Analysis of Prompt Engineering for Drug Toxicity Prediction

Clinical trials in the UK can cost up to £1.3 million, with approximately 90% drug failure rate. Toxicity is a major contributing factor in drug failure. Testing is time and cost intensive. In recent years, the use of artificial intelligence has been increasingly explored to aid in the prediction of drug toxicity, with extensive use of large language models (LLMs). However, LLMs can show considerable variation when minor changes are made to prompts, which raises concerns about their sensitivity to prompt engineering. Prompt engineering is used to optimise a prompt given to an LLM to generate the desired output. This paper proposes a method to analyse prompt engineering for drug toxicity prediction. The aim of the paper is to investigate the importance of prompt phrasing for drug toxicity prediction. LLMs were prompted to identify chemical properties of significance when predicting drug toxicity. Prompts were constructed to investigate; job role, prompt structuring, and rule interpretation. LLMs were then used to generate datasets, using the identified features from initial prompting, which were then passed to machine learning algorithms. The experiments show that the natural variance which occurs in LLMs outweighs any fine-tuning of prompts. There were, however, substantial improvements in model performance when using chemoinformatic code to extract features instead of using LLM-generated values. The proposed analysis methodology is applicable to a wide range of prompt types across different areas of bioinformatics.

An Edge-aware Prompt-enhanced SAM for Ultrasound Image Segmentation

Ultrasound image segmentation is essential for delineating anatomical structures and lesions, providing the foundation for accurate diagnosis. While the Segment Anything Model (SAM) has demonstrated remarkable success on natural images, its performance on ultrasound data is often hindered by poor boundary delineation. To address this limitation, we propose EP-SAM, an edge-aware and prompt-enhanced adaptation of SAM. Specifically, we leverage multi-block feature extraction from the image encoder to enrich coarse-to-fine semantic representations, while edge-aware supervision of the image encoder improves robustness to contour ambiguity and speckle noise. By integrating these complementary cues, EP-SAM generates high-quality prompts that effectively guide the model toward target regions of interest. Experimental results on multiple benchmarks demonstrate that EP-SAM consistently outperforms existing SAM-based methods.

Enhancing MedSAM with a Lightweight Box Predictor for Medical Image Segmentation

Semantic segmentation in medical imaging is a critical yet challenging task due to data scarcity and high variability across modalities. While foundation models like the Segment Anything Model (SAM) show promise, they often struggle with medical images without specific adaptation. Moreover, point prompts, despite being the most natural form of user interaction, provide insufficient spatial context for reliable segmentation, particularly when target structures are irregular or poorly contrasted. In this paper, we propose an enhanced segmentation framework that integrates a lightweight Box Predictor module into the MedSAM architecture. The Box Predictor estimates an approximate bounding box from a single user click using localized image embedding features, providing spatial guidance that reduces the ambiguity of point prompts, while introducing only 1.6M additional parameters and negligible inference overhead. We introduce a two-stage training pipeline where the Box Predictor is trained independently before being integrated into MedSAM. To validate the generalization capability of our method, we conduct extensive evaluations on four diverse datasets (FLARE22, BRISC, BUSI, LungSegDB) spanning distinct imaging modalities, including CT, MRI, and Ultrasound. Our method improves segmentation accuracy and robustness across varied anatomical structures and imaging domains, achieving Dice scores of 0.89 (BUSI), 0.93 (FLARE22), 0.88 (BRISC), and 0.98 (LungSegDB). Code is available at https://github.com/Amirhosseinmovahedi/MedSAM-BoxPredictor

Comparing LLM and Fine-Tuned Model Performance on NVDRS Circumstance Extraction with Varying Prompt Complexity

Suicide is a leading cause of death in the United States, and understanding the circumstances that precede it requires extracting structured information from death investigation narratives. Many of these circumstances require semantic inference beyond simple keyword matching. We develop a ``Complexity Score'' algorithm that analyzes coding manual structure to predict when detailed prompts with full coding guidelines improve over name-only prompts. We then construct a hybrid approach that selects prompt strategy per circumstance. We evaluate large language models (LLMs) against fine-tuned RoBERTa on 25 inferentially complex circumstances from the National Violent Death Reporting System (NVDRS). We found that LLMs substantially outperform on low-prevalence circumstances where training data is insufficient. We further demonstrate that our framework generalizes across frontier LLMs, with GPT-5.2, Gemini 2.5 Pro and Llama-3 70B showing consistent performance patterns. These findings support a hybrid architecture where LLMs handle rare, inferentially complex circumstances while fine-tuned models handle common ones.