mahmoodlab/hipt issues and pull requests

#75 - Feature Extraction

Issue - State: open - Opened by 18570481142 5 months ago

#74 - Pretrained 3. ViT?

Issue - State: open - Opened by vildesboe 9 months ago

#73 - Will the code for MCAT be updated in the survival prediction section?

Issue - State: open - Opened by rabberk 10 months ago - 2 comments

#72 - The tcga_brca_subset.csv.zip compressed file is corrupted.

Issue - State: open - Opened by s-xisx 11 months ago - 2 comments

#71 - dropout augmentation for second dino

Issue - State: open - Opened by jafarinia 11 months ago

#70 - what is the mean and std when using the pretrined dino vit-s to extract patch feature?

Issue - State: closed - Opened by weiaicunzai about 1 year ago - 1 comment

#69 - Poor performance on PRAD downstream

Issue - State: open - Opened by mbu93 about 1 year ago

#68 - Visualization Disturbing Original H&E

Issue - State: open - Opened by matthew-lee1 about 1 year ago

#67 - Pretraining Dataset

Issue - State: open - Opened by aCoalBall about 1 year ago

#66 - Duration of Feature Extraction Using hipt4k Pretrained Model

Issue - State: closed - Opened by XinyangHan about 1 year ago - 4 comments

#65 - 4k attention visualization output kind of weird

Issue - State: closed - Opened by yubin-ai over 1 year ago - 1 comment

#64 - How to determine the survival score when a patient has multiple WSIs?

Issue - State: closed - Opened by allgebra over 1 year ago - 1 comment

#63 - Data preprocessing

Issue - State: open - Opened by WinterPan2017 over 1 year ago

#62 - coordinates of 4k region embeddings

Issue - State: open - Opened by florianbuettner over 1 year ago

#61 - Setting patient_strat=FALSE in subtyping

Issue - State: closed - Opened by HanwenXuTHU over 1 year ago - 3 comments

#60 - dino4k pretraining

Issue - State: closed - Opened by Akihiko0123 over 1 year ago - 4 comments

#59 - The results of each inference are inconsistent

Issue - State: closed - Opened by yuzhuogu over 1 year ago - 2 comments

#58 - a WSI image with a higher resolution

Issue - State: open - Opened by yuzhuogu over 1 year ago

#57 - Hurry!!!How to slove this problem?

Issue - State: closed - Opened by wxyz-wjx over 1 year ago - 2 comments

#56 - Got different results when runing the example "Using the HIPT_4K API" two times

Issue - State: closed - Opened by weitinging over 1 year ago - 7 comments

#55 - .csv metadata file for colorectal dataset

Issue - State: open - Opened by umarikkar over 1 year ago

#54 - knn_classifier

Issue - State: open - Opened by xjc6666 over 1 year ago

#53 - Gradient accumulation not properly implemented

Issue - State: open - Opened by clemsgrs over 1 year ago - 2 comments

#52 - Change ckpt file extensions

Pull Request - State: open - Opened by scjjb over 1 year ago - 1 comment

#51 - Some issue about create patch.

Issue - State: closed - Opened by icherishxixi over 1 year ago - 14 comments

#50 - VIT-4096-WSI

Issue - State: closed - Opened by arjun11verma over 1 year ago - 1 comment

#49 - Creating patches and extracting features for [4096 x 4096]

Issue - State: open - Opened by nam1410 over 1 year ago - 3 comments

#48 - the reasoning behind attention heatmaps code

Issue - State: closed - Opened by clemsgrs over 1 year ago - 1 comment

#47 - name 'get_patch_attention_scores' is not defined

Issue - State: closed - Opened by Lewislou almost 2 years ago - 1 comment

#46 - Using the Features in CLAM

Issue - State: closed - Opened by shubhaminnani almost 2 years ago - 2 comments

#45 - Extracting features from 4096 x 4096 patches (M x L x D)

Issue - State: open - Opened by ekansh09 almost 2 years ago

#44 - Batch-wise extract features

Issue - State: closed - Opened by SongDoHou almost 2 years ago - 3 comments

#43 - WSI preprocessing

Issue - State: open - Opened by ghost almost 2 years ago - 5 comments

#42 - How can I get ’vits_tcga_pancancer_dino_pt_patch_features‘?

Issue - State: closed - Opened by qidog almost 2 years ago - 1 comment

#41 - Worse Performance in CAMELYON16 only

Issue - State: closed - Opened by bryanwong17 almost 2 years ago - 5 comments

#40 - Worse Performance in CAMELYON16 only

Issue - State: closed - Opened by bryanwong17 almost 2 years ago

#39 - Recommended GPUs

Issue - State: closed - Opened by usuyama almost 2 years ago - 2 comments

#38 - tar_patch_4096 with webdataset API

Issue - State: closed - Opened by JuanDuranMcgill almost 2 years ago - 2 comments

#37 - Pretrained ViTWSI-4096 model

Issue - State: closed - Opened by KiyoshiMu almost 2 years ago - 2 comments

#36 - cannot load pretrained model weights

Issue - State: closed - Opened by RedekopEP about 2 years ago - 2 comments

#35 - Process of training subtyping task on custom WSIs dataset using provided pretrained model

Issue - State: closed - Opened by SongDoHou about 2 years ago - 2 comments

#34 - 'Weakly-Supervised Training' task - Issue with fast_cluster_ids.pkl file

Issue - State: closed - Opened by gaiacervi about 2 years ago - 2 comments

#33 - Number of epochs required for finetuning

Issue - State: closed - Opened by bryanwong17 about 2 years ago - 1 comment

#32 - Stochastic behavior when extracting the features for one image

Issue - State: closed - Opened by maduc7 about 2 years ago - 4 comments

#31 - Fix attention notebook

Pull Request - State: closed - Opened by Arkkienkeli about 2 years ago

#30 - Some questions

Issue - State: closed - Opened by jasonyin20 about 2 years ago - 1 comment

#29 - Issue with Attention Visualization

Issue - State: closed - Opened by Arkkienkeli about 2 years ago - 2 comments

#28 - Getting raw patches after CLAM preprocessing

Issue - State: closed - Opened by bryanwong17 about 2 years ago - 5 comments

#27 - Some Questions

Issue - State: closed - Opened by bryanwong17 about 2 years ago - 1 comment

#26 - Inquiry about Dataset

Issue - State: closed - Opened by bryanwong17 about 2 years ago - 4 comments

#25 - subtyping: training loss not really decreasing

Issue - State: closed - Opened by clemsgrs about 2 years ago - 8 comments

#24 - average number of [4096,4096] regions per slide

Issue - State: closed - Opened by clemsgrs over 2 years ago - 9 comments

#23 - img_size argument

Issue - State: closed - Opened by clemsgrs over 2 years ago - 1 comment

#22 - Which mean "n" and "h" ?

Issue - State: closed - Opened by AndrewTal over 2 years ago - 2 comments

#21 - Training procedure for custom dataset?

Issue - State: closed - Opened by shatz01 over 2 years ago - 1 comment

#20 - Reshaping Vit256-16 output to be consistent with ViT4096-256 and following ViT-WSI

Issue - State: open - Opened by FabianHoerst over 2 years ago

#19 - All categories were classified into the same category

Issue - State: closed - Opened by SH-Diao123 over 2 years ago - 1 comment

#18 - ModuleNotFoundError: No module named 'utils.gpu_utils'

Issue - State: closed - Opened by mertgokpinar over 2 years ago - 1 comment

#17 - Remove repeated key in the kwargs dictionary

Pull Request - State: open - Opened by AymenSe over 2 years ago

#16 - Labels for cancer subtyping

Issue - State: closed - Opened by juanigp over 2 years ago - 9 comments

#15 - Unknow architecture: vit_small when running 1-Hierarchical-Pretraining/main_dino4k.py

Issue - State: closed - Opened by eran88 over 2 years ago - 1 comment

#14 - Question regarding Evaluation

Issue - State: closed - Opened by FabianHoerst over 2 years ago - 4 comments

#13 - Unable to find *.pt files for region_4096_pretraining

Issue - State: open - Opened by ramprs21 over 2 years ago - 5 comments

#12 - ModuleNotFoundError: No module named 'vision_transformer'

Issue - State: closed - Opened by giulianobertoti over 2 years ago - 6 comments

#11 - Datasets

Issue - State: closed - Opened by luojing1030 over 2 years ago - 4 comments

#10 - ModuleNotFoundError: No module named 'nn_encoder_arch'

Issue - State: closed - Opened by FarahHwang over 2 years ago - 1 comment

#9 - Survival Code

Issue - State: closed - Opened by pazadimo over 2 years ago - 2 comments

GitHub / mahmoodlab/hipt issues and pull requests