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Paper · 2403.06801 · 2024

CT2Rep: Automated Radiology Report Generation for 3D Medical Imaging

arXiv · PDF · Open in the Atlas

Code that ran

We lifted 10 functions out of this paper's own repositories and ran 10 of them in a sandbox. "Ran" means the function executed on a synthesized input and returned a value. It is not a reproduction of the paper's results.

RepositoryRoleRan
ibrahimethemhamamci/ct2rep canonical 10 of 10
FunctionStatusWhere it lives
attention Ran ibrahimethemhamamci/ct2rep/CT2Rep/modules/encoder_decoder.py
pointer only (licence: NONE) · get_code("83045338e170467c")
build_lr_scheduler Ran ibrahimethemhamamci/ct2rep/CT2Rep/modules/optimizers.py
pointer only (licence: NONE) · get_code("3cbefcc988ce7b35")
build_optimizer Ran ibrahimethemhamamci/ct2rep/CT2Rep/modules/optimizers.py
pointer only (licence: NONE) · get_code("13190f966b28dd15")
cast_num_frames Ran ibrahimethemhamamci/ct2rep/CT2Rep/modules/data_ct.py
pointer only (licence: NONE) · get_code("592dc2191cc05297")
clones Ran ibrahimethemhamamci/ct2rep/CT2Rep/modules/encoder_decoder.py
pointer only (licence: NONE) · get_code("6cdff690e29fd5e2")
compute_loss Ran ibrahimethemhamamci/ct2rep/CT2Rep/modules/loss.py
pointer only (licence: NONE) · get_code("0bc1f8b3524f6b1b")
pack_wrapper Ran ibrahimethemhamamci/ct2rep/CT2Rep/modules/att_model.py
pointer only (licence: NONE) · get_code("d2379d710eedc4ae")
pad_unsort_packed_sequence Ran ibrahimethemhamamci/ct2rep/CT2Rep/modules/att_model.py
pointer only (licence: NONE) · get_code("bfac58a04b6835f5")
sort_pack_padded_sequence Ran ibrahimethemhamamci/ct2rep/CT2Rep/modules/att_model.py
pointer only (licence: NONE) · get_code("e56d2f9cbd9cb8b1")
subsequent_mask Ran ibrahimethemhamamci/ct2rep/CT2Rep/modules/encoder_decoder.py
pointer only (licence: NONE) · get_code("66fbf162663d4cff")

Repositories linked to this paper

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Abstract

Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation. Automating report generation has emerged as a critical need to alleviate the workload of radiologists. While machine learning has facilitated report generation for 2D medical imaging, extending this to 3D has been unexplored due to computational complexity and data scarcity. We introduce the first method to generate radiology reports for 3D medical imaging, specifically targeting chest CT volumes. Given the absence of comparable methods, we establish a baseline using an advanced 3D vision encoder in medical imaging to demonstrate our method's effectiveness, which leverages a novel auto-regressive causal transformer. Furthermore, recognizing the benefits of leveraging information from previous visits, we augment CT2Rep with a cross-attention-based multi-modal fusion module and hierarchical memory, enabling the incorporation of longitudinal multimodal data. Access our code at https://github.com/ibrahimethemhamamci/CT2Rep

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