Sanjeev Kumar Karn

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.

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.

Sanjeev Kumar Karn, Francine Chen, Yan-Ying Chen et al.

Interleaved texts, where posts belonging to different threads occur in a sequence, commonly occur in online chat posts, so that it can be time-consuming to quickly obtain an overview of the discussions. Existing systems first disentangle the posts by threads and then extract summaries from those threads. A major issue with such systems is error propagation from the disentanglement component. While end-to-end trainable summarization system could obviate explicit disentanglement, such systems require a large amount of labeled data. To address this, we propose to pretrain an end-to-end trainable hierarchical encoder-decoder system using synthetic interleaved texts. We show that by fine-tuning on a real-world meeting dataset (AMI), such a system out-performs a traditional two-step system by 22%. We also compare against transformer models and observed that pretraining with synthetic data both the encoder and decoder outperforms the BertSumExtAbs transformer model which pretrains only the encoder on a large dataset.

Sanjeev Kumar Karn, Francine Chen, Yan-Ying Chen et al.

Interleaved texts, where posts belonging to different threads occur in one sequence, are a common occurrence, e.g., online chat conversations. To quickly obtain an overview of such texts, existing systems first disentangle the posts by threads and then extract summaries from those threads. The major issues with such systems are error propagation and non-fluent summary. To address those, we propose an end-to-end trainable hierarchical encoder-decoder system. We also introduce a novel hierarchical attention mechanism which combines three levels of information from an interleaved text, i.e, posts, phrases and words, and implicitly disentangles the threads. We evaluated the proposed system on multiple interleaved text datasets, and it out-performs a SOTA two-step system by 20-40%.

Sanjeev Kumar Karn, Mark Buckley, Ulli Waltinger et al.

In this work, we define the task of teaser generation and provide an evaluation benchmark and baseline systems for the process of generating teasers. A teaser is a short reading suggestion for an article that is illustrative and includes curiosity-arousing elements to entice potential readers to read particular news items. Teasers are one of the main vehicles for transmitting news to social media users. We compile a novel dataset of teasers by systematically accumulating tweets and selecting those that conform to the teaser definition. We have compared a number of neural abstractive architectures on the task of teaser generation and the overall best performing system is See et al.(2017)'s seq2seq with pointer network.