Mary Adewunmi

Muhammad Sohaib, Mary Adewunmi

In this proposed work, we identified the significant research issues on lung cancer risk factors. Capturing and defining symptoms at an early stage is one of the most difficult phases for patients. Based on the history of patients records, we reviewed a number of current research studies on lung cancer and its various stages. We identified that lung cancer is one of the significant research issues in predicting the early stages of cancer disease. This research aimed to develop a model that can detect lung cancer with a remarkably high level of accuracy using the deep learning approach (convolution neural network). This method considers and resolves significant gaps in previous studies. We compare the accuracy levels and loss values of our model with VGG16, InceptionV3, and Resnet50. We found that our model achieved an accuracy of 94% and a minimum loss of 0.1%. Hence physicians can use our convolution neural network models for predicting lung cancer risk factors in the real world. Moreover, this investigation reveals that squamous cell carcinoma, normal, adenocarcinoma, and large cell carcinoma are the most significant risk factors. In addition, the remaining attributes are also crucial for achieving the best performance.

Rezarta Islamaj, Joey Chan, Robert Leaman et al.

Multi-hop question answering (QA) remains a significant challenge in the biomedical domain, requiring systems to integrate information across multiple sources to answer complex questions. To address this problem, the BioCreative IX MedHopQA shared task was designed to benchmark in multi-hop reasoning for large language models (LLMs). We developed a novel dataset of 1,000 challenging QA pairs spanning diseases, genes, and chemicals, with particular emphasis on rare diseases. Each question was constructed to require two-hop reasoning through the integration of information from two distinct Wikipedia pages. The challenge attracted 48 submissions from 13 teams. Systems were evaluated using both surface string comparison and conceptual accuracy (MedCPT score). The results showed a substantial performance gap between baseline LLMs and enhanced systems. The top-ranked submission achieved an 89.30% F1 score on the MedCPT metric and an 87.30% exact match (EM) score, compared with 67.40% and 60.20%, respectively, for the zero-shot baseline. A central finding of the challenge was that retrieval-augmented generation (RAG) and related retrieval-based strategies were critical for strong performance. In addition, concept-level evaluation improved answer assessment when correct responses differed in surface form. The MedHopQA dataset is publicly available to support continued progress in this important area. Challenge materials: https://www.ncbi.nlm.nih.gov/research/bionlp/medhopqa and benchmark https://www.codabench.org/competitions/7609/

Fahad Ahmed, Reem Abdel-Salam, Leon Hamnett et al.

Breast cancer is one of the leading causes of death for women worldwide. Early screening is essential for early identification, but the chance of survival declines as the cancer progresses into advanced stages. For this study, the most recent BRACS dataset of histological (H\&E) stained images was used to classify breast cancer tumours, which contains both the whole-slide images (WSI) and region-of-interest (ROI) images, however, for our study we have considered ROI images. We have experimented using different pre-trained deep learning models, such as Xception, EfficientNet, ResNet50, and InceptionResNet, pre-trained on the ImageNet weights. We pre-processed the BRACS ROI along with image augmentation, upsampling, and dataset split strategies. For the default dataset split, the best results were obtained by ResNet50 achieving 66% f1-score. For the custom dataset split, the best results were obtained by performing upsampling and image augmentation which results in 96.2% f1-score. Our second approach also reduced the number of false positive and false negative classifications to less than 3% for each class. We believe that our study significantly impacts the early diagnosis and identification of breast cancer tumors and their subtypes, especially atypical and malignant tumors, thus improving patient outcomes and reducing patient mortality rates. Overall, this study has primarily focused on identifying seven (7) breast cancer tumor subtypes, and we believe that the experimental models can be fine-tuned further to generalize over previous breast cancer histology datasets as well.

Leon Hamnett, Mary Adewunmi, Modinat Abayomi et al.

Breast cancer remains a critical global health challenge, necessitating early and accurate detection for effective treatment. This paper introduces a methodology that combines automated image augmentation selection (RandAugment) with search optimisation strategies (Tree-based Parzen Estimator) to identify optimal values for the number of image augmentations and the magnitude of their associated augmentation parameters, leading to enhanced segmentation performance. We empirically validate our approach on breast cancer histology slides, focusing on the segmentation of cancer cells. A comparative analysis of state-of-the-art transformer-based segmentation models is conducted, including SegFormer, PoolFormer, and MaskFormer models, to establish a comprehensive baseline, before applying the augmentation methodology. Our results show that the proposed methodology leads to segmentation models that are more resilient to variations in histology slides whilst maintaining high levels of segmentation performance, and show improved segmentation of the tumour class when compared to previous research. Our best result after applying the augmentations is a Dice Score of 84.08 and an IoU score of 72.54 when segmenting the tumour class. The primary contribution of this paper is the development of a methodology that enhances segmentation performance while ensuring model robustness to data variances. This has significant implications for medical practitioners, enabling the development of more effective machine learning models for clinical applications to identify breast cancer cells from histology slides. Furthermore, the codebase accompanying this research will be released upon publication. This will facilitate further research and application development based on our methodology, thereby amplifying its impact.

Reem Abdel-Salam, Mary Adewunmi, Modinat A. Abayomi

Large language models (LLMs) are increasingly evident for accurate question answering across various domains. However, rigorous evaluation of their performance on complex question-answering (QA) capabilities is essential before deployment in real-world biomedical and healthcare applications. This paper presents our approach to the MedHopQA track of the BioCreative IX shared task, which focuses on multi-hop biomedical question answering involving diseases, genes, and chemicals. We adopt a supervised fine-tuning strategy leveraging LLaMA 3 8B, enhanced with a curated biomedical question-answer dataset compiled from external sources including BioASQ, MedQuAD, and TREC. Three experimental setups are explored: fine-tuning on combined short and long answers, short answers only, and long answers only. While our models demonstrate strong domain understanding, achieving concept-level accuracy scores of up to 0.8, their Exact Match (EM) scores remain significantly lower, particularly in the test phase. We introduce a two-stage inference pipeline for precise short-answer extraction to mitigate verbosity and improve alignment with evaluation metrics. Despite partial improvements, challenges persist in generating strictly formatted outputs. Our findings highlight the gap between semantic understanding and exact answer evaluation in biomedical LLM applications, motivating further research in output control and post-processing strategies.

Reem Abdel-Salam, Mary Adewunmi

Health Mention Classification (HMC) plays a critical role in leveraging social media posts for real-time tracking and public health monitoring. Nevertheless, the process of HMC presents significant challenges due to its intricate nature, primarily stemming from the contextual aspects of health mentions, such as figurative language and descriptive terminology, rather than explicitly reflecting a personal ailment. To address this problem, we argue that clearer mentions can be achieved through conventional fine-tuning with enhanced parameters of biomedical natural language methods (NLP). In this study, we explore different techniques such as the utilisation of part-of-speech (POS) tagger information, improving on PEFT techniques, and different combinations thereof. Extensive experiments are conducted on three widely used datasets: RHDM, PHM, and Illness. The results incorporated POS tagger information, and leveraging PEFT techniques significantly improves performance in terms of F1-score compared to state-of-the-art methods across all three datasets by utilising smaller models and efficient training. Furthermore, the findings highlight the effectiveness of incorporating POS tagger information and leveraging PEFT techniques for HMC. In conclusion, the proposed methodology presents a potentially effective approach to accurately classifying health mentions in social media posts while optimising the model size and training efficiency.