no code implementations • 18 Nov 2024 • Harshita Sharma, Valentina Salvatelli, Shaury Srivastav, Kenza Bouzid, Shruthi Bannur, Daniel C. Castro, Maximilian Ilse, Sam Bond-Taylor, Mercy Prasanna Ranjit, Fabian Falck, Fernando Pérez-García, Anton Schwaighofer, Hannah Richardson, Maria Teodora Wetscherek, Stephanie L. Hyland, Javier Alvarez-Valle
Subsequently, building on the architectures of MAIRA, a CXR-specialised model for report generation, we integrate a trainable segmentation tokens extractor that leverages these mask pseudolabels, and employ mask-aware prompting to generate draft radiology reports.
1 code implementation • 6 Jun 2024 • Shruthi Bannur, Kenza Bouzid, Daniel C. Castro, Anton Schwaighofer, Anja Thieme, Sam Bond-Taylor, Maximilian Ilse, Fernando Pérez-García, Valentina Salvatelli, Harshita Sharma, Felix Meissen, Mercy Ranjit, Shaury Srivastav, Julia Gong, Noel C. F. Codella, Fabian Falck, Ozan Oktay, Matthew P. Lungren, Maria Teodora Wetscherek, Javier Alvarez-Valle, Stephanie L. Hyland
Radiology reporting is a complex task requiring detailed medical image understanding and precise language generation, for which generative multimodal models offer a promising solution.
no code implementations • 8 May 2024 • Anja Thieme, Abhijith Rajamohan, Benjamin Cooper, Heather Groombridge, Robert Simister, Barney Wong, Nicholas Woznitza, Mark Ames Pinnock, Maria Teodora Wetscherek, Cecily Morrison, Hannah Richardson, Fernando Pérez-García, Stephanie L. Hyland, Shruthi Bannur, Daniel C. Castro, Kenza Bouzid, Anton Schwaighofer, Mercy Ranjit, Harshita Sharma, Matthew P. Lungren, Ozan Oktay, Javier Alvarez-Valle, Aditya Nori, Stephen Harris, Joseph Jacob
Nasogastric tubes (NGTs) are feeding tubes that are inserted through the nose into the stomach to deliver nutrition or medication.
no code implementations • 19 Jan 2024 • Fernando Pérez-García, Harshita Sharma, Sam Bond-Taylor, Kenza Bouzid, Valentina Salvatelli, Maximilian Ilse, Shruthi Bannur, Daniel C. Castro, Anton Schwaighofer, Matthew P. Lungren, Maria Wetscherek, Noel Codella, Stephanie L. Hyland, Javier Alvarez-Valle, Ozan Oktay
We introduce RAD-DINO, a biomedical image encoder pre-trained solely on unimodal biomedical imaging data that obtains similar or greater performance than state-of-the-art biomedical language-supervised models on a diverse range of benchmarks.
no code implementations • 20 Dec 2023 • Fernando Pérez-García, Sam Bond-Taylor, Pedro P. Sanchez, Boris van Breugel, Daniel C. Castro, Harshita Sharma, Valentina Salvatelli, Maria T. A. Wetscherek, Hannah Richardson, Matthew P. Lungren, Aditya Nori, Javier Alvarez-Valle, Ozan Oktay, Maximilian Ilse
Biomedical imaging datasets are often small and biased, meaning that real-world performance of predictive models can be substantially lower than expected from internal testing.
no code implementations • 22 Nov 2023 • Stephanie L. Hyland, Shruthi Bannur, Kenza Bouzid, Daniel C. Castro, Mercy Ranjit, Anton Schwaighofer, Fernando Pérez-García, Valentina Salvatelli, Shaury Srivastav, Anja Thieme, Noel Codella, Matthew P. Lungren, Maria Teodora Wetscherek, Ozan Oktay, Javier Alvarez-Valle
We present a radiology-specific multimodal model for the task for generating radiological reports from chest X-rays (CXRs).
no code implementations • 23 Oct 2023 • Qianchu Liu, Stephanie Hyland, Shruthi Bannur, Kenza Bouzid, Daniel C. Castro, Maria Teodora Wetscherek, Robert Tinn, Harshita Sharma, Fernando Pérez-García, Anton Schwaighofer, Pranav Rajpurkar, Sameer Tajdin Khanna, Hoifung Poon, Naoto Usuyama, Anja Thieme, Aditya V. Nori, Matthew P. Lungren, Ozan Oktay, Javier Alvarez-Valle
In this paper, we focus on assessing the performance of GPT-4, the most capable LLM so far, on the text-based applications for radiology reports, comparing against state-of-the-art (SOTA) radiology-specific models.
no code implementations • 9 May 2023 • Ho Hin Lee, Alberto Santamaria-Pang, Jameson Merkow, Ozan Oktay, Fernando Pérez-García, Javier Alvarez-Valle, Ivan Tarapov
We introduce a novel Region-based contrastive pretraining for Medical Image Retrieval (RegionMIR) that demonstrates the feasibility of medical image retrieval with similar anatomical regions.
no code implementations • 23 Mar 2023 • Fangyu Liu, Qianchu Liu, Shruthi Bannur, Fernando Pérez-García, Naoto Usuyama, Sheng Zhang, Tristan Naumann, Aditya Nori, Hoifung Poon, Javier Alvarez-Valle, Ozan Oktay, Stephanie L. Hyland
We evaluate DoT5 on the biomedical domain and the resource-lean subdomain of radiology, focusing on NLI, text summarisation and embedding learning.
1 code implementation • CVPR 2023 • Shruthi Bannur, Stephanie Hyland, Qianchu Liu, Fernando Pérez-García, Maximilian Ilse, Daniel C. Castro, Benedikt Boecking, Harshita Sharma, Kenza Bouzid, Anja Thieme, Anton Schwaighofer, Maria Wetscherek, Matthew P. Lungren, Aditya Nori, Javier Alvarez-Valle, Ozan Oktay
Prior work in biomedical VLP has mostly relied on the alignment of single image and report pairs even though clinical notes commonly refer to prior images.
2 code implementations • 23 Mar 2022 • Andres Diaz-Pinto, Sachidanand Alle, Vishwesh Nath, Yucheng Tang, Alvin Ihsani, Muhammad Asad, Fernando Pérez-García, Pritesh Mehta, Wenqi Li, Mona Flores, Holger R. Roth, Tom Vercauteren, Daguang Xu, Prerna Dogra, Sebastien Ourselin, Andrew Feng, M. Jorge Cardoso
MONAI Label allows researchers to make incremental improvements to their AI-based annotation application by making them available to other researchers and clinicians alike.
1 code implementation • 22 Jun 2021 • Fernando Pérez-García, Catherine Scott, Rachel Sparks, Beate Diehl, Sébastien Ourselin
We demonstrate that an STCNN trained on a HAR dataset can be used in combination with an RNN to accurately represent arbitrarily long videos of seizures.
1 code implementation • 24 May 2021 • Fernando Pérez-García, Reuben Dorent, Michele Rizzi, Francesco Cardinale, Valerio Frazzini, Vincent Navarro, Caroline Essert, Irène Ollivier, Tom Vercauteren, Rachel Sparks, John S. Duncan, Sébastien Ourselin
We fine-tuned our model on three small annotated datasets from different institutions and on the annotated images in EPISURG, comprising 20, 33, 19 and 133 subjects.
1 code implementation • 28 Jun 2020 • Fernando Pérez-García, Roman Rodionov, Ali Alim-Marvasti, Rachel Sparks, John S. Duncan, Sébastien Ourselin
In addition to EPISURG, we used three public datasets comprising 1813 preoperative MR images for training.
7 code implementations • 9 Mar 2020 • Fernando Pérez-García, Rachel Sparks, Sébastien Ourselin
Additionally, we provide a graphical interface within a TorchIO extension in 3D Slicer to visualize the effects of transforms.