Michael Adams

Satrajit Chakrabarty, Syed Amaan Abidi, Mina Mousa et al.

Efforts to utilize growing volumes of clinical imaging data to generate tumor evaluations continue to require significant manual data wrangling owing to the data heterogeneity. Here, we propose an artificial intelligence-based solution for the aggregation and processing of multisequence neuro-oncology MRI data to extract quantitative tumor measurements. Our end-to-end framework i) classifies MRI sequences using an ensemble classifier, ii) preprocesses the data in a reproducible manner, iii) delineates tumor tissue subtypes using convolutional neural networks, and iv) extracts diverse radiomic features. Moreover, it is robust to missing sequences and adopts an expert-in-the-loop approach, where the segmentation results may be manually refined by radiologists. Following the implementation of the framework in Docker containers, it was applied to two retrospective glioma datasets collected from the Washington University School of Medicine (WUSM; n = 384) and the M.D. Anderson Cancer Center (MDA; n = 30) comprising preoperative MRI scans from patients with pathologically confirmed gliomas. The scan-type classifier yielded an accuracy of over 99%, correctly identifying sequences from 380/384 and 30/30 sessions from the WUSM and MDA datasets, respectively. Segmentation performance was quantified using the Dice Similarity Coefficient between the predicted and expert-refined tumor masks. Mean Dice scores were 0.882 ($\pm$0.244) and 0.977 ($\pm$0.04) for whole tumor segmentation for WUSM and MDA, respectively. This streamlined framework automatically curated, processed, and segmented raw MRI data of patients with varying grades of gliomas, enabling the curation of large-scale neuro-oncology datasets and demonstrating a high potential for integration as an assistive tool in clinical practice.

Ala Jararweh, Michael Adams, Avinash Sahu et al.

Increasing complexity in software systems places a growing demand on reasoning tools that unlock vulnerabilities manifest in source code. Many current approaches focus on vulnerability analysis as a classifying task, oversimplifying the nuanced and context-dependent real-world scenarios. Even though current code large language models (LLMs) excel in code understanding, they often pay little attention to security-specific reasoning. We propose LLaVul, a multimodal LLM tailored to provide fine-grained reasoning about code through question-answering (QA). Our model is trained to integrate paired code and natural queries into a unified space, enhancing reasoning and context-dependent insights about code vulnerability. To evaluate our model performance, we construct a curated dataset of real-world vulnerabilities paired with security-focused questions and answers. Our model outperforms state-of-the-art general-purpose and code LLMs in the QA and detection tasks. We further explain decision-making by conducting qualitative analysis to highlight capabilities and limitations. By integrating code and QA, LLaVul enables more interpretable and security-focused code understanding.