Mariana Bento

Neha Gianchandani, Mahsa Dibaji, Johanna Ospel et al.

Brain aging is a regional phenomenon, a facet that remains relatively under-explored within the realm of brain age prediction research using machine learning methods. Voxel-level predictions can provide localized brain age estimates that can provide granular insights into the regional aging processes. This is essential to understand the differences in aging trajectories in healthy versus diseased subjects. In this work, a deep learning-based multitask model is proposed for voxel-level brain age prediction from T1-weighted magnetic resonance images. The proposed model outperforms the models existing in the literature and yields valuable clinical insights when applied to both healthy and diseased populations. Regional analysis is performed on the voxel-level brain age predictions to understand aging trajectories of known anatomical regions in the brain and show that there exist disparities in regional aging trajectories of healthy subjects compared to ones with underlying neurological disorders such as Dementia and more specifically, Alzheimer's disease. Our code is available at https://github.com/nehagianchandani/Voxel-level-brain-age-prediction.

Ezequiel de la Rosa, Ruisheng Su, Mauricio Reyes et al.

Accurate estimation of brain infarction (i.e., irreversibly damaged tissue) is critical for guiding treatment decisions in acute ischemic stroke. Reliable infarct prediction informs key clinical interventions, including the need for patient transfer to comprehensive stroke centers, the potential benefit of additional reperfusion attempts during mechanical thrombectomy, decisions regarding secondary neuroprotective treatments, and ultimately, prognosis of clinical outcomes. This work introduces the Ischemic Stroke Lesion Segmentation (ISLES) 2024 challenge, which focuses on the prediction of final infarct volumes from pre-interventional acute stroke imaging and clinical data. ISLES24 provides a comprehensive, multimodal setting where participants can leverage all clinically and practically available data, including full acute CT imaging, sub-acute follow-up MRI, and structured clinical information, across a train set of 150 cases. On the hidden test set of 98 cases, the top-performing model, a multimodal nnU-Net-based architecture, achieved a Dice score of 0.285 (+/- 0.213) and an absolute volume difference of 21.2 (+/- 37.2) mL, underlining the significant challenges posed by this task and the need for further advances in multimodal learning. This work makes two primary contributions: first, we establish a standardized, clinically realistic benchmark for post-treatment infarct prediction, enabling systematic evaluation of multimodal algorithmic strategies on a longitudinal stroke dataset; second, we analyze current methodological limitations and outline key research directions to guide the development of next-generation infarct prediction models.

Farzaneh Dehghani, Mahsa Dibaji, Fahim Anzum et al.

Artificial Intelligence (AI) has paved the way for revolutionary decision-making processes, which if harnessed appropriately, can contribute to advancements in various sectors, from healthcare to economics. However, its black box nature presents significant ethical challenges related to bias and transparency. AI applications are hugely impacted by biases, presenting inconsistent and unreliable findings, leading to significant costs and consequences, highlighting and perpetuating inequalities and unequal access to resources. Hence, developing safe, reliable, ethical, and Trustworthy AI systems is essential. Our team of researchers working with Trustworthy and Responsible AI, part of the Transdisciplinary Scholarship Initiative within the University of Calgary, conducts research on Trustworthy and Responsible AI, including fairness, bias mitigation, reproducibility, generalization, interpretability, and authenticity. In this paper, we review and discuss the intricacies of AI biases, definitions, methods of detection and mitigation, and metrics for evaluating bias. We also discuss open challenges with regard to the trustworthiness and widespread application of AI across diverse domains of human-centric decision making, as well as guidelines to foster Responsible and Trustworthy AI models.

Neha Gianchandani, Mahsa Dibaji, Mariana Bento et al.

Deep learning models have achieved state-of-the-art results in estimating brain age, which is an important brain health biomarker, from magnetic resonance (MR) images. However, most of these models only provide a global age prediction, and rely on techniques, such as saliency maps to interpret their results. These saliency maps highlight regions in the input image that were significant for the model's predictions, but they are hard to be interpreted, and saliency map values are not directly comparable across different samples. In this work, we reframe the age prediction problem from MR images to an image-to-image regression problem where we estimate the brain age for each brain voxel in MR images. We compare voxel-wise age prediction models against global age prediction models and their corresponding saliency maps. The results indicate that voxel-wise age prediction models are more interpretable, since they provide spatial information about the brain aging process, and they benefit from being quantitative.

Ronnie de Souza Santos, Italo Santos, Mariana Bento et al.

Background: Cheating in university education is commonly described as context dependent and influenced by assessment design, institutional norms, and student interpretation. In software engineering education, programming oriented coursework has historically involved ambiguity around collaboration, reuse, and external assistance. Recently, large language models (LLMs) have introduced additional mediation in the production of code and related artifacts. Aims: This study investigates how software engineering students describe experiences of using LLMs in ways they perceived as inappropriate, disallowed, or misaligned with course expectations. Method: A cross sectional survey was conducted with 116 undergraduate software engineering students from multiple countries, combining quantitative summaries with qualitative data. Results: Reported LLM cheating practices occurred primarily in programming assignments, routine coursework, and documentation tasks, often in contexts of time pressure and unclear guidance. Use during quizzes and exams was less frequent and more consistently identified as a violation. Students reported awareness of academic and professional consequences regarding LLM cheating, while formal sanctions were perceived as limited. Conclusions: Our study indicates that reported LLM misuse in software engineering is associated with assessment and instructional conditions, suggesting a need for clearer alignment between assessment design, learning objectives, and expectations for LLM use.

Mahsa Dibaji, Neha Gianchandani, Akhil Nair et al.

While utilizing machine learning models, one of the most crucial aspects is how bias and fairness affect model outcomes for diverse demographics. This becomes especially relevant in the context of machine learning for medical imaging applications as these models are increasingly being used for diagnosis and treatment planning. In this paper, we study biases related to sex when developing a machine learning model based on brain magnetic resonance images (MRI). We investigate the effects of sex by performing brain age prediction considering different experimental designs: model trained using only female subjects, only male subjects and a balanced dataset. We also perform evaluation on multiple MRI datasets (Calgary-Campinas(CC359) and CamCAN) to assess the generalization capability of the proposed models. We found disparities in the performance of brain age prediction models when trained on distinct sex subgroups and datasets, in both final predictions and decision making (assessed using interpretability models). Our results demonstrated variations in model generalizability across sex-specific subgroups, suggesting potential biases in models trained on unbalanced datasets. This underlines the critical role of careful experimental design in generating fair and reliable outcomes.

Amirmohammad Shamaei, Alexander Stebner, Salome et al.

Magnetic resonance imaging (MRI) is a crucial medical imaging modality. However, long acquisition times remain a significant challenge, leading to increased costs, and reduced patient comfort. Recent studies have shown the potential of using deep learning models that incorporate information from prior subject-specific MRI scans to improve reconstruction quality of present scans. Integrating this prior information requires registration of the previous scan to the current image reconstruction, which can be time-consuming. We propose a novel deep-learning-based MRI reconstruction framework which consists of an initial reconstruction network, a deep registration model, and a transformer-based enhancement network. We validated our method on a longitudinal dataset of T1-weighted MRI scans with 2,808 images from 18 subjects at four acceleration factors (R5, R10, R15, R20). Quantitative metrics confirmed our approach's superiority over existing methods (p < 0.05, Wilcoxon signed-rank test). Furthermore, we analyzed the impact of our MRI reconstruction method on the downstream task of brain segmentation and observed improved accuracy and volumetric agreement with reference segmentations. Our approach also achieved a substantial reduction in total reconstruction time compared to methods that use traditional registration algorithms, making it more suitable for real-time clinical applications. The code associated with this work is publicly available at https://github.com/amirshamaei/longitudinal-mri-deep-recon.

Roberto Souza, Mariana Bento, Nikita Nogovitsyn et al.

The U-net is a deep-learning network model that has been used to solve a number of inverse problems. In this work, the concatenation of two-element U-nets, termed the W-net, operating in k-space (K) and image (I) domains, were evaluated for multi-channel magnetic resonance (MR) image reconstruction. The two element network combinations were evaluated for the four possible image-k-space domain configurations: a) W-net II, b) W-net KK, c) W-net IK, and d) W-net KI were evaluated. Selected promising four element networks (WW-nets) were also examined. Two configurations of each network were compared: 1) Each coil channel processed independently, and 2) all channels processed simultaneously. One hundred and eleven volumetric, T1-weighted, 12-channel coil k-space datasets were used in the experiments. Normalized root mean squared error, peak signal to noise ratio, visual information fidelity and visual inspection were used to assess the reconstructed images against the fully sampled reference images. Our results indicated that networks that operate solely in the image domain are better suited when processing individual channels of multi-channel data independently. Dual domain methods are more advantageous when simultaneously reconstructing all channels of multi-channel data. Also, the appropriate cascade of U-nets compared favorably (p < 0.01) to the previously published, state-of-the-art Deep Cascade model in in three out of four experiments.

Hugo J. Kuijf, J. Matthijs Biesbroek, Jeroen de Bresser et al.

Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are often still obtained from manual segmentations on brain MR images, which is a laborious procedure. Automatic WMH segmentation methods exist, but a standardized comparison of the performance of such methods is lacking. We organized a scientific challenge, in which developers could evaluate their method on a standardized multi-center/-scanner image dataset, giving an objective comparison: the WMH Segmentation Challenge (https://wmh.isi.uu.nl/). Sixty T1+FLAIR images from three MR scanners were released with manual WMH segmentations for training. A test set of 110 images from five MR scanners was used for evaluation. Segmentation methods had to be containerized and submitted to the challenge organizers. Five evaluation metrics were used to rank the methods: (1) Dice similarity coefficient, (2) modified Hausdorff distance (95th percentile), (3) absolute log-transformed volume difference, (4) sensitivity for detecting individual lesions, and (5) F1-score for individual lesions. Additionally, methods were ranked on their inter-scanner robustness. Twenty participants submitted their method for evaluation. This paper provides a detailed analysis of the results. In brief, there is a cluster of four methods that rank significantly better than the other methods, with one clear winner. The inter-scanner robustness ranking shows that not all methods generalize to unseen scanners. The challenge remains open for future submissions and provides a public platform for method evaluation.