Sabeen Ahmed

Sabeen Ahmed, Ian E. Nielsen, Aakash Tripathi et al.

Transformer architecture has widespread applications, particularly in Natural Language Processing and computer vision. Recently Transformers have been employed in various aspects of time-series analysis. This tutorial provides an overview of the Transformer architecture, its applications, and a collection of examples from recent research papers in time-series analysis. We delve into an explanation of the core components of the Transformer, including the self-attention mechanism, positional encoding, multi-head, and encoder/decoder. Several enhancements to the initial, Transformer architecture are highlighted to tackle time-series tasks. The tutorial also provides best practices and techniques to overcome the challenge of effectively training Transformers for time-series analysis.

Sabeen Ahmed, Nathan Parker, Margaret Park et al.

Cancer cachexia is a multifactorial syndrome characterized by progressive muscle wasting, metabolic dysfunction, and systemic inflammation, leading to reduced quality of life and increased mortality. Despite extensive research, no single definitive biomarker exists, as cachexia-related indicators such as serum biomarkers, skeletal muscle measurements, and metabolic abnormalities often overlap with other conditions. Existing composite indices, including the Cancer Cachexia Index (CXI), Modified CXI (mCXI), and Cachexia Score (CASCO), integrate multiple biomarkers but lack standardized thresholds, limiting their clinical utility. This study proposes a multimodal AI-based biomarker for early cancer cachexia detection, leveraging open-source large language models (LLMs) and foundation models trained on medical data. The approach integrates heterogeneous patient data, including demographics, disease status, lab reports, radiological imaging (CT scans), and clinical notes, using a machine learning framework that can handle missing data. Unlike previous AI-based models trained on curated datasets, this method utilizes routinely collected clinical data, enhancing real-world applicability. Additionally, the model incorporates confidence estimation, allowing the identification of cases requiring expert review for precise clinical interpretation. Preliminary findings demonstrate that integrating multiple data modalities improves cachexia prediction accuracy at the time of cancer diagnosis. The AI-based biomarker dynamically adapts to patient-specific factors such as age, race, ethnicity, weight, cancer type, and stage, avoiding the limitations of fixed-threshold biomarkers. This multimodal AI biomarker provides a scalable and clinically viable solution for early cancer cachexia detection, facilitating personalized interventions and potentially improving treatment outcomes and patient survival.

Asim Waqas, Aakash Tripathi, Sabeen Ahmed et al.

Multi-omics research has enhanced our understanding of cancer heterogeneity and progression. Investigating molecular data through multi-omics approaches is crucial for unraveling the complex biological mechanisms underlying cancer, thereby enabling more effective diagnosis, treatment, and prevention strategies. However, predicting patient outcomes through the integration of all available multi-omics data is still an under-study research direction. Here, we present SeNMo, a foundation model that has been trained on multi-omics data across 33 cancer types. SeNMo is particularly efficient in handling multi-omics data characterized by high-width and low-length attributes. We trained SeNMo for the task of overall survival of patients using pan-cancer multi-omics data involving 33 cancer sites from the GDC. The training multi-omics data includes gene expression, DNA methylation, miRNA expression, DNA mutations, protein expression modalities, and clinical data. SeNMo was validated on two independent cohorts: Moffitt Cancer Center and CPTAC lung squamous cell carcinoma. We evaluated the model's performance in predicting patient's overall survival using the C-Index. SeNMo performed consistently well in the training regime, reflected by the validation C-Index of 0.76 on GDC's public data. In the testing regime, SeNMo performed with a C-Index of 0.758 on a held-out test set. The model showed an average accuracy of 99.8% on the task of classifying the primary cancer type on the pan-cancer test cohort. SeNMo demonstrated robust performance on the classification task of predicting the primary cancer type of patients. SeNMo further demonstrated significant performance in predicting tertiary lymph structures from multi-omics data, showing generalizability across cancer types, molecular data types, and clinical endpoints.

Sabeen Ahmed, Nathan Parker, Margaret Park et al.

Cancer cachexia is a common metabolic disorder characterized by severe muscle atrophy which is associated with poor prognosis and quality of life. Monitoring skeletal muscle area (SMA) longitudinally through computed tomography (CT) scans, an imaging modality routinely acquired in cancer care, is an effective way to identify and track this condition. However, existing tools often lack full automation and exhibit inconsistent accuracy, limiting their potential for integration into clinical workflows. To address these challenges, we developed SMAART-AI (Skeletal Muscle Assessment-Automated and Reliable Tool-based on AI), an end-to-end automated pipeline powered by deep learning models (nnU-Net 2D) trained on mid-third lumbar level CT images with 5-fold cross-validation, ensuring generalizability and robustness. SMAART-AI incorporates an uncertainty-based mechanism to flag high-error SMA predictions for expert review, enhancing reliability. We combined the SMA, skeletal muscle index, BMI, and clinical data to train a multi-layer perceptron (MLP) model designed to predict cachexia at the time of cancer diagnosis. Tested on the gastroesophageal cancer dataset, SMAART-AI achieved a Dice score of 97.80% +/- 0.93%, with SMA estimated across all four datasets in this study at a median absolute error of 2.48% compared to manual annotations with SliceOmatic. Uncertainty metrics-variance, entropy, and coefficient of variation-strongly correlated with SMA prediction errors (0.83, 0.76, and 0.73 respectively). The MLP model predicts cachexia with 79% precision, providing clinicians with a reliable tool for early diagnosis and intervention. By combining automation, accuracy, and uncertainty awareness, SMAART-AI bridges the gap between research and clinical application, offering a transformative approach to managing cancer cachexia.