Search Results for author: Parisa Boodaghi Malidarreh

Found 8 papers, 3 papers with code

Predicting Future States with Spatial Point Processes in Single Molecule Resolution Spatial Transcriptomics

no code implementations4 Jan 2024 Parisa Boodaghi Malidarreh, Biraaj Rout, Mohammad Sadegh Nasr, Priyanshi Borad, Jillur Rahman Saurav, Jai Prakash Veerla, Kelli Fenelon, Theodora Koromila, Jacob M. Luber

In this paper, we introduce a pipeline based on Random Forest Regression to predict the future distribution of cells that are expressed by the Sog-D gene (active cells) in both the Anterior to posterior (AP) and the Dorsal to Ventral (DV) axis of the Drosophila in embryogenesis process.

Point Processes regression +1

Multimodal Pathology Image Search Between H&E Slides and Multiplexed Immunofluorescent Images

no code implementations11 Jun 2023 Amir Hajighasemi, MD Jillur Rahman Saurav, Mohammad S Nasr, Jai Prakash Veerla, Aarti Darji, Parisa Boodaghi Malidarreh, Michael Robben, Helen H Shang, Jacob M Luber

We present an approach for multimodal pathology image search, using dynamic time warping (DTW) on Variational Autoencoder (VAE) latent space that is fed into a ranked choice voting scheme to retrieve multiplexed immunofluorescent imaging (mIF) that is most similar to a query H&E slide.

Dynamic Time Warping Image Retrieval

Generalizability of PRS313 for breast cancer risk amongst non-Europeans in a Los Angeles biobank

no code implementations6 May 2023 Helen Shang, Yi Ding, Vidhya Venkateswaran, Kristin Boulier, Nikhita Kathuria-Prakash, Parisa Boodaghi Malidarreh, Jacob M. Luber, Bogdan Pasaniuc

We found that the PRS313 achieved overlapping Areas under the ROC Curve (AUCs) in females of Lantix (AUC, 0. 68; 95 CI, 0. 65-0. 71) and European ancestry (AUC, 0. 70; 95 CI, 0. 69-0. 71) but lower AUCs for the AFR and EAA populations (AFR: AUC, 0. 61; 95 CI, 0. 56-0. 65; EAA: AUC, 0. 64; 95 CI, 0. 60-0. 680).

Clinically Relevant Latent Space Embedding of Cancer Histopathology Slides through Variational Autoencoder Based Image Compression

1 code implementation23 Mar 2023 Mohammad Sadegh Nasr, Amir Hajighasemi, Paul Koomey, Parisa Boodaghi Malidarreh, Michael Robben, Jillur Rahman Saurav, Helen H. Shang, Manfred Huber, Jacob M. Luber

We generate and visualize embeddings from the compressed latent space and demonstrate how they are useful for clinical interpretation of data, and how in the future such latent embeddings can be used to accelerate search of clinical imaging data.

Image Compression

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