Browsing by Subject "Artificial Intelligence"
Results Per Page
Sort Options
Item Open Access Accelerating crystal structure determination with iterative AlphaFold prediction.(Acta crystallographica. Section D, Structural biology, 2023-03) Terwilliger, Thomas C; Afonine, Pavel V; Liebschner, Dorothee; Croll, Tristan I; McCoy, Airlie J; Oeffner, Robert D; Williams, Christopher J; Poon, Billy K; Richardson, Jane S; Read, Randy J; Adams, Paul DExperimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold. Here, an automatic procedure requiring only sequence information and crystallographic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. Iterating through cycles of structure prediction is a key element of this procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. In 87% of cases our procedure yielded a model with at least 50% of Cα atoms matching those in the deposited models within 2 Å. Predictions from the iterative template-guided prediction procedure were more accurate than those obtained without templates. It is concluded that AlphaFold predictions obtained based on sequence information alone are usually accurate enough to solve the crystallographic phase problem with molecular replacement, and a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization is suggested.Item Open Access ADVANCING VISION INTELLIGENCE THROUGH THE DEVELOPMENT OF EFFICIENCY, INTERPRETABILITY AND FAIRNESS IN DEEP LEARNING MODELS(2024) Kong, FanjieDeep learning has demonstrated remarkable success in developing vision intelligence across a variety of application domains, including autonomous driving, facial recognition, medical image analysis, \etc.However, developing such vision systems poses significant challenges, particularly in relation to ensuring efficiency, interpretability, and fairness. Efficiency requires a model to leverage the least possible computational resources while preserving performance relative to more computationally-demanding alternatives, which is essential for the practical deployment of large-scale models in real-time applications. Interpretability demands a model to align with the domain-specific knowledge of the task it addresses while having the capability for case-based reasoning. This characteristic is especially crucial in high-stakes areas such as healthcare, criminal justice, and financial investment. Fairness ensures that computer vision models do not perpetuate or exacerbate societal biases in downstream applications such as web image search, text-guided image generation, \etc. In this dissertation, I will discuss the contributions that I have made in advancing vision intelligence regarding to efficiency, interpretability and fairness in computer vision models.
The first part of this dissertation will focus on how to design computer vision models to efficiently process very large images.We propose a novel CNN architecture termed { \em Zoom-In Network} that leverages a hierarchical attention sampling mechanisms to select important regions of images to process. Such approach without processing the entire image yields outstanding memory efficiency while maintaining classification accuracy on various tiny object image classification datasets.
The second part of this dissertation will discuss how to build post-hoc interpretation method for deep learning models to obtain insights reasoned from the predictions.We propose a novel image and text insight-generation framework based on attributions from deep neural nets. We test our approach on an industrial dataset and demonstrate our method outperforms competing methods.
Finally, we study fairness in large vision-language models.More specifically, we examined gender and racial bias in text-based image retrieval for neutral text queries. In an attempt to address bias in the test-time phase, we proposed post-hoc bias mitigation to actively balance the demographic group in the image search results. Experiments on multiple datasets show that our method can significantly reduce bias while maintaining satisfactory retrieval accuracy at the same time.
My research in enhancing vision intelligence via developments in efficiency, interpretability, and fairness, has undergone rigorous validation using publicly available benchmarks and has been recognized at leading peer-reviewed machine learning conferences.This dissertation has sparked interest within the AI community, emphasizing the importance of improving computer vision models through these three critical dimensions, namely, efficiency, interpretability and fairness.
Item Open Access An active learning approach for rapid characterization of endothelial cells in human tumors.(PLoS One, 2014) Padmanabhan, Raghav K; Somasundar, Vinay H; Griffith, Sandra D; Zhu, Jianliang; Samoyedny, Drew; Tan, Kay See; Hu, Jiahao; Liao, Xuejun; Carin, Lawrence; Yoon, Sam S; Flaherty, Keith T; Dipaola, Robert S; Heitjan, Daniel F; Lal, Priti; Feldman, Michael D; Roysam, Badrinath; Lee, William MFCurrently, no available pathological or molecular measures of tumor angiogenesis predict response to antiangiogenic therapies used in clinical practice. Recognizing that tumor endothelial cells (EC) and EC activation and survival signaling are the direct targets of these therapies, we sought to develop an automated platform for quantifying activity of critical signaling pathways and other biological events in EC of patient tumors by histopathology. Computer image analysis of EC in highly heterogeneous human tumors by a statistical classifier trained using examples selected by human experts performed poorly due to subjectivity and selection bias. We hypothesized that the analysis can be optimized by a more active process to aid experts in identifying informative training examples. To test this hypothesis, we incorporated a novel active learning (AL) algorithm into FARSIGHT image analysis software that aids the expert by seeking out informative examples for the operator to label. The resulting FARSIGHT-AL system identified EC with specificity and sensitivity consistently greater than 0.9 and outperformed traditional supervised classification algorithms. The system modeled individual operator preferences and generated reproducible results. Using the results of EC classification, we also quantified proliferation (Ki67) and activity in important signal transduction pathways (MAP kinase, STAT3) in immunostained human clear cell renal cell carcinoma and other tumors. FARSIGHT-AL enables characterization of EC in conventionally preserved human tumors in a more automated process suitable for testing and validating in clinical trials. The results of our study support a unique opportunity for quantifying angiogenesis in a manner that can now be tested for its ability to identify novel predictive and response biomarkers.Item Open Access Applying active learning to high-throughput phenotyping algorithms for electronic health records data.(Journal of the American Medical Informatics Association : JAMIA, 2013-12) Chen, Yukun; Carroll, Robert J; Hinz, Eugenia R McPeek; Shah, Anushi; Eyler, Anne E; Denny, Joshua C; Xu, HuaObjectives
Generalizable, high-throughput phenotyping methods based on supervised machine learning (ML) algorithms could significantly accelerate the use of electronic health records data for clinical and translational research. However, they often require large numbers of annotated samples, which are costly and time-consuming to review. We investigated the use of active learning (AL) in ML-based phenotyping algorithms.Methods
We integrated an uncertainty sampling AL approach with support vector machines-based phenotyping algorithms and evaluated its performance using three annotated disease cohorts including rheumatoid arthritis (RA), colorectal cancer (CRC), and venous thromboembolism (VTE). We investigated performance using two types of feature sets: unrefined features, which contained at least all clinical concepts extracted from notes and billing codes; and a smaller set of refined features selected by domain experts. The performance of the AL was compared with a passive learning (PL) approach based on random sampling.Results
Our evaluation showed that AL outperformed PL on three phenotyping tasks. When unrefined features were used in the RA and CRC tasks, AL reduced the number of annotated samples required to achieve an area under the curve (AUC) score of 0.95 by 68% and 23%, respectively. AL also achieved a reduction of 68% for VTE with an optimal AUC of 0.70 using refined features. As expected, refined features improved the performance of phenotyping classifiers and required fewer annotated samples.Conclusions
This study demonstrated that AL can be useful in ML-based phenotyping methods. Moreover, AL and feature engineering based on domain knowledge could be combined to develop efficient and generalizable phenotyping methods.Item Open Access Artificial intelligence clustering of adult spinal deformity sagittal plane morphology predicts surgical characteristics, alignment, and outcomes.(European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society, 2021-08) Durand, Wesley M; Lafage, Renaud; Hamilton, D Kojo; Passias, Peter G; Kim, Han Jo; Protopsaltis, Themistocles; Lafage, Virginie; Smith, Justin S; Shaffrey, Christopher; Gupta, Munish; Kelly, Michael P; Klineberg, Eric O; Schwab, Frank; Gum, Jeffrey L; Mundis, Gregory; Eastlack, Robert; Kebaish, Khaled; Soroceanu, Alex; Hostin, Richard A; Burton, Doug; Bess, Shay; Ames, Christopher; Hart, Robert A; Daniels, Alan H; International Spine Study Group (ISSG)Purpose
AI algorithms have shown promise in medical image analysis. Previous studies of ASD clusters have analyzed alignment metrics-this study sought to complement these efforts by analyzing images of sagittal anatomical spinopelvic landmarks. We hypothesized that an AI algorithm would cluster preoperative lateral radiographs into groups with distinct morphology.Methods
This was a retrospective review of a multicenter, prospectively collected database of adult spinal deformity. A total of 915 patients with adult spinal deformity and preoperative lateral radiographs were included. A 2 × 3, self-organizing map-a form of artificial neural network frequently employed in unsupervised classification tasks-was developed. The mean spine shape was plotted for each of the six clusters. Alignment, surgical characteristics, and outcomes were compared.Results
Qualitatively, clusters C and D exhibited only mild sagittal plane deformity. Clusters B, E, and F, however, exhibited marked positive sagittal balance and loss of lumbar lordosis. Cluster A had mixed characteristics, likely representing compensated deformity. Patients in clusters B, E, and F disproportionately underwent 3-CO. PJK and PJF were particularly prevalent among clusters A and E. Among clusters B and F, patients who experienced PJK had significantly greater positive sagittal balance than those who did not.Conclusions
This study clustered preoperative lateral radiographs of ASD patients into groups with highly distinct overall spinal morphology and association with sagittal alignment parameters, baseline HRQOL, and surgical characteristics. The relationship between SVA and PJK differed by cluster. This study represents significant progress toward incorporation of computer vision into clinically relevant classification systems in adult spinal deformity.Level of evidence iv
Diagnostic: individual cross-sectional studies with the consistently applied reference standard and blinding.Item Open Access Artificial Intelligence Models Predict Operative Versus Nonoperative Management of Patients with Adult Spinal Deformity with 86% Accuracy.(World neurosurgery, 2020-09) Durand, Wesley M; Daniels, Alan H; Hamilton, David K; Passias, Peter; Kim, Han Jo; Protopsaltis, Themistocles; LaFage, Virginie; Smith, Justin S; Shaffrey, Christopher; Gupta, Munish; Klineberg, Eric; Schwab, Frank; Burton, Doug; Bess, Shay; Ames, Christopher; Hart, Robert; International Spine Study GroupObjective
Patients with ASD show complex and highly variable disease. The decision to manage patients operatively is largely subjective and varies based on surgeon training and experience. We sought to develop models capable of accurately discriminating between patients receiving operative versus nonoperative treatment based only on baseline radiographic and clinical data at enrollment.Methods
This study was a retrospective analysis of a multicenter consecutive cohort of patients with ASD. A total of 1503 patients were included, divided in a 70:30 split for training and testing. Patients receiving operative treatment were defined as those undergoing surgery up to 1 year after their baseline visit. Potential predictors included available demographics, past medical history, patient-reported outcome measures, and premeasured radiographic parameters from anteroposterior and lateral films. In total, 321 potential predictors were included. Random forest, elastic net regression, logistic regression, and support vector machines (SVMs) with radial and linear kernels were trained.Results
Of patients in the training and testing sets, 69.0% (n = 727) and 69.1% (n = 311), respectively, received operative management. On evaluation with the testing dataset, performance for SVM linear (area under the curve =0.910), elastic net (0.913), and SVM radial (0.914) models was excellent, and the logistic regression (0.896) and random forest (0.830) models performed very well for predicting operative management of patients with ASD. The SVM linear model showed 86% accuracy.Conclusions
This study developed models showing excellent discrimination (area under the curve >0.9) between patients receiving operative versus nonoperative management, based solely on baseline study enrollment values. Future investigations may evaluate the implementation of such models for decision support in the clinical setting.Item Open Access Automatic annotation of spatial expression patterns via sparse Bayesian factor models.(PLoS Comput Biol, 2011-07) Pruteanu-Malinici, Iulian; Mace, Daniel L; Ohler, UweAdvances in reporters for gene expression have made it possible to document and quantify expression patterns in 2D-4D. In contrast to microarrays, which provide data for many genes but averaged and/or at low resolution, images reveal the high spatial dynamics of gene expression. Developing computational methods to compare, annotate, and model gene expression based on images is imperative, considering that available data are rapidly increasing. We have developed a sparse Bayesian factor analysis model in which the observed expression diversity of among a large set of high-dimensional images is modeled by a small number of hidden common factors. We apply this approach on embryonic expression patterns from a Drosophila RNA in situ image database, and show that the automatically inferred factors provide for a meaningful decomposition and represent common co-regulation or biological functions. The low-dimensional set of factor mixing weights is further used as features by a classifier to annotate expression patterns with functional categories. On human-curated annotations, our sparse approach reaches similar or better classification of expression patterns at different developmental stages, when compared to other automatic image annotation methods using thousands of hard-to-interpret features. Our study therefore outlines a general framework for large microscopy data sets, in which both the generative model itself, as well as its application for analysis tasks such as automated annotation, can provide insight into biological questions.Item Open Access Development of a neuro-fuzzy technique for automated parameter optimization of inverse treatment planning.(Radiation oncology (London, England), 2009-01) Stieler, Florian; Yan, Hui; Lohr, Frank; Wenz, Frederik; Yin, Fang-FangBACKGROUND: Parameter optimization in the process of inverse treatment planning for intensity modulated radiation therapy (IMRT) is mainly conducted by human planners in order to create a plan with the desired dose distribution. To automate this tedious process, an artificial intelligence (AI) guided system was developed and examined. METHODS: The AI system can automatically accomplish the optimization process based on prior knowledge operated by several fuzzy inference systems (FIS). Prior knowledge, which was collected from human planners during their routine trial-and-error process of inverse planning, has first to be "translated" to a set of "if-then rules" for driving the FISs. To minimize subjective error which could be costly during this knowledge acquisition process, it is necessary to find a quantitative method to automatically accomplish this task. A well-developed machine learning technique, based on an adaptive neuro fuzzy inference system (ANFIS), was introduced in this study. Based on this approach, prior knowledge of a fuzzy inference system can be quickly collected from observation data (clinically used constraints). The learning capability and the accuracy of such a system were analyzed by generating multiple FIS from data collected from an AI system with known settings and rules. RESULTS: Multiple analyses showed good agreements of FIS and ANFIS according to rules (error of the output values of ANFIS based on the training data from FIS of 7.77 +/- 0.02%) and membership functions (3.9%), thus suggesting that the "behavior" of an FIS can be propagated to another, based on this process. The initial experimental results on a clinical case showed that ANFIS is an effective way to build FIS from practical data, and analysis of ANFIS and FIS with clinical cases showed good planning results provided by ANFIS. OAR volumes encompassed by characteristic percentages of isodoses were reduced by a mean of between 0 and 28%. CONCLUSION: The study demonstrated a feasible way to automatically perform parameter optimization of inverse treatment planning under guidance of prior knowledge without human intervention other than providing a set of constraints that have proven clinically useful in a given setting.Item Open Access Evaluation High-Quality of Information from ChatGPT (Artificial Intelligence-Large Language Model) Artificial Intelligence on Shoulder Stabilization Surgery.(Arthroscopy : the journal of arthroscopic & related surgery : official publication of the Arthroscopy Association of North America and the International Arthroscopy Association, 2024-03) Hurley, Eoghan T; Crook, Bryan S; Lorentz, Samuel G; Danilkowicz, Richard M; Lau, Brian C; Taylor, Dean C; Dickens, Jonathan F; Anakwenze, Oke; Klifto, Christopher SPurpose
To analyze the quality and readability of information regarding shoulder stabilization surgery available using an online AI software (ChatGPT), using standardized scoring systems, as well as to report on the given answers by the AI.Methods
An open AI model (ChatGPT) was used to answer 23 commonly asked questions from patients on shoulder stabilization surgery. These answers were evaluated for medical accuracy, quality, and readability using The JAMA Benchmark criteria, DISCERN score, Flesch-Kincaid Reading Ease Score (FRES) & Grade Level (FKGL).Results
The JAMA Benchmark criteria score was 0, which is the lowest score, indicating no reliable resources cited. The DISCERN score was 60, which is considered a good score. The areas that open AI model did not achieve full marks were also related to the lack of available source material used to compile the answers, and finally some shortcomings with information not fully supported by the literature. The FRES was 26.2, and the FKGL was considered to be that of a college graduate.Conclusions
There was generally high quality in the answers given on questions relating to shoulder stabilization surgery, but there was a high reading level required to comprehend the information presented. However, it is unclear where the answers came from with no source material cited. It is important to note that the ChatGPT software repeatedly references the need to discuss these questions with an orthopaedic surgeon and the importance of shared discussion making, as well as compliance with surgeon treatment recommendations.Clinical relevance
As shoulder instability is an injury that predominantly affects younger individuals who may use the Internet for information, this study shows what information patients may be getting online.Item Open Access Gene selection using iterative feature elimination random forests for survival outcomes.(IEEE/ACM Trans Comput Biol Bioinform, 2012-09) Pang, Herbert; George, Stephen L; Hui, Ken; Tong, TiejunAlthough many feature selection methods for classification have been developed, there is a need to identify genes in high-dimensional data with censored survival outcomes. Traditional methods for gene selection in classification problems have several drawbacks. First, the majority of the gene selection approaches for classification are single-gene based. Second, many of the gene selection procedures are not embedded within the algorithm itself. The technique of random forests has been found to perform well in high-dimensional data settings with survival outcomes. It also has an embedded feature to identify variables of importance. Therefore, it is an ideal candidate for gene selection in high-dimensional data with survival outcomes. In this paper, we develop a novel method based on the random forests to identify a set of prognostic genes. We compare our method with several machine learning methods and various node split criteria using several real data sets. Our method performed well in both simulations and real data analysis.Additionally, we have shown the advantages of our approach over single-gene-based approaches. Our method incorporates multivariate correlations in microarray data for survival outcomes. The described method allows us to better utilize the information available from microarray data with survival outcomes.Item Open Access Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.(PLoS Comput Biol, 2010-10-07) Gnanakaran, S; Daniels, MG; Bhattacharya, T; Lapedes, AS; Sethi, A; Li, M; Tang, H; Greene, K; Gao, H; Haynes, BF; Cohen, MS; Shaw, GM; Seaman, MS; Kumar, A; Gao, F; Montefiori, DC; Korber, BA steady increase in knowledge of the molecular and antigenic structure of the gp120 and gp41 HIV-1 envelope glycoproteins (Env) is yielding important new insights for vaccine design, but it has been difficult to translate this information to an immunogen that elicits broadly neutralizing antibodies. To help bridge this gap, we used phylogenetically corrected statistical methods to identify amino acid signature patterns in Envs derived from people who have made potently neutralizing antibodies, with the hypothesis that these Envs may share common features that would be useful for incorporation in a vaccine immunogen. Before attempting this, essentially as a control, we explored the utility of our computational methods for defining signatures of complex neutralization phenotypes by analyzing Env sequences from 251 clonal viruses that were differentially sensitive to neutralization by the well-characterized gp120-specific monoclonal antibody, b12. We identified ten b12-neutralization signatures, including seven either in the b12-binding surface of gp120 or in the V2 region of gp120 that have been previously shown to impact b12 sensitivity. A simple algorithm based on the b12 signature pattern was predictive of b12 sensitivity/resistance in an additional blinded panel of 57 viruses. Upon obtaining these reassuring outcomes, we went on to apply these same computational methods to define signature patterns in Env from HIV-1 infected individuals who had potent, broadly neutralizing responses. We analyzed a checkerboard-style neutralization dataset with sera from 69 HIV-1-infected individuals tested against a panel of 25 different Envs. Distinct clusters of sera with high and low neutralization potencies were identified. Six signature positions in Env sequences obtained from the 69 samples were found to be strongly associated with either the high or low potency responses. Five sites were in the CD4-induced coreceptor binding site of gp120, suggesting an important role for this region in the elicitation of broadly neutralizing antibody responses against HIV-1.Item Open Access Intelligent career planning via stochastic subsampling reinforcement learning.(Scientific reports, 2022-05) Guo, Pengzhan; Xiao, Keli; Ye, Zeyang; Zhu, Hengshu; Zhu, WeiCareer planning consists of a series of decisions that will significantly impact one's life. However, current recommendation systems have serious limitations, including the lack of effective artificial intelligence algorithms for long-term career planning, and the lack of efficient reinforcement learning (RL) methods for dynamic systems. To improve the long-term recommendation, this work proposes an intelligent sequential career planning system featuring a career path rating mechanism and a new RL method coined as the stochastic subsampling reinforcement learning (SSRL) framework. After proving the effectiveness of this new recommendation system theoretically, we evaluate it computationally by gauging it against several benchmarks under different scenarios representing different user preferences in career planning. Numerical results have demonstrated that our system is superior to other benchmarks in locating promising optimal career paths for users in long-term planning. Case studies have further revealed that our SSRL career path recommendation system would encourage people to gradually improve their career paths to maximize long-term benefits. Moreover, we have shown that the initial state (i.e., the first job) can have a significant impact, positively or negatively, on one's career, while in the long-term view, a carefully planned career path following our recommendation system may mitigate the negative impact of a lackluster beginning in one's career life.Item Open Access Machine wanting.(Studies in history and philosophy of biological and biomedical sciences, 2013-12) McShea, Daniel WWants, preferences, and cares are physical things or events, not ideas or propositions, and therefore no chain of pure logic can conclude with a want, preference, or care. It follows that no pure-logic machine will ever want, prefer, or care. And its behavior will never be driven in the way that deliberate human behavior is driven, in other words, it will not be motivated or goal directed. Therefore, if we want to simulate human-style interactions with the world, we will need to first understand the physical structure of goal-directed systems. I argue that all such systems share a common nested structure, consisting of a smaller entity that moves within and is driven by a larger field that contains it. In such systems, the smaller contained entity is directed by the field, but also moves to some degree independently of it, allowing the entity to deviate and return, to show the plasticity and persistence that is characteristic of goal direction. If all this is right, then human want-driven behavior probably involves a behavior-generating mechanism that is contained within a neural field of some kind. In principle, for goal directedness generally, the containment can be virtual, raising the possibility that want-driven behavior could be simulated in standard computational systems. But there are also reasons to believe that goal-direction works better when containment is also physical, suggesting that a new kind of hardware may be necessary.Item Open Access The role of machine learning in clinical research: transforming the future of evidence generation.(Trials, 2021-08) Weissler, E Hope; Naumann, Tristan; Andersson, Tomas; Ranganath, Rajesh; Elemento, Olivier; Luo, Yuan; Freitag, Daniel F; Benoit, James; Hughes, Michael C; Khan, Faisal; Slater, Paul; Shameer, Khader; Roe, Matthew; Hutchison, Emmette; Kollins, Scott H; Broedl, Uli; Meng, Zhaoling; Wong, Jennifer L; Curtis, Lesley; Huang, Erich; Ghassemi, MarzyehBackground
Interest in the application of machine learning (ML) to the design, conduct, and analysis of clinical trials has grown, but the evidence base for such applications has not been surveyed. This manuscript reviews the proceedings of a multi-stakeholder conference to discuss the current and future state of ML for clinical research. Key areas of clinical trial methodology in which ML holds particular promise and priority areas for further investigation are presented alongside a narrative review of evidence supporting the use of ML across the clinical trial spectrum.Results
Conference attendees included stakeholders, such as biomedical and ML researchers, representatives from the US Food and Drug Administration (FDA), artificial intelligence technology and data analytics companies, non-profit organizations, patient advocacy groups, and pharmaceutical companies. ML contributions to clinical research were highlighted in the pre-trial phase, cohort selection and participant management, and data collection and analysis. A particular focus was paid to the operational and philosophical barriers to ML in clinical research. Peer-reviewed evidence was noted to be lacking in several areas.Conclusions
ML holds great promise for improving the efficiency and quality of clinical research, but substantial barriers remain, the surmounting of which will require addressing significant gaps in evidence.Item Open Access Theological Librarian vs. Machine: Taking on the Amazon Alexa Show (with Some Reflections on the Future of the Profession)(Theological Librarianship, 2017-10) Sheppard, BMItem Open Access Training a Diffusion-GAN With Modified Loss Functions to Improve the Head-and-Neck Intensity Modulated Radiation Therapy Fluence Generator(2024) Reid, Scott WilliamIntroduction: The current head-and-neck (HN) fluence map generator tends to producehighly modulated fluence maps and therefore high monitor units (MUs) for each beam, which leads to more delivery uncertainty and leakage dose. This project implements diffu- sion into the training process and modifies the loss functions to mitigate this effect.
Methods: The dataset consists of 200 head-and-neck (HN) patients receiving intensity mod-ulated radiation therapy (IMRT) for training, 16 for validation, and 15 for testing. Two models were trained, one with-diffusion and one without. The original model was a con- ditional generative adversarial network (GAN) written in TensorFlow, the model without diffusion was written to be the PyTorch equivalent of the original model. After confirming the model was properly converted to PyTorch by comparing outputs, both new models were modified to use binary cross entropy for the GAN loss and mean absolute error as a third loss function for the generator. Hyperparameters were carefully selected based on the training script for the original model, and further tuned with trial and error. The diffusion was implemented based on Diffusion-GAN and the associated GitHub repository. The two new models were compared by plotting training loss vs epoch over 500 epochs. The two models were compared to the original model by comparing the output fluence maps to the ground truth using similarity index and comparing DVH statistics among the three models.
Results: The with-diffusion model and no-diffusion model achieved similar training loss.The diffusion model and no-diffusion model consistently delivered better parotid sparing than the original model and delivered less dose to four of the six tested OAR. The with- diffusion model delivered less dose to five of the six tested OAR. The diffusion model had the least MUs: 23% less than the original model and 3% less than the no-diffusion model. The diffusion model had lower D2cc: 4% less than the original model and 1% less than the no-diffusion model on average. All three plans deliver 95% of the prescription dose to nearly the same percentage of PTV volume.
Conclusion: Implementing diffusion does not provide a significant impact on training timeand training loss. However, it does enable comparable dose performance to both the no- diffusion and original models, while significantly reducing the total MU’s and 3D max 2cc relative to the original model and slightly reducing these metrics relative to the no-diffusion model, indicating smoother fluence modulation. In addition, both new models reduced dose to the right and left parotids relative to the original model, and to four of six tested OAR total, while the with-diffusion model consistently delivers less dose to OAR than the no- diffusion model. This indicates that both the new loss functions and diffusion reduce the overall dose to the OARs while preserving dose conformity around the target.