Neda Tavakoli

Foundation models can streamline imaging workflows, improve diagnostic accuracy, enable personalized treatment, and, via integrated generative artificial intelligence, create synthetic images to augment scarce real-world data; however, successful adoption requires explainability, trust, and workflow integration.

Background: Late Gadolinium Enhancement (LGE) imaging is the gold standard for assessing myocardial fibrosis and scarring, with left ventricular (LV) LGE extent predicting major adverse cardiac events (MACE). Despite its importance, routine LGE-based LV scar quantification is hindered by labor-intensive manual segmentation and inter-observer variability. Methods: We propose ScarNet, a hybrid model combining a transformer-based encoder from the Medical Segment Anything Model (MedSAM) with a convolution-based U-Net decoder, enhanced by tailored attention blocks. ScarNet was trained on 552 ischemic cardiomyopathy patients with expert segmentations of myocardial and scar boundaries and tested on 184 separate patients. Results: ScarNet achieved robust scar segmentation in 184 test patients, yielding a median Dice score of 0.912 (IQR: 0.863--0.944), significantly outperforming MedSAM (median Dice = 0.046, IQR: 0.043--0.047) and nnU-Net (median Dice = 0.638, IQR: 0.604--0.661). ScarNet demonstrated lower bias (-0.63%) and coefficient of variation (4.3%) compared to MedSAM (bias: -13.31%, CoV: 130.3%) and nnU-Net (bias: -2.46%, CoV: 20.3%). In Monte Carlo simulations with noise perturbations, ScarNet achieved significantly higher scar Dice (0.892 \pm 0.053, CoV = 5.9%) than MedSAM (0.048 \pm 0.112, CoV = 233.3%) and nnU-Net (0.615 \pm 0.537, CoV = 28.7%). Conclusion: ScarNet outperformed MedSAM and nnU-Net in accurately segmenting myocardial and scar boundaries in LGE images. The model exhibited robust performance across diverse image qualities and scar patterns.

Modern genomic datasets, like those generated under the 1000 Genome Project, contain millions of variants belonging to known haplotypes. Although these datasets are more representative than a single reference sequence and can alleviate issues like reference bias, they are significantly more computationally burdensome to work with, often involving large-indexed genome graph data structures for tasks such as read mapping. The construction, preprocessing, and mapping algorithms can require substantial computational resources depending on the size of these variant sets. Moreover, the accuracy of mapping algorithms has been shown to decrease when working with complete variant sets. Therefore, a drastically reduced set of variants that preserves important properties of the original set is desirable. This work provides a technique for finding a minimal subset of variants S such that for given parameters α and δ , all substrings up to length α in the haplotypes are guaranteed to be still alignable to the appropriate locations with either Hamming or edit distance at most δ , using only S . Our contributions include showing the NP-hardness and inapproximability of these optimization problems and providing Integer Linear Programming (ILP) formulations. Our edit distance ILP formulation carefully decomposes the problem according to variant locations, which allows it to scale to support all of chromosome 22’s variants from the 1000 Genome Project. Our experiments also demonstrate a significant reduction in the number of variants. For example, for moderately long reads, e.g., α = 1000, over 75% of the variants can be removed while preserving read mappability with edit distance at most one.

Background The recent release of large language models (LLMs) for public use, such as ChatGPT and Google Bard, has opened up a multitude of potential benefits as well as challenges. Purpose To evaluate and compare the accuracy and consistency of responses generated by publicly available ChatGPT-3.5 and Google Bard to non-expert questions related to lung cancer prevention, screening, and terminology commonly used in radiology reports based on the recommendation of Lung Imaging Reporting and Data System (Lung-RADS) v2022 from American College of Radiology and Fleischner society. Materials and Methods Forty of the exact same questions were created and presented to ChatGPT-3.5 and Google Bard experimental version as well as Bing and Google search engines by three different authors of this paper. Each answer was reviewed by two radiologists for accuracy. Responses were scored as correct, partially correct, incorrect, or unanswered. Consistency was also evaluated among the answers. Here, consistency was defined as the agreement between the three answers provided by ChatGPT-3.5, Google Bard experimental version, Bing, and Google search engines regardless of whether the concept conveyed was correct or incorrect. The accuracy among different tools were evaluated using Stata. Results ChatGPT-3.5 answered 120 questions with 85 (70.8%) correct, 14 (11.7%) partially correct, and 21 (17.5%) incorrect. Google Bard did not answer 23 (19.1%) questions. Among the 97 questions answered by Google Bard, 62 (51.7%) were correct, 11 (9.2%) were partially correct, and 24 (20%) were incorrect. Bing answered 120 questions with 74 (61.7%) correct, 13 (10.8%) partially correct, and 33 (27.5%) incorrect. Google search engine answered 120 questions with 66 (55%) correct, 27 (22.5%) partially correct, and 27 (22.5%) incorrect. The ChatGPT-3.5 is more likely to provide correct or partially answer than Google Bard, approximately by 1.5 folds (OR = 1.55, P = 0.004). ChatGPT-3.5 and Google search engine were more likely to be consistent than Google Bard by approximately 7 and 29 folds (OR = 6.65, P = 0.002 for ChatGPT and OR = 28.83, P = 0.002 for Google search engine, respectively). Conclusion Although ChatGPT-3.5 had a higher accuracy in comparison with the other tools, neither ChatGPT nor Google Bard, Bing and Google search engines answered all questions correctly and with 100% consistency.