Nooshin Maghsoodi

Dilakshan Srikanthan, Amoon Jamzad, Paul Wilson et al.

Whether attention maps from pathology foundation models capture genuine biology remains unknown, yet this question is critical for clinical trust and regulatory approval. We propose a spatial transcriptomics-based framework for orthogonal, hypothesis-free evaluation of attention and apply it to five pathology foundation models (CONCH v1.5, UNI v2, Virchow2, GigaPath, H-Optimus-1) and a ResNet50 baseline. Using attention-based multiple instance learning, we train single-task and multi-task models to predict five molecular alterations in glioblastoma on the CPTAC cohort, validate on an independent TCGA cohort, and evaluate biological coherence of attention maps against 87 transcriptional signatures using co-registered Visium spatial transcriptomics data from 18 samples. Internally, no single encoder dominates across all tasks, and external validation inverts internal performance rankings. Attention maps show a five-fold enrichment gradient from pathways (Cohen's d=0.329) to individual genes (d=0.055), indicating that attention captures emergent multi-gene transcriptional programs rather than individual molecular events. Spatially smooth attention maps do not imply biological coherence, and different encoders attend to distinct biological compartments. Our framework provides objective, quantitative assessment of what foundation models learn from histopathology, moving the field beyond qualitative saliency map review.

Sarah Nassar, Nooshin Maghsoodi, Sophia Mannina et al.

Objective: Atrial fibrillation (AF) is the most common cardiac arrhythmia experienced by intensive care unit (ICU) patients and can cause adverse health effects. In this study, we publish a labelled ICU dataset and benchmarks for AF detection. Methods: We compared machine learning models across three data-driven artificial intelligence (AI) approaches: feature-based classifiers, deep learning (DL), and ECG foundation models (FMs). This comparison addresses a critical gap in the literature and aims to pinpoint which AI approach is best for accurate AF detection. Electrocardiograms (ECGs) from a Canadian ICU and the 2021 PhysioNet/Computing in Cardiology Challenge were used to conduct the experiments. Multiple training configurations were tested, ranging from zero-shot inference to transfer learning. Results: On average and across both datasets, ECG FMs performed best, followed by DL, then feature-based classifiers. The model that achieved the top F1 score on our ICU test set was ECG-FM through a transfer learning strategy (F1=0.89). Conclusion: This study demonstrates promising potential for using AI to build an automatic patient monitoring system. Significance: By publishing our labelled ICU dataset (LinkToBeAdded) and performance benchmarks, this work enables the research community to continue advancing the state-of-the-art in AF detection in the ICU.

Faranak Akbarifar, Nooshin Maghsoodi, Sean P Dukelow et al.

Purpose: Visually Guided Reaching (VGR) on the Kinarm robot yields sensitive kinematic biomarkers but requires 40-64 reaches, imposing time and fatigue burdens. We evaluate whether time-series foundation models can replace unrecorded trials from an early subset of reaches while preserving the reliability of standard Kinarm parameters. Methods: We analyzed VGR speed signals from 461 stroke and 599 control participants across 4- and 8-target reaching protocols. We withheld all but the first 8 or 16 reaching trials and used ARIMA, MOMENT, and Chronos models, fine-tuned on 70 percent of subjects, to forecast synthetic trials. We recomputed four kinematic features of reaching (reaction time, movement time, posture speed, maximum speed) on combined recorded plus forecasted trials and compared them to full-length references using ICC(2,1). Results: Chronos forecasts restored ICC >= 0.90 for all parameters with only 8 recorded trials plus forecasts, matching the reliability of 24-28 recorded reaches (Delta ICC <= 0.07). MOMENT yielded intermediate gains, while ARIMA improvements were minimal. Across cohorts and protocols, synthetic trials replaced reaches without materially compromising feature reliability. Conclusion: Foundation-model forecasting can greatly shorten Kinarm VGR assessment time. For the most impaired stroke survivors, sessions drop from 4-5 minutes to about 1 minute while preserving kinematic precision. This forecast-augmented paradigm promises efficient robotic evaluations for assessing motor impairments following stroke.

Hanna Hoffmann, Setareh Bady, Claas de Boer et al.

Achieving high levels of surgical skill through effective training is essential for optimal patient outcomes. Automated, data-driven skill assessment holds significant potential to improve surgical training. While machine learning-based methods are increasingly popular for assessing skills in minimally invasive surgery, their application to open surgery remains limited. We present the results of a dedicated MICCAI challenge designed to benchmark and advance vision-based skill assessment in open surgery. The challenge dataset comprises videos of an open suturing training task recorded with a static GoPro camera in a dry-lab setting, with instrument trajectories available in addition to the primary video modality. The OSS Challenge was hosted over two consecutive years, comprising two and three independent tasks, respectively: (1) classifying skill level into four classes, (2) predicting the full Objective Structured Assessment of Technical Skills across eight categories, and (3) tracking hands and surgical tools. Participants submitted diverse solutions including deep learning-based video models, tracking-driven methods, and hybrid approaches. General-purpose spatiotemporal video models consistently achieved the strongest performance, though conceptually diverse approaches reached competitive levels when well-executed. Predicting fine-grained OSATS scores remains challenging but benefits substantially from increased training data. Keypoint tracking proves difficult given frequent occlusions and out-of-frame instances, limiting current applicability for motion-based skill analysis. This work benchmarks innovative and diverse solutions for surgical skill assessment, highlighting both the promise and current limitations of video-based evaluation in open surgery and identifying critical directions for advancing automated skill assessment toward clinical impact.

Nooshin Maghsoodi, Sarah Nassar, Paul F R Wilson et al.

Objective: Electrocardiograms (ECGs) play a crucial role in diagnosing heart conditions; however, the effectiveness of artificial intelligence (AI)-based ECG analysis is often hindered by the limited availability of labeled data. Self-supervised learning (SSL) can address this by leveraging large-scale unlabeled data. We introduce PhysioCLR (Physiology-aware Contrastive Learning Representation for ECG), a physiology-aware contrastive learning framework that incorporates domain-specific priors to enhance the generalizability and clinical relevance of ECG-based arrhythmia classification. Methods: During pretraining, PhysioCLR learns to bring together embeddings of samples that share similar clinically relevant features while pushing apart those that are dissimilar. Unlike existing methods, our method integrates ECG physiological similarity cues into contrastive learning, promoting the learning of clinically meaningful representations. Additionally, we introduce ECG- specific augmentations that preserve the ECG category post augmentation and propose a hybrid loss function to further refine the quality of learned representations. Results: We evaluate PhysioCLR on two public ECG datasets, Chapman and Georgia, for multilabel ECG diagnoses, as well as a private ICU dataset labeled for binary classification. Across the Chapman, Georgia, and private cohorts, PhysioCLR boosts the mean AUROC by 12% relative to the strongest baseline, underscoring its robust cross-dataset generalization. Conclusion: By embedding physiological knowledge into contrastive learning, PhysioCLR enables the model to learn clinically meaningful and transferable ECG eatures. Significance: PhysioCLR demonstrates the potential of physiology-informed SSL to offer a promising path toward more effective and label-efficient ECG diagnostics.

Nooshin Maghsoodi, Hossein Sameti, Hossein Zeinali et al.

In this paper, we combine Hidden Markov Models (HMMs) with i-vector extractors to address the problem of text-dependent speaker recognition with random digit strings. We employ digit-specific HMMs to segment the utterances into digits, to perform frame alignment to HMM states and to extract Baum-Welch statistics. By making use of the natural partition of input features into digits, we train digit-specific i-vector extractors on top of each HMM and we extract well-localized i-vectors, each modelling merely the phonetic content corresponding to a single digit. We then examine ways to perform channel and uncertainty compensation, and we propose a novel method for using the uncertainty in the i-vector estimates. The experiments on RSR2015 part III show that the proposed method attains 1.52\% and 1.77\% Equal Error Rate (EER) for male and female respectively, outperforming state-of-the-art methods such as x-vectors, trained on vast amounts of data. Furthermore, these results are attained by a single system trained entirely on RSR2015, and by a simple score-normalized cosine distance. Moreover, we show that the omission of channel compensation yields only a minor degradation in performance, meaning that the system attains state-of-the-art results even without recordings from multiple handsets per speaker for training or enrolment. Similar conclusions are drawn from our experiments on the RedDots corpus, where the same method is evaluated on phrases. Finally, we report results with bottleneck features and show that further improvement is attained when fusing them with spectral features.

Hossein Zeinali, Hossein Sameti, Nooshin Maghsoodi

This paper describes the submission to fixed condition of NIST SRE 2016 by Sharif University of Technology (SUT) team. We provide a full description of the systems that were included in our submission. We start with an overview of the datasets that were used for training and development. It is followed by describing front-ends which contain different VAD and feature types. UBM and i-vector extractor training are the next details in this paper. As one of the important steps in system preparation, preconditioning the i-vectors are explained in more details. Then, we describe the classifier and score normalization methods. And finally, some results on SRE16 evaluation dataset are reported and analyzed.