Vidya Sankar Viswanathan’s research while affiliated with Emory University and other places

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Publications (57)


Fig. 1 | UMAP visualizations of feature separation in pneumonitis and subtypes. a UMAP visualizations for illustrating the separation of features between pneumonitis occurrence and non-occurrence, and b RTP and IIP. The UMAP plots reveal relatively distinct clusters for differentiating pneumonitis occurrence from nonoccurrence and RTP from IIP.
Fig. 2 | AUROC curves and nomogram for predicting pneumonitis in stage III NSCLC. a AUCROC curve for predicting the development of pneumonitis in the internal training set (D 1 ), b the internal validation set (D 2 ), and c the external validation set (D 3 ). d A nomogram that quantifies the probability of developing pneumonitis in unresectable stage III NSCLC patients treated with chemoradiation followed by consolidative durvalumab. e Calibration curve for predictive model. The
Fig. 3 | AUROC Curves, radiomic heatmaps, and spiderweb plots for analyzing pneumonitis risk and subtypes. a AUROC curves for distinguishing between RTP and IIP in the training set (D 4 ), and b the validation set (D 5 ). c Radiomic heatmap of Law L*E feature shows differences between tumor regions for patients with high risk of developing pneumonitis as compared to patients who will not develop pneumonitis. d Radiomic heatmap of Law L*E feature from multiple inflammatory lesions of patients who have experienced IIP as compared to patients who have experienced RTP. c Spiderweb plot for the specific image phenotypes associated with IIP or RTP and d the same concept in those who do and do not develop pneumonitis. e spiderweb plot of specific radiomic feature phenotypes linked to IIP or RTP, and f spiderweb plot of specific radiomic feature phenotypes linked to the presence or absence of pneumonitis. Each spoke on the spider webplot (labeled f1 through f7) corresponds to one of the seven most predictive features selected through LASSO for constructing the PRS or DRS models. The lengths of each spoke reflect the magnitude of each radiomic feature's contribution, with higher values indicating stronger expression of specific textures, such as edge detection or speckled patterns, in the CT scans.
Fig. 5 | UMAP embeddings highlighting radiomic feature separation by pneumonitis grades. a UMAP plot for distinguishing pneumonitis grades from baseline CT scans, reflecting a complex and heterogeneous imaging phenotype with overlapping clusters that do not clearly differentiate pneumonitis risk. b UMAP plot for distinguishing pneumonitis grades from post-treatment CT scans, where pneumonitis has developed, showing distinct separation among clusters that capture the severity and texture changes associated with different pneumonitis grades. This indicates that post-treatment scans are more effective in identifying pneumonitisrelated alterations based on radiomic signatures.
Fig. 6 | Molecular characteristics associated with PRS and DRS. Gene set enrichment analysis identified a PRS-positively correlated (pneumonitis induced) biological pathways, b PRS-negatively correlated (no evidence of pneumonitis) biological pathways, c Volcano plotshowing the differential expressed genes between pneumonitis induced and no pneumonitis occurrence component. The top positively correlated genes with the PRS for pneumonitis include IL6, TNF, and CCL2, which are known to play critical roles in inflammatory responses. Conversely, negatively correlated genes such as TP53 and VEGF are associated with tumor suppression and angiogenesisregulation. d DRS-positively correlated (IO induced) biological pathways, and e DRS-negatively correlated (RT induced) biological pathways from KEGG pathway database (FDR < 0.05).

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Novel radiogenomics approach to predict and characterize pneumonitis in stage III NSCLC
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December 2024

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31 Reads

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1 Citation

npj Precision Oncology

Lukas Delasos

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Vidya S. Viswanathan

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Unresectable stage III NSCLC is now treated with chemoradiation (CRT) followed by immune checkpoint inhibitors (ICI). Pneumonitis, a common CRT complication, has heightened risk with ICI, potentially causing severe outcomes. Currently, there are no biomarkers to predict pneumonitis risk or differentiate between radiation-induced pneumonitis (RTP) and ICI-induced pneumonitis (IIP). This study analyzed 293 patients from two institutions, with 140 experiencing pneumonitis (RTP: 84, IIP: 56). Two models were developed: M1 predicted pneumonitis risk using seven radiomic features, achieving high accuracy across internal and external datasets (AUCs: 0.76 and 0.85). M2 differentiated RTP from IIP, with strong performance (AUCs: 0.86 and 0.81). Gene set enrichment analysis linked high pneumonitis risk to pathways such as ECM-receptor interaction and T-cell signaling, while high IIP risk correlated with MAPK and JAK-STAT pathways. Radiomic models show promise in early pneumonitis risk stratification and distinguishing pneumonitis types, potentially guiding personalized NSCLC treatment.

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Towards equitable AI in oncology

June 2024

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65 Reads

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15 Citations

Nature Reviews Clinical Oncology

Artificial intelligence (AI) stands at the threshold of revolutionizing clinical oncology, with considerable potential to improve early cancer detection and risk assessment, and to enable more accurate personalized treatment recommendations. However, a notable imbalance exists in the distribution of the benefits of AI, which disproportionately favour those living in specific geographical locations and in specific populations. In this Perspective, we discuss the need to foster the development of equitable AI tools that are both accurate in and accessible to a diverse range of patient populations, including those in low-income to middle-income countries. We also discuss some of the challenges and potential solutions in attaining equitable AI, including addressing the historically limited representation of diverse populations in existing clinical datasets and the use of inadequate clinical validation methods. Additionally, we focus on extant sources of inequity including the type of model approach (such as deep learning, and feature engineering-based methods), the implications of dataset curation strategies, the need for rigorous validation across a variety of populations and settings, and the risk of introducing contextual bias that comes with developing tools predominantly in high-income countries.


Correlation of the combination of CT-derived tumor texture and vessel tortuosity on survival outcomes for immunotherapy but not for chemotherapy in metastatic non-small cell lung cancer (mNSCLC): Results from a CheckMate227 (CM227) subset.

June 2024

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9 Reads

Journal of Clinical Oncology

8610 Background: CM227 (NCT02477826) is a large multi-center phase 3 trial that evaluated the benefit of immunotherapy (IO) over chemotherapy (Ch) as first line therapy in stage IV NSCLC. While PD-L1 and tumor mutational burden (TMB) initially emerged as promising biomarkers, CM227 showed benefit of IO over Ch regardless of PD-L1 or TMB status. There is an unmet clinical need for predictive biomarkers to identify patients (pts) who will respond to IO. In this study, we report initial blinded validation results of a CT-derived biomarker combining change in textural radiomics (Δ-Rad) and quantitative vessel tortuosity (Δ-QVT) between baseline and 6-week post-treatment for predicting response and survival outcome of IO and Ch alone in a subset of patients enrolled in CM227. Methods: This retrospective study included baseline (B) and 6-week post-treatment (TP1) CT scans from (a) a multi-center training set (D tr , N=110) of first line IO-treated mNSCLC pts and (b) a validation set consisting of a subset of mNSCLC from CM227 (D v , N=224), of which 178 pts were treated with IO (D v IO ) and 36 pts (D v Ch ) with Ch. Intra-tumoral, peri-tumoral texture radiomic (Khorrami et al., Cancer Immunol Res 2020) and QVT (Alilou et al., Sci Adv 2022) features were extracted from up to the two largest measurable lung lesions on each CT using an in-house MATLAB pipeline. Δ-Rad and Δ-QVT features were computed as the feature difference between B and TP1. A best objective IO response classifier, M Combo was trained on D tr using a combination of Δ-Rad and Δ-QVT features. Kaplan-Meier analyses with log rank p-values, hazard ratio (HR) and its confidence interval (CI) were computed to assess the predictive benefit of M Combo with overall survival (OS) and progression free survival (PFS) in D v , D v IO and D v Ch . We also report area under the receiver operating characteristic (AUC) of IO response predictions compared against best overall response in D v , D v IO and D v Ch . Results: M Combo predicted best overall response with an AUC of 0.67, 0.68, 0.74 in D v , D v IO , and D v Ch , respectively. M Combo was statistically significantly associated with OS and PFS in D v and D v IO but not in D v Ch (Table). Conclusions: Our preliminary findings reveal that combination of CT-based textural and vessel tortuosity features are predictive of IO response over chemotherapy in a subset of CM227 pts. Validation on the entire CM277 cohort is warranted. [Table: see text]


Association of combination tumor texture and vessel tortuosity with progression free survival across PD-L1 subgroups in durvalumab treated non-small cell lung cancer (NSCLC): Blinded validation results from CP1108.

June 2024

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15 Reads

Journal of Clinical Oncology

8600 Background: Immunotherapy (IO) has shown a durable response with minimal toxicity in the treatment of metastatic NSCLC. However, only 30-50% of these patients (pts) actually respond. Despite initial optimism surrounding PD-L1 expression as a potential biomarker, IO provides benefit across PD-L1 low (<25%) and high (≥25%) status. This highlights a critical need for more effective biomarkers to guide treatment decisions. Here, we present blinded validation results of a CT-based biomarker of change in quantitative vessel tortuosity (1) (Δ-QVT) and texture radiomics (2) (Δ-Rad) between baseline (B) and 6 weeks post-treatment (TP1) for predicting response, overall survival (OS) and progression free survival (PFS) in CP1108 (NCT01693562). Methods: CT scans at B and TP1 were retrospectively analyzed from two studies (a) a multi-center training set (S tr , N=110) of metastatic NSCLC pts treated with first line IO and (b) a blinded NSCLC cohort of N = 151 pts treated with Durvalumab in CP1108 study (S v ). In S v , N=75 pts were PD-L1 high (S v ⁺ ) whereas N=65 pts were PD-L1 low (S v ⁻ ). An in-house MATLAB based algorithm was used to extract intra-tumoral, peri-tumoral texture and QVT features from up to two largest measurable tumors in each CT. A classifier (M Combo ) was trained on S tr to predict best overall response defined as per the RECIST v1.1 criteria using combination of Δ-QVT and Δ-Rad features. Area under the receiver operating characteristic (AUC) was used to evaluate M Combo against RECIST response whereas univariable and multivariable Cox regression models with log-rank test, hazard ratio (HR) with confidence interval (CI) and concordance index (C-index) were used to study the association of M Combo with OS and PFS in S v , S v ⁺ , and S v ⁻ . Results: M Combo predicted objective response with an AUC of 0.78 in S v and was statistically significantly associated with PFS (Table) in S v , S v ⁺ , and S v ⁻ . M Combo was associated with OS in S v , S v ⁺ , but not in S v ⁻ . Multivariable analysis with PD-L1 status, histological subtype, ECOG status, liver metastasis, line of therapy and sex showed independent association of M Combo across OS and PFS. Conclusions: Our results indicate that combination of radiomics and vessel tortuosity biomarker from CT is independently prognostic of response and PFS across PD-L1 levels. Prospective validation of this biomarker is needed. 1. Alilou et al. Sci Adv 2022. 2. Khorrami et al. Cancer Immunol Res 2020. [Table: see text]





Failing to Make the Grade: Conventional Cardiac Allograft Rejection Grading Criteria Are Inadequate for Predicting Rejection Severity

February 2024

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23 Reads

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2 Citations

Circulation Heart Failure

BACKGROUND Cardiac allograft rejection is the leading cause of early graft failure and is a major focus of postheart transplant patient care. While histological grading of endomyocardial biopsy samples remains the diagnostic standard for acute rejection, this standard has limited diagnostic accuracy. Discordance between biopsy rejection grade and patient clinical trajectory frequently leads to both overtreatment of indolent processes and delayed treatment of aggressive ones, spurring the need to investigate the adequacy of the current histological criteria for assessing clinically important rejection outcomes. METHODS N=2900 endomyocardial biopsy images were assigned a rejection grade label (high versus low grade) and a clinical trajectory label (evident versus silent rejection). Using an image analysis approach, n=370 quantitative morphology features describing the lymphocytes and stroma were extracted from each slide. Two models were constructed to compare the subset of features associated with rejection grades versus those associated with clinical trajectories. A proof-of-principle machine learning pipeline—the cardiac allograft rejection evaluator—was then developed to test the feasibility of identifying the clinical severity of a rejection event. RESULTS The histopathologic findings associated with conventional rejection grades differ substantially from those associated with clinically evident allograft injury. Quantitative assessment of a small set of well-defined morphological features can be leveraged to more accurately reflect the severity of rejection compared with that achieved by the International Society of Heart and Lung Transplantation grades. CONCLUSIONS Conventional endomyocardial samples contain morphological information that enables accurate identification of clinically evident rejection events, and this information is incompletely captured by the current, guideline-endorsed, rejection grading criteria.


Rank Acquisition Impact on Radiomics Estimation (AсquIRE) in Chest CT Imaging: A Retrospective Multi-Site, Multi-Use-Case Study

December 2023

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24 Reads

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3 Citations

Computer Methods and Programs in Biomedicine

Background Radiomics is a method within medical image analysis that involves the extraction of quantitative data from radiologic scans, often in conjunction with machine learning algorithms to phenotype disease appearance, prognosticate disease outcome, and predict treatment response. However, variance in CT scanner acquisition parameters, such as convolution kernels or pixel spacing, can impact radiomics texture feature values. Purpose The extent to which the parameters influence radiomics features continues to be an active area of investigation. In this study, we describe a novel approach, Acquisition Impact on Radiomics Estimation (AcquIRE), to rank the impact of CT acquisition parameters on radiomic texture features. Methods In this work, we used three chest CT imaging datasets (n = 749 patients) from nine sites comprising: i) lung granulomas and adenocarcinomas (D1) (10 and 52 patients, respectively); ii) minimal and frank invasive adenocarcinoma (D2) (74 and 145 patients); and iii) early-stage NSCLC patients (D3) (315 patients). Datasets D2 and D3 were collected from four sites each, and D1 from a single site. For each patient, 744 texture features and nine acquisition parameters were extracted and utilized to evaluate which parameters impact radiomic features the most. The AcquIRE method establishes a relative assessment between acquisition parameters and radiomic texture featuresa through the creation of a classification model, which is then utilized to assess the rank of the acquisition parameters. Results Across the use cases, CT software version and convolution kernel parameters were found to have the most variance. In D1, it was observed that the Haralick texture feature family was the least affected by variations in acquisition parameters, while the Gabor feature family was the most impacted. However, in datasets D2 and D3, the Gabor features were found to be the least affected. Our findings suggest that the impact on radiomic parameters is as much a function of the problem in question as it is acquisition parameters. Conclusions The software version and convolution kernel parameters impacted the radiomics feature the most.


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Computational Image and Molecular Analysis Reveal Unique Prognostic Features of Immune Architecture in African Versus European American Women with Endometrial Cancer

November 2023

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28 Reads

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1 Citation

Endometrial cancer (EC) disproportionately affects African American (AA) women in terms of progression and death. In our study, we sought to employ computerized image and bioinformatic analysis to tease out morphologic and molecular differences in EC between AA and European-American (EA) populations. We identified the differences in immune cell spatial patterns between AA and EA populations with markers of tumor biology, including histologic and molecular subtypes. The models performed best when they were trained and validated using data from the same population. Unsupervised clustering revealed a distinct association between immune cell features and known molecular subtypes of endometrial cancer that varied between AA and EA populations. Our genomic analysis revealed two distinct and novel gene sets with mutations associated with improved prognosis in AA and EA patients. Our study findings suggest the need for population-specific risk prediction models for women with endometrial cancer.


Citations (29)


... The scarcity of high-quality and suitable datasets is a major challenge for the application of AI algorithms to tumor drug resistance [145]. Currently, AI models based on in vitro cancer cell lines show limited translational potential in forecasting clinical drug responses in real-world scenarios [146]. ...

Reference:

Emerging artificial intelligence-driven precision therapies in tumor drug resistance: recent advances, opportunities, and challenges
Towards equitable AI in oncology
  • Citing Article
  • June 2024

Nature Reviews Clinical Oncology

... In the field of medical imaging analysis, deep learning has emerged as a powerful tool. [13][14][15] By utilizing deep learning technology, doctors can more comprehensively and accurately analyze patients' imaging data, and get assistance in disease diagnosis, disease severity assessment, prognosis prediction, and treatment decisions. 16,17 Deep learning diagnostic models based on computed tomography (CT) images have been widely applied in research on the diagnosis of various diseases. ...

Deep Learning reveals lung shape differences on baseline chest CT between mild and severe COVID-19: A multi-site retrospective study
  • Citing Article
  • May 2024

Computers in Biology and Medicine

... Additionally, Arabyarmohammadi et al. (2024) address the challenges associated with cardiac allograft rejection grading, advocating for AI-enabled digital pathology as a means to surmount the limitations inherent in conventional grading criteria [3]. This is substantiated by Alymai et al. (2024), who showcase AI's ability to match and surpass traditional diagnostic methods when detecting fibrosis in Crohn's disease through molecular imaging [4]. ...

Failing to Make the Grade: Conventional Cardiac Allograft Rejection Grading Criteria Are Inadequate for Predicting Rejection Severity
  • Citing Article
  • February 2024

Circulation Heart Failure

... The integration of bioinformatics and computational tools in EC research has significantly advanced our understanding of the disease's molecular underpinnings [84]. These tools have enabled the discovery of novel biomarkers, molecular subtypes, and therapeutic targets, paving the way for personalized medicine [85]. ...

Computational Image and Molecular Analysis Reveal Unique Prognostic Features of Immune Architecture in African Versus European American Women with Endometrial Cancer

... Novel AI applications in CMR: Magnetic Resonance Fingerprinting (MRF) is a new technique that allows the quantifica-tion of multiple tissue properties in a single scan. A recent study investigated the use of cardiac MRF (cMRF) for myocardial T1, T2 and Extracellular Volume (ECV) quantification in 9 patients with non-ischemic cardiomyopathy compared with traditional mapping methods [40]. Due to the potential of cMRF to overcome variations in heart rate s and system properties, cMRF may achieve more reproducible T1 and T2 quantification, and therefore holds promise for application in cardiomyopathy patients [41]. ...

Rank Acquisition Impact on Radiomics Estimation (AсquIRE) in Chest CT Imaging: A Retrospective Multi-Site, Multi-Use-Case Study

Computer Methods and Programs in Biomedicine

... Several studies have been published [7][8][9][10][11][12][13][14][15][16], depicted in more detail in Table 1. Moreover, commercial products are available on the market with often reported outstanding performance values [17,18], but when applied in clinical practice, the same performance values are hard to repeat [19]. The lack of a publicly accessible reference test set or a test set protected by a certification body stands in the way of an objective and comparable measurement of performance characteristics among different AI solutions [20]. ...

Assessing the Potential of a Deep Learning Tool to Improve Fracture Detection by Radiologists and Emergency Physicians on Extremity Radiographs
  • Citing Article
  • November 2023

Academic Radiology

... In addition, AI approaches are being embedded as part of prospective IO-related clinical trials. 163 The establishment of global standards for data and resource sharing will pave the way for a more cohesive and inclusive approach to IO discoveries. Ultimately, the collective endeavor in compIO seeks to break the conventional boundaries of science and technology, toward building a future where every patient can benefit from the promise of immunotherapies. ...

175P Radiomic biomarker of vessel tortuosity for monitoring treatment change: Preliminary findings in prospective evaluation of ECOG-ACRIN EA5163
  • Citing Article
  • October 2023

Annals of Oncology

... Recent works have demonstrated the value of 3D mapping of large biospecimens for understanding tissue structure, capturing the inter-and intra-sample heterogeneity, identifying rare events, and improving pathological classification and tumor grading. [17][18][19][20][21][22] In this paper, we use CODA 23 , a novel imaging workflow that creates volumetric reconstruction of mm 3 to cm 3 -scale tissue samples at single-cell resolution. CODA utilizes histological image registration and semantic segmentation to create 3D quantifiable maps of normal and diseased microanatomy from hematoxylin and eosin (H&E) staining alone. ...

Visual assessment of 2D levels within 3D pathology datasets of prostate needle biopsies reveals substantial spatial heterogeneity
  • Citing Article
  • October 2023

Laboratory Investigation

... Recent years have witnessed a decline in CUP incidence, potentially attributable to enhanced success rates in identifying primary site tumors (13,14). While liver metastases with known primary sites have been extensively studied (15,16), liver metastases with unknown primary sites remain scarcely explored. Presently, this phenomenon is primarily documented in a limited number of case reports (17). ...

Identifying primary tumor site of origin for liver metastases via a combination of handcrafted and deep learning features