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Randomized Sparse Matrix Compression for Large-Scale Constrained Optimization in Cancer Radiotherapy

Neural Information Processing Systems

Radiation therapy, treating over half of all cancer patients, involves using specialized machines to direct high-energy beams at tumors, aiming to damage cancer cells while minimizing harm to nearby healthy tissues. Customizing the shape and intensity of radiation beams for each patient leads to solving large-scale constrained optimization problems that need to be solved within tight clinical time-frame. At the core of these challenges is a large matrix that is commonly sparsified for computational efficiency by neglecting small elements. Such a crude approximation can degrade the quality of treatment, potentially causing unnecessary radiation exposure to healthy tissues--this may lead to significant radiation-induced side effects--or delivering inadequate radiation to the tumor, which is crucial for effective tumor treatment. In this work, we demonstrate, for the first time, that randomized sketch tools can effectively sparsify this matrix without sacrificing treatment quality. We also develop a novel randomized sketch method with desirable theoretical guarantees that outperforms existing techniques in practical application. Beyond developing a novel randomized sketch method, this work emphasizes the potential of harnessing scientific computing tools, crucial in today's big data analysis, to tackle computationally intensive challenges in healthcare. The application of these tools could have a profound impact on the lives of numerous cancer patients.


Methodology for Comparing Machine Learning Algorithms for Survival Analysis

Cardoso, Lucas Buk, Angelo, Simone Aldrey, Bonilha, Yasmin Pacheco Gil, Maia, Fernando, Ribeiro, Adeylson Guimarães, Curado, Maria Paula, Fernandes, Gisele Aparecida, Parro, Vanderlei Cunha, Cipparrone, Flávio Almeida de Magalhães, Filho, Alexandre Dias Porto Chiavegatto, Filho, Victor Wünsch, Toporcov, Tatiana Natasha

arXiv.org Artificial Intelligence

This study presents a comparative methodological analysis of six machine learning models for survival analysis (MLSA). Using data from nearly 45,000 colorectal cancer patients in the Hospital-Based Cancer Registries of São Paulo, we evaluated Random Survival Forest (RSF), Gradient Boosting for Survival Analysis (GBSA), Survival SVM (SSVM), XGBoost-Cox (XGB-Cox), XGBoost-AFT (XGB-AFT), and LightGBM (LGBM), capable of predicting survival considering censored data. Hyperparameter optimization was performed with different samplers, and model performance was assessed using the Concordance Index (C-Index), C-Index IPCW, time-dependent AUC, and Integrated Brier Score (IBS). Survival curves produced by the models were compared with predictions from classification algorithms, and predictor interpretation was conducted using SHAP and permutation importance. XGB-AFT achieved the best performance (C-Index = 0.7618; IPCW = 0.7532), followed by GBSA and RSF. The results highlight the potential and applicability of MLSA to improve survival prediction and support decision making.


Dutch Metaphor Extraction from Cancer Patients' Interviews and Forum Data using LLMs and Human in the Loop

Han, Lifeng, Lindevelt, David, Puts, Sander, van Mulligen, Erik, Verberne, Suzan

arXiv.org Artificial Intelligence

Metaphors and metaphorical language (MLs) play an important role in healthcare communication between clinicians, patients, and patients' family members. In this work, we focus on Dutch language data from cancer patients. We extract metaphors used by patients using two data sources: (1) cancer patient storytelling interview data and (2) online forum data, including patients' posts, comments, and questions to professionals. We investigate how current state-of-the-art large language models (LLMs) perform on this task by exploring different prompting strategies such as chain of thought reasoning, few-shot learning, and self-prompting. With a human-in-the-loop setup, we verify the extracted metaphors and compile the outputs into a corpus named HealthQuote.NL. We believe the extracted metaphors can support better patient care, for example shared decision making, improved communication between patients and clinicians, and enhanced patient health literacy. They can also inform the design of personalized care pathways. We share prompts and related resources at https://github.com/aaronlifenghan/HealthQuote.NL


Diffusion Transformer-based Universal Dose Denoising for Pencil Beam Scanning Proton Therapy

Ding, Yuzhen, Holmes, Jason, Feng, Hongying, Bues, Martin, McGee, Lisa A., Rwigema, Jean-Claude M., Yu, Nathan Y., Sio, Terence S., Keole, Sameer R., Wong, William W., Schild, Steven E., Ashman, Jonathan B., Vora, Sujay A., Ma, Daniel J., Patel, Samir H., Liu, Wei

arXiv.org Artificial Intelligence

Purpose: Intensity-modulated proton therapy (IMPT) offers precise tumor coverage while sparing organs at risk (OARs) in head and neck (H&N) cancer. However, its sensitivity to anatomical changes requires frequent adaptation through online adaptive radiation therapy (oART), which depends on fast, accurate dose calculation via Monte Carlo (MC) simulations. Reducing particle count accelerates MC but degrades accuracy. To address this, denoising low-statistics MC dose maps is proposed to enable fast, high-quality dose generation. Methods: We developed a diffusion transformer-based denoising framework. IMPT plans and 3D CT images from 80 H&N patients were used to generate noisy and high-statistics dose maps using MCsquare (1 min and 10 min per plan, respectively). Data were standardized into uniform chunks with zero-padding, normalized, and transformed into quasi-Gaussian distributions. Testing was done on 10 H&N, 10 lung, 10 breast, and 10 prostate cancer cases, preprocessed identically. The model was trained with noisy dose maps and CT images as input and high-statistics dose maps as ground truth, using a combined loss of mean square error (MSE), residual loss, and regional MAE (focusing on top/bottom 10% dose voxels). Performance was assessed via MAE, 3D Gamma passing rate, and DVH indices. Results: The model achieved MAEs of 0.195 (H&N), 0.120 (lung), 0.172 (breast), and 0.376 Gy[RBE] (prostate). 3D Gamma passing rates exceeded 92% (3%/2mm) across all sites. DVH indices for clinical target volumes (CTVs) and OARs closely matched the ground truth. Conclusion: A diffusion transformer-based denoising framework was developed and, though trained only on H&N data, generalizes well across multiple disease sites.


Randomized Sparse Matrix Compression for Large-Scale Constrained Optimization in Cancer Radiotherapy

Neural Information Processing Systems

Radiation therapy, treating over half of all cancer patients, involves using specialized machines to direct high-energy beams at tumors, aiming to damage cancer cells while minimizing harm to nearby healthy tissues. Customizing the shape and intensity of radiation beams for each patient leads to solving large-scale constrained optimization problems that need to be solved within tight clinical time-frame. At the core of these challenges is a large matrix that is commonly sparsified for computational efficiency by neglecting small elements. Such a crude approximation can degrade the quality of treatment, potentially causing unnecessary radiation exposure to healthy tissues--this may lead to significant radiation-induced side effects--or delivering inadequate radiation to the tumor, which is crucial for effective tumor treatment. In this work, we demonstrate, for the first time, that randomized sketch tools can effectively sparsify this matrix without sacrificing treatment quality.


AI tool scans faces to predict biological age and cancer survival

FOX News

Fox News anchor Bret Baier has the latest on the Murdoch Children's Research Institute's partnership with the Gladstone Institutes for the'Decoding Broken Hearts' initiative on'Special Report.' A simple selfie could hold hidden clues to one's biological age -- and even how long they'll live. That's according to researchers from Mass General Brigham, who developed a deep-learning algorithm called FaceAge. Using a photo of someone's face, the artificial intelligence tool generates predictions of the subject's biological age, which is the rate at which they are aging as opposed to their chronological age. FaceAge also predicts survival outcomes for people with cancer, according to a press release from MGB.


Predicting Survivability of Cancer Patients with Metastatic Patterns Using Explainable AI

Nalela, Polycarp, Rao, Deepthi, Rao, Praveen

arXiv.org Artificial Intelligence

Cancer remains a leading global health challenge and a major cause of mortality. This study leverages machine learning (ML) to predict the survivability of cancer patients with metastatic patterns using the comprehensive MSK-MET dataset, which includes genomic and clinical data from 25,775 patients across 27 cancer types. We evaluated five ML models-XGBoost, Naïve Bayes, Decision Tree, Logistic Regression, and Random Fores using hyperparameter tuning and grid search. XGBoost emerged as the best performer with an area under the curve (AUC) of 0.82. To enhance model interpretability, SHapley Additive exPlanations (SHAP) were applied, revealing key predictors such as metastatic site count, tumor mutation burden, fraction of genome altered, and organ-specific metastases. Further survival analysis using Kaplan-Meier curves, Cox Proportional Hazards models, and XGBoost Survival Analysis identified significant predictors of patient outcomes, offering actionable insights for clinicians. These findings could aid in personalized prognosis and treatment planning, ultimately improving patient care.


Reliable Radiologic Skeletal Muscle Area Assessment -- A Biomarker for Cancer Cachexia Diagnosis

Ahmed, Sabeen, Parker, Nathan, Park, Margaret, Jeong, Daniel, Peres, Lauren, Davis, Evan W., Permuth, Jennifer B., Siegel, Erin, Schabath, Matthew B., Yilmaz, Yasin, Rasool, Ghulam

arXiv.org Artificial Intelligence

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.


AI-Driven Automated Tool for Abdominal CT Body Composition Analysis in Gastrointestinal Cancer Management

Nan, Xinyu, He, Meng, Chen, Zifan, Dong, Bin, Tang, Lei, Zhang, Li

arXiv.org Artificial Intelligence

The incidence of gastrointestinal cancers remains significantly high, particularly in China, emphasizing the importance of accurate prognostic assessments and effective treatment strategies. Research shows a strong correlation between abdominal muscle and fat tissue composition and patient outcomes. However, existing manual methods for analyzing abdominal tissue composition are time-consuming and costly, limiting clinical research scalability. To address these challenges, we developed an AI-driven tool for automated analysis of abdominal CT scans to effectively identify and segment muscle, subcutaneous fat, and visceral fat. Our tool integrates a multi-view localization model and a high-precision 2D nnUNet-based segmentation model, demonstrating a localization accuracy of 90% and a Dice Score Coefficient of 0.967 for segmentation. Furthermore, it features an interactive interface that allows clinicians to refine the segmentation results, ensuring high-quality outcomes effectively. Our tool offers a standardized method for effectively extracting critical abdominal tissues, potentially enhancing the management and treatment for gastrointestinal cancers. The code is available at https://github.com/NanXinyu/AI-Tool4Abdominal-Seg.git}{https://github.com/NanXinyu/AI-Tool4Abdominal-Seg.git.


RECOVER: Designing a Large Language Model-based Remote Patient Monitoring System for Postoperative Gastrointestinal Cancer Care

Yang, Ziqi, Lu, Yuxuan, Bagdasarian, Jennifer, Swain, Vedant Das, Agarwal, Ritu, Campbell, Collin, Al-Refaire, Waddah, El-Bayoumi, Jehan, Gao, Guodong, Wang, Dakuo, Yao, Bingsheng, Shara, Nawar

arXiv.org Artificial Intelligence

Cancer surgery is a key treatment for gastrointestinal (GI) cancers, a group of cancers that account for more than 35% of cancer-related deaths worldwide, but postoperative complications are unpredictable and can be life-threatening. In this paper, we investigate how recent advancements in large language models (LLMs) can benefit remote patient monitoring (RPM) systems through clinical integration by designing RECOVER, an LLM-powered RPM system for postoperative GI cancer care. To closely engage stakeholders in the design process, we first conducted seven participatory design sessions with five clinical staff and interviewed five cancer patients to derive six major design strategies for integrating clinical guidelines and information needs into LLM-based RPM systems. We then designed and implemented RECOVER, which features an LLM-powered conversational agent for cancer patients and an interactive dashboard for clinical staff to enable efficient postoperative RPM. Finally, we used RECOVER as a pilot system to assess the implementation of our design strategies with four clinical staff and five patients, providing design implications by identifying crucial design elements, offering insights on responsible AI, and outlining opportunities for future LLM-powered RPM systems.