domain.

Rikhiya Ghosh, Oladimeji Farri, Hans-Martin von Stockhausen et al.

The healthcare industry is currently experiencing an unprecedented wave of cybersecurity attacks, impacting millions of individuals. With the discovery of thousands of vulnerabilities each month, there is a pressing need to drive the automation of vulnerability assessment processes for medical devices, facilitating rapid mitigation efforts. Generative AI systems have revolutionized various industries, offering unparalleled opportunities for automation and increased efficiency. This paper presents a solution leveraging Large Language Models (LLMs) to learn from historical evaluations of vulnerabilities for the automatic assessment of vulnerabilities in the medical devices industry. This approach is applied within the portfolio of a single manufacturer, taking into account device characteristics, including existing security posture and controls. The primary contributions of this paper are threefold. Firstly, it provides a detailed examination of the best practices for training a vulnerability Language Model (LM) in an industrial context. Secondly, it presents a comprehensive comparison and insightful analysis of the effectiveness of Language Models in vulnerability assessment. Finally, it proposes a new human-in-the-loop framework to expedite vulnerability evaluation processes.

Cuong Nhat Ha, Shima Asaadi, Sanjeev Kumar Karn et al.

Vision-language models, while effective in general domains and showing strong performance in diverse multi-modal applications like visual question-answering (VQA), struggle to maintain the same level of effectiveness in more specialized domains, e.g., medical. We propose a medical vision-language model that integrates large vision and language models adapted for the medical domain. This model goes through three stages of parameter-efficient training using three separate biomedical and radiology multi-modal visual and text datasets. The proposed model achieves state-of-the-art performance on the SLAKE 1.0 medical VQA (MedVQA) dataset with an overall accuracy of 87.5% and demonstrates strong performance on another MedVQA dataset, VQA-RAD, achieving an overall accuracy of 73.2%.

Rikhiya Ghosh, Hans-Martin von Stockhausen, Martin Schmitt et al.

The National Vulnerability Database (NVD) publishes over a thousand new vulnerabilities monthly, with a projected 25 percent increase in 2024, highlighting the crucial need for rapid vulnerability identification to mitigate cybersecurity attacks and save costs and resources. In this work, we propose using large language models (LLMs) to learn vulnerability evaluation from historical assessments of medical device vulnerabilities in a single manufacturer's portfolio. We highlight the effectiveness and challenges of using LLMs for automatic vulnerability evaluation and introduce a method to enrich historical data with cybersecurity ontologies, enabling the system to understand new vulnerabilities without retraining the LLM. Our LLM system integrates with the in-house application - Cybersecurity Management System (CSMS) - to help Siemens Healthineers (SHS) product cybersecurity experts efficiently assess the vulnerabilities in our products. Also, we present guidelines for efficient integration of LLMs into the cybersecurity tool.

Manuela Daniela Danu, George Marica, Constantin Suciu et al.

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.

Rajeev Bhatt Ambati, Ahmed Ada Hanifi, Ramya Vunikili et al.

Multi-label sentences (text) in the clinical domain result from the rich description of scenarios during patient care. The state-of-theart methods for assertion detection mostly address this task in the setting of a single assertion label per sentence (text). In addition, few rules based and deep learning methods perform negation/assertion scope detection on single-label text. It is a significant challenge extending these methods to address multi-label sentences without diminishing performance. Therefore, we developed a convolutional neural network (CNN) architecture to localize multiple labels and their scopes in a single stage end-to-end fashion, and demonstrate that our model performs atleast 12% better than the state-of-the-art on multi-label clinical text.

Reza Ghaeini, Sadid A. Hasan, Vivek Datla et al.

We present a novel deep learning architecture to address the natural language inference (NLI) task. Existing approaches mostly rely on simple reading mechanisms for independent encoding of the premise and hypothesis. Instead, we propose a novel dependent reading bidirectional LSTM network (DR-BiLSTM) to efficiently model the relationship between a premise and a hypothesis during encoding and inference. We also introduce a sophisticated ensemble strategy to combine our proposed models, which noticeably improves final predictions. Finally, we demonstrate how the results can be improved further with an additional preprocessing step. Our evaluation shows that DR-BiLSTM obtains the best single model and ensemble model results achieving the new state-of-the-art scores on the Stanford NLI dataset.

Aaditya Prakash, Siyuan Zhao, Sadid A. Hasan et al.

Diagnosis of a clinical condition is a challenging task, which often requires significant medical investigation. Previous work related to diagnostic inferencing problems mostly consider multivariate observational data (e.g. physiological signals, lab tests etc.). In contrast, we explore the problem using free-text medical notes recorded in an electronic health record (EHR). Complex tasks like these can benefit from structured knowledge bases, but those are not scalable. We instead exploit raw text from Wikipedia as a knowledge source. Memory networks have been demonstrated to be effective in tasks which require comprehension of free-form text. They use the final iteration of the learned representation to predict probable classes. We introduce condensed memory neural networks (C-MemNNs), a novel model with iterative condensation of memory representations that preserves the hierarchy of features in the memory. Experiments on the MIMIC-III dataset show that the proposed model outperforms other variants of memory networks to predict the most probable diagnoses given a complex clinical scenario.

Aaditya Prakash, Sadid A. Hasan, Kathy Lee et al.

In this paper, we propose a novel neural approach for paraphrase generation. Conventional para- phrase generation methods either leverage hand-written rules and thesauri-based alignments, or use statistical machine learning principles. To the best of our knowledge, this work is the first to explore deep learning models for paraphrase generation. Our primary contribution is a stacked residual LSTM network, where we add residual connections between LSTM layers. This allows for efficient training of deep LSTMs. We evaluate our model and other state-of-the-art deep learning models on three different datasets: PPDB, WikiAnswers and MSCOCO. Evaluation results demonstrate that our model outperforms sequence to sequence, attention-based and bi- directional LSTM models on BLEU, METEOR, TER and an embedding-based sentence similarity metric.