Browsing by Author "Li, Xinyi"
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Item Open Access A Collimator Setting Optimization Algorithm for Dual-arc Volumetric Modulated Arc Therapy in Pancreas Stereotactic Body Radiation Therapy(2019) Li, XinyiPurpose: To develop an automatic collimator setting optimization algorithm to improve dosimetric quality of pancreas Volumetric Modulated Arc Therapy (VMAT) plans for Stereotactic Body Radiation Therapy (SBRT).
Methods: Fifty-five pancreas SBRT cases were retrospectively studied. Different from the conventional practice of initializing collimator settings manually, the proposed algorithm simultaneously optimizes the collimator angles and jaw positions which are customized to the patient geometry. This algorithm includes two key steps: an iterative optimization algorithm via simulated annealing that generates a set of collimator settings candidates, and a scoring system that choose the final collimator settings based on organs-at-risk (OARs) sparing criteria and dose prescription. The scoring system penalizes 3 factors: 1) jaw opening ratio on Y direction to X direction; 2) unmodulated MLC area within the jaw aperture in a dynamic MLC sequence; 3) OAR shielding capability by MLC with MLC aperture control constraints. For validation, the other 16 pancreas SBRT cases were analyzed. Two dual-arc plans were generated for each validation case, an optimized plan (Planopt) and a conventional plan (Planconv). Each plan was generated by a same set of auxiliary planning structures and dose-volume-histogram (DVH) constraints in inverse optimization. Dosimetric results were analyzed and compared. All results were tested by Wilcoxon signed-rank tests.
Results: Both plan groups had no statistical differences in target dose coverage V95% (p=0.84) and Root Conformity Index (p=0.30). Mean doses of OARs were improved or comparable. In comparison with Planconv, Planopt reduced maximum dose (D0.03cc) to stomach (-49.5cGy, p=0.03), duodenum (-63.5cGy, p<0.01), and bowel (-62.5cGy, p=0.01). Planopt also showed lower modulation complexity score (p=0.02), which implies its higher modulation complexity of the dynamic MLC sequence.
Conclusions: The proposed collimator settings optimization algorithm successfully improved dosimetric performance for dual-arc VMAT plans in pancreas SBRT. The proposed algorithm was demonstrated with great clinical feasibility and readiness.
Item Open Access A Collimator Setting Optimization Algorithm for Dual-Arc Volumetric Modulated Arc Therapy in Pancreas Stereotactic Body Radiation Therapy.(Technology in cancer research & treatment, 2019-01) Li, Xinyi; Wu, Jackie; Palta, Manisha; Zhang, You; Sheng, Yang; Zhang, Jiahan; Wang, ChunhaoPURPOSE:To optimize collimator setting to improve dosimetric quality of pancreas volumetric modulated arc therapy plan for stereotactic body radiation therapy. MATERIALS AND METHODS:Fifty-five volumetric modulated arc therapy cases in stereotactic body radiation therapy of pancreas were retrospectively included in this study with internal review board approval. Different from the routine practice of initializing collimator settings with a template, the proposed algorithm simultaneously optimizes the collimator angles and jaw positions that are customized to the patient geometry. Specifically, this algorithm includes 2 key steps: (1) an iterative optimization algorithm via simulated annealing that generates a set of potential collimator settings from 39 cases with pancreas stereotactic body radiation therapy, and (2) a multi-leaf collimator modulation scoring system that makes the final decision of the optimal collimator settings (collimator angles and jaw positions) based on organs at risk sparing criteria. For validation, the other 16 cases with pancreas stereotactic body radiation therapy were analyzed. Two plans were generated for each validation case, with one plan optimized using the proposed algorithm (Planopt) and the other plan with the template setting (Planconv). Each plan was optimized with 2 full arcs and the same set of constraints for the same case. Dosimetric results were analyzed and compared, including target dose coverage, conformity, organs at risk maximum dose, and modulation complexity score. All results were tested by Wilcoxon signed rank tests, and the statistical significance level was set to .05. RESULTS:Both plan groups had comparable target dose coverage and mean doses of all organs at risk. However, organs at risk (stomach, duodenum, large/small bowel) maximum dose sparing (D0.1 cc and D0.03 cc) was improved in Planopt compared to Planconv. Planopt also showed lower modulation complexity score, which suggests better capability of handling complex shape and sparing organs at risk . CONCLUSIONS:The proposed collimator settings optimization algorithm successfully improved dosimetric performance for dual-arc pancreas volumetric modulated arc therapy plans in stereotactic body radiation therapy of pancreas. This algorithm has the capability of immediate clinical application.Item Embargo Artificial Intelligence-Driven Planning Agents for Real-Time IMRT Plan Generation(2023) Li, XinyiArtificial intelligence (AI) has been rapidly developing in various fields, featuring automation in complex tasks with superior efficiency. This feature meets the urgent need for the automation of resource-intensive tasks in clinics. In radiation oncology, AI has been investigated for almost every process in patient management and treatment. Among these, radiotherapy treatment planning is one of the most time-consuming and labor-intensive processes. This dissertation work focuses on AI-based planning agents for intensity-modulated radiation therapy (IMRT) for various treatment sites. Fluence map prediction for prostate simultaneous integrated boost (SIB) or Stereotactic Body Radiotherapy (SBRT) cases was selected for a feasibility study. Prostate cases have one of the most consistent anatomic geometries and dosimetric constraints among all treatment sites. The developed prostate AI planning agent employed a customized convolutional neuro network (CNN), Dense-Res Hybrid Network (DRHN). DRHN was trained to predict optimal fluence maps from patient anatomic information. The proposed method avoids the time-consuming inverse planning process and thus could make fluence map predictions in seconds and generate IMRT plans in a few minutes. The resulting AI plan quality met institutional clinical guidelines. This preliminary study demonstrated the feasibility of the proposed AI strategy in automatic treatment planning and provided a solid foundation for the following studies. As a step forward, a more sophisticated AI agent for oropharyngeal cases was developed based on the prostate AI agent. This AI agent had the following two upgrades to adapt to the much more complex geometry in head-and-neck (H&N) treatment site: 1) conditional generative adversarial networks (cGAN) training architecture; 2) the generator, PyraNet, was a customized CNN network with more complicated network structure design in the shape of pyramids. This H&N AI agent demonstrated encouraging plan quality, especially that organs-at-risk (OAR) dosimetric outcomes achieved expectations. A graphical user interface (GUI) was developed and commissioned to make this AI tool available for clinical implementation. In summary, a DL-based fluence map prediction was developed for prostate and H&N cases. The H&N AI agent was implemented for clinical use, and more related research and applications are around the corner.
Item Open Access Challenges of COVID-19 Case Forecasting in the US, 2020-2021.(PLoS computational biology, 2024-05) Lopez, Velma K; Cramer, Estee Y; Pagano, Robert; Drake, John M; O'Dea, Eamon B; Adee, Madeline; Ayer, Turgay; Chhatwal, Jagpreet; Dalgic, Ozden O; Ladd, Mary A; Linas, Benjamin P; Mueller, Peter P; Xiao, Jade; Bracher, Johannes; Castro Rivadeneira, Alvaro J; Gerding, Aaron; Gneiting, Tilmann; Huang, Yuxin; Jayawardena, Dasuni; Kanji, Abdul H; Le, Khoa; Mühlemann, Anja; Niemi, Jarad; Ray, Evan L; Stark, Ariane; Wang, Yijin; Wattanachit, Nutcha; Zorn, Martha W; Pei, Sen; Shaman, Jeffrey; Yamana, Teresa K; Tarasewicz, Samuel R; Wilson, Daniel J; Baccam, Sid; Gurung, Heidi; Stage, Steve; Suchoski, Brad; Gao, Lei; Gu, Zhiling; Kim, Myungjin; Li, Xinyi; Wang, Guannan; Wang, Lily; Wang, Yueying; Yu, Shan; Gardner, Lauren; Jindal, Sonia; Marshall, Maximilian; Nixon, Kristen; Dent, Juan; Hill, Alison L; Kaminsky, Joshua; Lee, Elizabeth C; Lemaitre, Joseph C; Lessler, Justin; Smith, Claire P; Truelove, Shaun; Kinsey, Matt; Mullany, Luke C; Rainwater-Lovett, Kaitlin; Shin, Lauren; Tallaksen, Katharine; Wilson, Shelby; Karlen, Dean; Castro, Lauren; Fairchild, Geoffrey; Michaud, Isaac; Osthus, Dave; Bian, Jiang; Cao, Wei; Gao, Zhifeng; Lavista Ferres, Juan; Li, Chaozhuo; Liu, Tie-Yan; Xie, Xing; Zhang, Shun; Zheng, Shun; Chinazzi, Matteo; Davis, Jessica T; Mu, Kunpeng; Pastore Y Piontti, Ana; Vespignani, Alessandro; Xiong, Xinyue; Walraven, Robert; Chen, Jinghui; Gu, Quanquan; Wang, Lingxiao; Xu, Pan; Zhang, Weitong; Zou, Difan; Gibson, Graham Casey; Sheldon, Daniel; Srivastava, Ajitesh; Adiga, Aniruddha; Hurt, Benjamin; Kaur, Gursharn; Lewis, Bryan; Marathe, Madhav; Peddireddy, Akhil Sai; Porebski, Przemyslaw; Venkatramanan, Srinivasan; Wang, Lijing; Prasad, Pragati V; Walker, Jo W; Webber, Alexander E; Slayton, Rachel B; Biggerstaff, Matthew; Reich, Nicholas G; Johansson, Michael ADuring the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub (https://covid19forecasthub.org). We evaluated approximately 9.7 million forecasts of weekly state-level COVID-19 cases for predictions 1-4 weeks into the future submitted by 24 teams from August 2020 to December 2021. We assessed coverage of central prediction intervals and weighted interval scores (WIS), adjusting for missing forecasts relative to a baseline forecast, and used a Gaussian generalized estimating equation (GEE) model to evaluate differences in skill across epidemic phases that were defined by the effective reproduction number. Overall, we found high variation in skill across individual models, with ensemble-based forecasts outperforming other approaches. Forecast skill relative to the baseline was generally higher for larger jurisdictions (e.g., states compared to counties). Over time, forecasts generally performed worst in periods of rapid changes in reported cases (either in increasing or decreasing epidemic phases) with 95% prediction interval coverage dropping below 50% during the growth phases of the winter 2020, Delta, and Omicron waves. Ideally, case forecasts could serve as a leading indicator of changes in transmission dynamics. However, while most COVID-19 case forecasts outperformed a naïve baseline model, even the most accurate case forecasts were unreliable in key phases. Further research could improve forecasts of leading indicators, like COVID-19 cases, by leveraging additional real-time data, addressing performance across phases, improving the characterization of forecast confidence, and ensuring that forecasts were coherent across spatial scales. In the meantime, it is critical for forecast users to appreciate current limitations and use a broad set of indicators to inform pandemic-related decision making.Item Open Access Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States.(Proceedings of the National Academy of Sciences of the United States of America, 2022-04) Cramer, Estee Y; Ray, Evan L; Lopez, Velma K; Bracher, Johannes; Brennen, Andrea; Castro Rivadeneira, Alvaro J; Gerding, Aaron; Gneiting, Tilmann; House, Katie H; Huang, Yuxin; Jayawardena, Dasuni; Kanji, Abdul H; Khandelwal, Ayush; Le, Khoa; Mühlemann, Anja; Niemi, Jarad; Shah, Apurv; Stark, Ariane; Wang, Yijin; Wattanachit, Nutcha; Zorn, Martha W; Gu, Youyang; Jain, Sansiddh; Bannur, Nayana; Deva, Ayush; Kulkarni, Mihir; Merugu, Srujana; Raval, Alpan; Shingi, Siddhant; Tiwari, Avtansh; White, Jerome; Abernethy, Neil F; Woody, Spencer; Dahan, Maytal; Fox, Spencer; Gaither, Kelly; Lachmann, Michael; Meyers, Lauren Ancel; Scott, James G; Tec, Mauricio; Srivastava, Ajitesh; George, Glover E; Cegan, Jeffrey C; Dettwiller, Ian D; England, William P; Farthing, Matthew W; Hunter, Robert H; Lafferty, Brandon; Linkov, Igor; Mayo, Michael L; Parno, Matthew D; Rowland, Michael A; Trump, Benjamin D; Zhang-James, Yanli; Chen, Samuel; Faraone, Stephen V; Hess, Jonathan; Morley, Christopher P; Salekin, Asif; Wang, Dongliang; Corsetti, Sabrina M; Baer, Thomas M; Eisenberg, Marisa C; Falb, Karl; Huang, Yitao; Martin, Emily T; McCauley, Ella; Myers, Robert L; Schwarz, Tom; Sheldon, Daniel; Gibson, Graham Casey; Yu, Rose; Gao, Liyao; Ma, Yian; Wu, Dongxia; Yan, Xifeng; Jin, Xiaoyong; Wang, Yu-Xiang; Chen, YangQuan; Guo, Lihong; Zhao, Yanting; Gu, Quanquan; Chen, Jinghui; Wang, Lingxiao; Xu, Pan; Zhang, Weitong; Zou, Difan; Biegel, Hannah; Lega, Joceline; McConnell, Steve; Nagraj, VP; Guertin, Stephanie L; Hulme-Lowe, Christopher; Turner, Stephen D; Shi, Yunfeng; Ban, Xuegang; Walraven, Robert; Hong, Qi-Jun; Kong, Stanley; van de Walle, Axel; Turtle, James A; Ben-Nun, Michal; Riley, Steven; Riley, Pete; Koyluoglu, Ugur; DesRoches, David; Forli, Pedro; Hamory, Bruce; Kyriakides, Christina; Leis, Helen; Milliken, John; Moloney, Michael; Morgan, James; Nirgudkar, Ninad; Ozcan, Gokce; Piwonka, Noah; Ravi, Matt; Schrader, Chris; Shakhnovich, Elizabeth; Siegel, Daniel; Spatz, Ryan; Stiefeling, Chris; Wilkinson, Barrie; Wong, Alexander; Cavany, Sean; España, Guido; Moore, Sean; Oidtman, Rachel; Perkins, Alex; Kraus, David; Kraus, Andrea; Gao, Zhifeng; Bian, Jiang; Cao, Wei; Lavista Ferres, Juan; Li, Chaozhuo; Liu, Tie-Yan; Xie, Xing; Zhang, Shun; Zheng, Shun; Vespignani, Alessandro; Chinazzi, Matteo; Davis, Jessica T; Mu, Kunpeng; Pastore Y Piontti, Ana; Xiong, Xinyue; Zheng, Andrew; Baek, Jackie; Farias, Vivek; Georgescu, Andreea; Levi, Retsef; Sinha, Deeksha; Wilde, Joshua; Perakis, Georgia; Bennouna, Mohammed Amine; Nze-Ndong, David; Singhvi, Divya; Spantidakis, Ioannis; Thayaparan, Leann; Tsiourvas, Asterios; Sarker, Arnab; Jadbabaie, Ali; Shah, Devavrat; Della Penna, Nicolas; Celi, Leo A; Sundar, Saketh; Wolfinger, Russ; Osthus, Dave; Castro, Lauren; Fairchild, Geoffrey; Michaud, Isaac; Karlen, Dean; Kinsey, Matt; Mullany, Luke C; Rainwater-Lovett, Kaitlin; Shin, Lauren; Tallaksen, Katharine; Wilson, Shelby; Lee, Elizabeth C; Dent, Juan; Grantz, Kyra H; Hill, Alison L; Kaminsky, Joshua; Kaminsky, Kathryn; Keegan, Lindsay T; Lauer, Stephen A; Lemaitre, Joseph C; Lessler, Justin; Meredith, Hannah R; Perez-Saez, Javier; Shah, Sam; Smith, Claire P; Truelove, Shaun A; Wills, Josh; Marshall, Maximilian; Gardner, Lauren; Nixon, Kristen; Burant, John C; Wang, Lily; Gao, Lei; Gu, Zhiling; Kim, Myungjin; Li, Xinyi; Wang, Guannan; Wang, Yueying; Yu, Shan; Reiner, Robert C; Barber, Ryan; Gakidou, Emmanuela; Hay, Simon I; Lim, Steve; Murray, Chris; Pigott, David; Gurung, Heidi L; Baccam, Prasith; Stage, Steven A; Suchoski, Bradley T; Prakash, B Aditya; Adhikari, Bijaya; Cui, Jiaming; Rodríguez, Alexander; Tabassum, Anika; Xie, Jiajia; Keskinocak, Pinar; Asplund, John; Baxter, Arden; Oruc, Buse Eylul; Serban, Nicoleta; Arik, Sercan O; Dusenberry, Mike; Epshteyn, Arkady; Kanal, Elli; Le, Long T; Li, Chun-Liang; Pfister, Tomas; Sava, Dario; Sinha, Rajarishi; Tsai, Thomas; Yoder, Nate; Yoon, Jinsung; Zhang, Leyou; Abbott, Sam; Bosse, Nikos I; Funk, Sebastian; Hellewell, Joel; Meakin, Sophie R; Sherratt, Katharine; Zhou, Mingyuan; Kalantari, Rahi; Yamana, Teresa K; Pei, Sen; Shaman, Jeffrey; Li, Michael L; Bertsimas, Dimitris; Skali Lami, Omar; Soni, Saksham; Tazi Bouardi, Hamza; Ayer, Turgay; Adee, Madeline; Chhatwal, Jagpreet; Dalgic, Ozden O; Ladd, Mary A; Linas, Benjamin P; Mueller, Peter; Xiao, Jade; Wang, Yuanjia; Wang, Qinxia; Xie, Shanghong; Zeng, Donglin; Green, Alden; Bien, Jacob; Brooks, Logan; Hu, Addison J; Jahja, Maria; McDonald, Daniel; Narasimhan, Balasubramanian; Politsch, Collin; Rajanala, Samyak; Rumack, Aaron; Simon, Noah; Tibshirani, Ryan J; Tibshirani, Rob; Ventura, Valerie; Wasserman, Larry; O'Dea, Eamon B; Drake, John M; Pagano, Robert; Tran, Quoc T; Ho, Lam Si Tung; Huynh, Huong; Walker, Jo W; Slayton, Rachel B; Johansson, Michael A; Biggerstaff, Matthew; Reich, Nicholas GShort-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multimodel ensemble forecast that combined predictions from dozens of groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naïve baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-wk horizon three to five times larger than when predicting at a 1-wk horizon. This project underscores the role that collaboration and active coordination between governmental public-health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks.Item Open Access Fluence Map Prediction Using Deep Learning Models - Direct Plan Generation for Pancreas Stereotactic Body Radiation Therapy.(Frontiers in artificial intelligence, 2020-01) Wang, Wentao; Sheng, Yang; Wang, Chunhao; Zhang, Jiahan; Li, Xinyi; Palta, Manisha; Czito, Brian; Willett, Christopher G; Wu, Qiuwen; Ge, Yaorong; Yin, Fang-Fang; Wu, Q JackiePurpose: Treatment planning for pancreas stereotactic body radiation therapy (SBRT) is a difficult and time-consuming task. In this study, we aim to develop a novel deep learning framework to generate clinical-quality plans by direct prediction of fluence maps from patient anatomy using convolutional neural networks (CNNs). Materials and Methods: Our proposed framework utilizes two CNNs to predict intensity-modulated radiation therapy fluence maps and generate deliverable plans: (1) Field-dose CNN predicts field-dose distributions in the region of interest using planning images and structure contours; (2) a fluence map CNN predicts the final fluence map per beam using the predicted field dose projected onto the beam's eye view. The predicted fluence maps were subsequently imported into the treatment planning system for leaf sequencing and final dose calculation (model-predicted plans). One hundred patients previously treated with pancreas SBRT were included in this retrospective study, and they were split into 85 training cases and 15 test cases. For each network, 10% of training data were randomly selected for model validation. Nine-beam benchmark plans with standardized target prescription and organ-at-risk constraints were planned by experienced clinical physicists and used as the gold standard to train the model. Model-predicted plans were compared with benchmark plans in terms of dosimetric endpoints, fluence map deliverability, and total monitor units. Results: The average time for fluence-map prediction per patient was 7.1 s. Comparing model-predicted plans with benchmark plans, target mean dose, maximum dose (0.1 cc), and D95% absolute differences in percentages of prescription were 0.1, 3.9, and 2.1%, respectively; organ-at-risk mean dose and maximum dose (0.1 cc) absolute differences were 0.2 and 4.4%, respectively. The predicted plans had fluence map gamma indices (97.69 ± 0.96% vs. 98.14 ± 0.74%) and total monitor units (2,122 ± 281 vs. 2,265 ± 373) that were comparable to the benchmark plans. Conclusions: We develop a novel deep learning framework for pancreas SBRT planning, which predicts a fluence map for each beam and can, therefore, bypass the lengthy inverse optimization process. The proposed framework could potentially change the paradigm of treatment planning by harnessing the power of deep learning to generate clinically deliverable plans in seconds.