TrimLLaMA: Progressive Layer Dropping for Domain-SpecificLLMs
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Engineering topics
Publications and source records attributed to Zhang, H.
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Explore the source record for details and available documents.
Explore the source record for details and available documents.
Explore the source record for details and available documents.
Explore the source record for details and available documents.
Purpose: To compare linear and deformable registration methods for evaluation of tumor response to Chemoradiation therapy (CRT) in patients with esophageal cancer. Methods: Linear and multi-resolution BSpline deformable registration were performed on Pre-Post-CRT CT/PET images of 20 patients with esophageal cancer. For both registration methods, we registered CT using Mean Square Error (MSE) metric, however to register PET we used transformation obtained using Mutual Information (MI) from the same CT due to being multi-modality. Similarity of Warped-CT/PET was quantitatively evaluated using Normalized Mutual Information and plausibility of DF was assessed using inverse consistency Error. To evaluate tumor response four groups of tumor features were examined: (1) Conventional PET/CT e.g. SUV, diameter (2) Clinical parameters e.g. TNM stage, histology (3)spatial-temporal PET features that describe intensity, texture and geometry of tumor (4)all features combined. Dominant features were identified using 10-fold cross-validation and Support Vector Machine (SVM) was deployed for tumor response prediction while the accuracy was evaluated by ROC Area Under Curve (AUC). Results: Average and standard deviation of Normalized mutual information for deformable registration using MSE was 0.2±0.054 and for linear registration was 0.1±0.026, showing higher NMI for deformable registration. Likewise for MI metric, deformable registration had 0.13±0.035 comparing to linear counterpart with 0.12±0.037. Inverse consistency error for deformable registration for MSE metric was 4.65±2.49 and for linear was 1.32±2.3 showing smaller value for linear registration. The same conclusion was obtained for MI in terms of inverse consistency error. AUC for both linear and deformable registration was 1 showing no absolute difference in terms of response evaluation. Conclusion: Deformable registration showed better NMI comparing to linear registration, however inverse consistency of transformation was lower in linear registration. We do not expect to see significant difference when warping PET images using deformable or linear registration. This work was supported in part by the National Cancer Institute Grants R01CA172638.
Purpose: To develop a quantitative radiomics approach for survival prediction of glioblastoma (GBM) patients treated with chemoradiotherapy (CRT). Methods: 28 GBM patients who received CRT at our institution were retrospectively studied. 255 radiomic features were extracted from 3 gadolinium-enhanced T1 weighted MRIs for 2 regions of interest (ROIs) (the surgical cavity and its surrounding enhancement rim). The 3 MRIs were at pre-treatment, 1-month and 3-month post-CRT. The imaging features comprehensively quantified the intensity, spatial variation (texture), geometric property and their spatial-temporal changes for the 2 ROIs. 3 demographics features (age, race, gender) and 12 clinical parameters (KPS, extent of resection, whether concurrent temozolomide was adjusted/stopped and radiotherapy related information) were also included. 4 Machine learning models (logistic regression (LR), support vector machine (SVM), decision tree (DT), neural network (NN)) were applied to predict overall survival (OS) and progression-free survival (PFS). The number of cases and percentage of cases predicted correctly were collected and AUC (area under the receiver operating characteristic (ROC) curve) were determined after leave-one-out cross-validation. Results: From univariate analysis, 27 features (1 demographic, 1 clinical and 25 imaging) were statistically significant (p<0.05) for both OS and PFS. Two sets of features (each contained 24 features) were algorithmically selected from all features to predict OS and PFS. High prediction accuracy of OS was achieved by using NN (96%, 27 of 28 cases were correctly predicted, AUC = 0.99), LR (93%, 26 of 28 cases were correctly predicted, AUC = 0.95) and SVM (93%, 26 of 28 cases were correctly predicted, AUC = 0.90). When predicting PFS, NN obtained the highest prediction accuracy (89%, 25 of 28 cases were correctly predicted, AUC = 0.92). Conclusion: Radiomics approach combined with patients’ demographics and clinical parameters can accurately predict survival in GBM patients treated with CRT.
Purpose: The shape of the Positron Emission Tomography (PET) image represents the heterogeneity of tumor growth in various directions, and thus could be associated with tumor malignancy. We have proposed a median geodesic distance (MGD) to represent the local complexity of the shape and use a normalized MGD (NMGD) to quantify the shape, and found a potential correlation of NMGD to survival in a 20-patient pilot study. This study was to verify the finding in a larger patient cohort. Methods: Geodesic distance of two vertices on a surface is defined as the shortest path on the surface connecting the two vertices. The MGD was calculated for each vertex on the surface to display the local complexity of the shape. The NMGD was determined as: NMGD = 100*standard deviation(MGDs)/mean(MGDs). We applied the NMGD to 40 NSCLC patients who were enrolled in prospective PET image protocols and received radiotherapy. Each patient had a pre-treatment PET scan with the resolution of 4mm*4mm*5mm. Tumors were contoured by a professional radiation oncologist and triangulation meshes were built up based on the contours. Results: The mean and standard deviation of NMGD was 6.4±3.0. The OS was 33.1±16.9 months for low NMGD group, and 15.4±15.6 months for the high NMGD group. The low NMGD group had significant better OS than the high NMGD group (p=0.0013). Conclusion: NMGD could be used as a shape biomarker to predict survival and the MGD could be combined with image texture in future to increase prediction accuracy. This study was supported by Award Number 1R01CA166948 from the NIH and National Cancer Institute.
Purpose: The feasibility of dose measurement using new generation EBT3 film was explored in a water phantom for a ring and tandem HDR applicator for measurements tracking mucosal dose during cervical brachytherapy. Methods: An experimental fixture was assembled to position the applicator in a water phantom. Prior to measurement, calibration curves for EBT3 film in water and in solidwater were verified. EBT3 film was placed at different known locations around the applicator in the water tank. A CT scan of the phantom with applicator was performed using clinical protocol. A typical cervical cancer treatment plan was then generated by Oncentra brachytherapy planning system. A dose of 500 cGy was prescribed to point A (2 cm, 2 cm). Locations measured by film included the outer surface of the ring, measurement point A-m (2.2 cm, 2.2 cm), and profiles extending from point A-m parallel to the tandem. Three independent measurements were conducted. The doses recorded by film were carefully analyzed and compared with values calculated by the treatment planning system. Results: Assessment of the EBT3 films indicate that the dose at point A matches the values predicted by the planning system. Dose to the point A-m was 411.5 cGy, and the outer circumferential surface dose of the ring was between 500 and 1150 cGy. It was found that from the point A-m, the dose drops 60% within 4.5 cm on the line parallel to the tandem. The measurement doses agree with the treatment planning system. Conclusion: Use of EBT3 film is feasible for in-water measurements for brachytherapy. A carefully machined apparatus will likely improve measurement accuracy. In a typical plan, our study found that the ring surface dose can be 2.5 times larger than the point A prescription dose. EBT3 film can be used to monitor mucosal dose in brachytherapy treatments.
Purpose: To evaluate the dosimetric metrics of HDR Ring and Tandem applicator Brachytherapy for primary cervical cancers. Methods: The dosimetric metrics of high-risk clinical target volumes (HDR-CTV) of 12 patients (in total 60 fractions/plans) treated with the HDR ring and tandem applicators were retrospectively analyzed. Ring diameter is from 2.6 to 3.4 cm, tandem length is from 4 to 6 cm, and the angle is either 45 or 60 degrees. The first fraction plan was MR guided, the MR images were then used as a reference for contouring the HR-CTV in CT images of following 4 fractions. The nominal prescription dose was between 5.2 and 5.8 Gy at the point A. The plans were adjusted to cover at least 90% of the HR-CTV by 90% of the prescription dose and to reduce the doses to the bladder, rectum and bowel-bag. Minimum target dose of D100 and D90 were converted into the biologically equivalent EBRT dose D90-iso and D100-iso (using α/β=10 Gy, 2 Gy/fx). Equivalent uniform doses (EUD) based on the average cancer killing across the target volume were calculated by the modified linear quadratic model (MLQ) from the differential dose volume histogram (DVH) tables. Results: The average D90iso of all plans is 8.1 Gy (ranging from 6.2 to 15 Gy, median 7.8 Gy); the average D100iso is just 4.1 Gy (ranging from 1.8 to 7.8 Gy; median 3.9 Gy). The average EUD is 7.0 Gy (ranging from 6.1 to 9.6 Gy, median 6.9 Gy), which is 87% of the D90iso, and 170% of the D100iso. Conclusion: The EUDs is smaller than D90iso but greater than D100iso. Because the EUD takes into account the intensive cancer cell killing in the high dose zone of HR-CTV, MLQ calculated EUD apparently is more relevant than D90 and D100 to describe the HDR brachytherapy treatment quality.
Purpose: Superficial lesions in the conjunctiva are frequently treated with en face electrons, using a hanging block to spare dose to the lens of the eye. Dose to the tumor and lens depend on the design and setup of the block and supporting apparatus. We performed in phantom measurements in order to characterize the dose sparing effects of the block as well as the under-dosing effect under the supporting apparatus for 6 MeV treatment. Methods: The commercial hanging block studied uses a 1.2 cm diameter tungsten cylinder supported by a 3 mm diameter acrylic rod. Point dose measurements under the hanging block, under an unblocked part of the field, and under the acrylic rod were performed using MOSFET detectors. In addition, EBT3 film was used for both PDD and profile measurements at a depth in phantom of 3 mm for both 105 and 103 cm SSD. Results: MOSFET measurements reported a dose reduction of 95% under the tungsten block when using an SSD of 103 cm, and 86% when using an SSD of 105 cm at a depth in phantom of 3 mm. Film measurements showed that the area under the acrylic rod may be under-dosed by as much as 30% when using 103 SSD. MOSFET measurements confirmed that when using an SSD of 103 cm, the area under the acrylic rod is under-dosed by up to 30% at 3mm depth, compared to the unblocked part of the field. Conclusion: The effectiveness of the commercial hanging block apparatus depends on setup, with 95% lens sparing possible with an SSD of 103 cm. This short SSD is necessary for sharp penumbra. At this SSD, substantial under-dosing under the acrylic support rod is possible. This must be mitigated with either feathering, or using an alternative method of support for the tungsten block.
Purpose: Three dimensional (3D) Grid Therapy using MLC-based inverse-planning has been proposed to achieve the features of both conformal radiotherapy and spatially fractionated radiotherapy, which may deliver very high dose in a single fraction to portions of a large tumor with relatively low normal tissue dose. However, the technique requires relatively long delivery time. This study aims to develop a collimator-based 3D grid therapy technique. Here we report the development of the technique in a small animal radiation research platform. Methods: Similar as in the MLC-based technique, 9 non-coplanar beams in special channeling directions were used for the 3D grid therapy technique. Two specially designed grid collimators were fabricated, and one of them was selectively used to match the corresponding gantry/couch angles so that the grid opening of all 9 beams are met in the 3D space in the target. A stack of EBT3 films were used as 3D dosimetry to demonstrate the 3D grid-like dose distribution in the target. Three 1-mm beams were delivered to the stack of films in the area outside the target for alignment when all the films were scanned to reconstruct the 3D dosimtric image. Results: 3D film dosimetry showed a lattice-like dose distribution in the 3D target as well as in the axial, sagittal and coronal planes. The dose outside the target also showed a grid like dose distribution, and the average dose gradually decreased with the distance to the target. The peak to valley ratio was approximately 5:1. The delivery time was 7 minutes for 18 Gy peak dose, comparing to 6 minutes to deliver a 18-Gy 3D conformal plan. Conclusion: We have demonstrated the feasibility of the collimator-based 3D grid therapy technique which can significantly reduce delivery time comparing to MLC-based inverse planning technique.
Purpose: To present a novel multi-criteria optimization (MCO) solution approach that generates treatment plans with deliverable apertures using column generation. Methods: We demonstrate our method with 10 locally advanced head-and-neck cancer cases retrospectively. In our MCO formulation, we defined an objective function for each structure in the treatment volume. This resulted in 9 objective functions, including 3 distinct objectives for primary target volume, high-risk and low-risk target volumes, 5 objectives for each of the organs-at-risk (OARs) (two parotid glands, spinal cord, brain stem and oral cavity), and one for the non-target non-OAR normal tissue. Conditional value-at-risk (CVaR) constraints were utilized to ensure at least certain fraction of the target volumes receiving the prescription doses. To directly generate deliverable plans, column generation algorithm was embedded within our MCO approach for aperture shape generation. Final dose distributions for all plans were generated using a Monte Carlo kernel-superposition dose calculation. We compared the MCO plans with the clinical plans, which were created by clinicians. Results: At least 95% target coverage was achieved by both MCO plans and clinical plans. However, the average conformity indices of clinical plans and the MCO plans were 1.95 and 1.35, respectively (31% reduction, p<0.01). Compared to the conventional clinical plan, the proposed MCO method achieved average reductions in left parotid mean dose of 5% (p=0.06), right parotid mean dose of 18% (p<0.01), oral cavity mean dose of 21% (p=0.03), spinal cord maximum dose of 20% (p<0.01), brain stem maximum dose of 61% (p<0.01), and normal tissue maximum dose of 5% (p<0.01), respectively. Conclusion: We demonstrated that the proposed MCO method was able to obtain deliverable IMRT treatment plans while achieving significant improvements in dosimetric plan quality.
Purpose: Cone-beam (CB) computed tomography (CT) is used for image guidance during radiotherapy treatment delivery. Conventional Feldkamp and compressed sensing (CS) based CBCT recon-struction techniques are compared for image registration. This study is to evaluate the image registration accuracy of conventional and CS CBCT for head-and-neck (HN) patients. Methods: Ten HN patients with oropharyngeal tumors were retrospectively selected. Each HN patient had one planning CT (CTP) and three CBCTs were acquired during an adaptive radiotherapy proto-col. Each CBCT was reconstructed by both the conventional (CBCTCON) and compressed sens-ing (CBCTCS) methods. Two oncologists manually labeled 23 landmarks of normal tissue and implanted gold markers on both the CTP and CBCTCON. Subsequently, landmarks on CTp were propagated to CBCTs, using a b-spline-based deformable image registration (DIR) and rigid registration (RR). The errors of these registration methods between two CBCT methods were calcu-lated. Results: For DIR, the mean distance between the propagated and the labeled landmarks was 2.8 mm ± 0.52 for CBCTCS, and 3.5 mm ± 0.75 for CBCTCON. For RR, the mean distance between the propagated and the labeled landmarks was 6.8 mm ± 0.92 for CBCTCS, and 8.7 mm ± 0.95 CBCTCON. Conclusion: This study has demonstrated that CS CBCT is more accurate than conventional CBCT in image registration by both rigid and non-rigid methods. It is potentially suggested that CS CBCT is an improved image modality for image guided adaptive applications.
Purpose: To investigate the incorporation of pre-therapy regional ventilation function in predicting radiation fibrosis (RF) in stage III non-small-cell lung cancer (NSCLC) patients treated with concurrent thoracic chemoradiotherapy. Methods: 37 stage III NSCLC patients were retrospectively studied. Patients received one cycle of cisplatin-gemcitabine, followed by two to three cycles of cisplatin-etoposide concurrently with involved-field thoracic radiotherapy between 46 and 66 Gy (2 Gy per fraction). Pre-therapy regional ventilation images of the lung were derived from 4DCT via a density-change-based image registration algorithm with mass correction. RF was evaluated at 6-months post-treatment using radiographic scoring based on airway dilation and volume loss. Three types of ipsilateral lung metrics were studied: (1) conventional dose-volume metrics (V20, V30, V40, and mean-lung-dose (MLD)), (2) dose-function metrics (fV20, fV30, fV40, and functional mean-lung-dose (fMLD) generated by combining regional ventilation and dose), and (3) dose-subvolume metrics (sV20, sV30, sV40, and subvolume mean-lung-dose (sMLD) defined as the dose-volume metrics computed on the sub-volume of the lung with at least 60% of the quantified maximum ventilation status). Receiver operating characteristic (ROC) curve analysis and logistic regression analysis were used to evaluate the predictability of these metrics for RF. Results: In predicting airway dilation, the area under the ROC curve (AUC) values for (V20, MLD), (fV20, fMLD), and (sV20, and sMLD) were (0.76, 0.70), (0.80, 0.74) and (0.82, 0.80), respectively. The logistic regression p-values were (0.09, 0.18), (0.02, 0.05) and (0.004, 0.006), respectively. With regard to volume loss, the corresponding AUC values for these metrics were (0.66, 0.57), (0.67, 0.61) and (0.71, 0.69), and p-values were (0.95, 0.90), (0.43, 0.64) and (0.08, 0.12), respectively. Conclusion: The inclusion of regional ventilation function improved predictability of radiation fibrosis. Dose-subvolume metrics provided a promising method for incorporating functional information into the conventional dose-volume parameters for outcome assessment.
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