Rename to decipher

.flake8

@@ -69,7 +69,6 @@ exclude =
     docs/_build,
     dist,
     experiments,
-    spider/wsi/hover_net
 per-file-ignores =
     tests/*: D
     */__init__.py: F401

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,15 +1,15 @@
 ---
 name: Bug report
-about: Spider doesn’t do what it should? Please help us fix it!
+about: DECIPHER doesn’t do what it should? Please help us fix it!
 title: ''
 labels: bug
 assignees: ''
 ---
 
 ### Please ensure:
 
-- [ ] I have confirmed this bug exists on the **latest** version of Spider. See https://github.com/gao-lab/spider
-- [ ] I follow the tutorial from the [Spider tutorial](https://github.com/gao-lab/spider).
+- [ ] I have confirmed this bug exists on the **latest** version of DECIPHER. See https://github.com/gao-lab/decipher
+- [ ] I follow the tutorial from the [DECIPHER tutorial](https://github.com/gao-lab/decipher).
 
 -----------
 
@@ -24,7 +24,7 @@ assignees: ''
 - Python version: <!-- e.g. 3.9.1 -->
 - Torch version: <!-- e.g. 2.0.1 -->
 - Pytorch geometric version: <!-- e.g. 2.3.0 -->
-- Spider version: <!-- e.g. 0.1.0 -->
+- DECIPHER version: <!-- e.g. 0.1.0 -->
 - Others: <!-- Other unconventional env setup -->
 
 **Data information:**

.github/ISSUE_TEMPLATE/enhancement-request.md

@@ -1,6 +1,6 @@
 ---
 name: Enhancement request
-about: Anything you’d like to see in Spider?
+about: Anything you’d like to see in DECIPHER?
 title: ''
 labels: enhancement
 assignees: ''

.github/workflows/release.yml

@@ -75,4 +75,4 @@ jobs:
           context: .
           dockerfile: ./Dockerfile
           push: true
-          tags: huhansan666666/spider:latest
+          tags: huhansan666666/decipher:latest

.gitignore

@@ -85,4 +85,4 @@ experiments/**/*.yaml
 !resource/README.md
 !.vscode/*
 !Dockerfile
-!spider/data/*
+!decipher/data/*

.pre-commit-config.yaml

@@ -3,8 +3,8 @@ fail_fast: false
 default_language_version:
     python: python3
 default_stages:
-    - commit
-    - push
+    - pre-commit
+    - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black

DEVELOPER.md

@@ -5,7 +5,7 @@
 
 ## Full install
 ```sh
-git clone [email protected]:gao-lab/Spider-dev.git && cd Spider-dev
+git clone [email protected]:gao-lab/DECIPHER.git && cd DECIPHER
 mamba create -p ./conda -c conda-forge -c rapidsai -c nvidia -c bioconda python=3.11 rapids=24.04 cuda-version=11.8 cudnn cutensor cusparselt pandoc snakemake==7.32.4 -y && conda activate ./conda
 pip install -e ".[dev, docs]"
 install_pyg_dependencies
@@ -35,6 +35,6 @@ py-spy record -o profile.svg -- python -m <YOUR_SCRIPT.py>
 
 ## Build docker image
 ```sh
-cd Spider-dev/
-docker image build --no-cache . -t huhansan666666/spider:v0.1.0 --network=host
+# cd DECIPHER/
+docker image build --no-cache . -t huhansan666666/decipher:v0.1.0 --network=host
 ```

Dockerfile

@@ -7,10 +7,10 @@ RUN apt-get update \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-# Copy Spider package and install
+# Copy DECIPHER package and install
 USER rapids
 WORKDIR /app
-COPY ./spider ./spider
+COPY ./decipher ./decipher
 COPY ./README.md ./README.md
 COPY ./pyproject.toml ./pyproject.toml
 RUN pip --no-cache-dir install -e "." && install_pyg_dependencies && rm -rf /tmp/*

README.md

@@ -1,47 +1,49 @@
-<!-- [![stars-badge](https://img.shields.io/github/stars/gao-lab/Spider-dev?logo=GitHub&color=yellow)](https://github.com/gao-lab/Spider-dev/stargazers) -->
+<!-- [![stars-badge](https://img.shields.io/github/stars/gao-lab/DECIPHER?logo=GitHub&color=yellow)](https://github.com/gao-lab/DECIPHER/stargazers) -->
+[![build-badge](https://github.com/gao-lab/DECIPHER/actions/workflows/build.yml/badge.svg)](https://github.com/gao-lab/DECIPHER/actions/workflows/build.yml)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![build-badge](https://github.com/gao-lab/Spider-dev/actions/workflows/build.yml/badge.svg)](https://github.com/gao-lab/Spider-dev/actions/workflows/build.yml)
 [![license-badge](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 ![Python 3.10|3.11|3.12](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12-blue.svg)
 
 
-# Spider: SPatial IDentity and Environment Representation
+# DECIPHER
 <div align="center">
 
-[Installation](#Installation) • [Documentation](#Documentation) • [Citation](#Citation) • [FAQ](#FAQ) • [Acknowledgement](#Acknowledgement)
+[Installation](#Installation) • [Documentation](#Documentation) • [Manuscript](#Manuscript) • [FAQ](#FAQ) • [Acknowledgement](#Acknowledgement)
 
 </div>
 
-`Spider` aims to learn cells’ embeddings from omics feature and spatial environment aspects independently, from single-cell spatial omics data.
+`DECIPHER` aims to learn cells’ disentangled embeddings from intracellular state and extracellular contexts view based on single-cell spatial omics data.
+
+![DECIPHER](./docs/_static/Model.png)
 
 ## Installation
 > [!IMPORTANT]
 > Requires Python >= 3.10 and CUDA-enabled GPU (not recommend using CPU because it‘s too slow).
 
 ### PyPI
-We recommend to install `Spider` to a new conda environment with [RAPIDS](https://docs.rapids.ai/install) dependencies.
+We recommend to install `cell-decipher` to a new conda environment with [RAPIDS](https://docs.rapids.ai/install) dependencies.
 
 ```sh
 mamba create -p ./conda -c conda-forge -c rapidsai -c nvidia python=3.11 rapids=24.04 cuda-version=11.8 cudnn cutensor cusparselt -y && conda activate ./conda
-pip install spider
+pip install cell-decipher
 install_pyg_dependencies
 ```
 
 ### Docker
 Build docker image from [Dockerfile](./Dockerfile) or pull the latest image from Docker Hub by:
 ```sh
-docker pull huhansan666666/spider:latest
+docker pull huhansan666666/decipher:latest
 ```
 
 ## Documentation
-Here is a minimal example for quick start. Please check our [**documentation**](https://slat.readthedocs.io/en/latest/) for detailed tutorial and information.
+Here is a minimal example for quick start. Please check our [**documentation**](https://slat.readthedocs.io/en/latest/) for advanced tutorials.
 
 ```python
 import scanpy as sc
-from spider import Spider
+from decipher import DECIPHER
 
 # Init model
-model = Spider(work_dir='/path/to/work_dir')
+model = DECIPHER(work_dir='/path/to/work_dir')
 
 # Register data
 adata = sc.read_h5ad('/path/to/adata.h5ad')
@@ -50,12 +52,12 @@ model.register_data(adata)
 # Fit model
 model.fit_omics()
 
-# Get independent omics and spatial embeddings
+# Get disentangled omics and spatial embeddings
 omics_emb = model.center_emb
 spatial_emb = model.nbr_emb
 ```
 
-## Citation
+## Manuscript
 TBD
 
 > If you want to repeat our benchmarks and case studies, please check the [**benchmark**](./benchmark/README.md) and [**experiments**](./experiments/README.md) folder.

benchmark/README.md

@@ -12,7 +12,7 @@ All datasets used in benchmark are public available. Here is a summary:
 
 
 ## Methods
-- Spider
+- DECIPHER
 - SLAT
 - BANKSY
 - STAGATE
@@ -24,15 +24,15 @@ All datasets used in benchmark are public available. Here is a summary:
 ## Reproducibility
 
 ### Setup environment
-Following the [guide](./env/README.md). You can also check absolute version of install packages in [conda.yaml](env/conda.yaml) file.
+Follow the [guide](./env/README.md) to set up the environment. The absolute version of packages is also provided in [conda.yaml](env/conda.yaml).
 
 ### Prepare data
 
 Download the datasets and move them into `./input` folder.
 
 ### Run the workflow in slurm cluster
 
-> Take about 12 hours when using 4 GPU nodes (64 cores, 1TB mem and 8 A100-GPUs).
+> Take about 12 hours when using 32 A100 GPUs.
 
 We use `snakemake` to run benchmark workflows in Slurm cluster. Firstly, you need modify `partition` name in [`config`](./profiles/hpc/hpc.yaml) according to your cluster settings, then run:
 

benchmark/analysis/benchmark_analysis.R

@@ -24,7 +24,7 @@ library(patchwork)
 
 # %% vscode={"languageId": "r"}
 data <- read_csv('../results/benchmark_results.csv')
-data$method <- factor(data$method, levels = c('spider', 'scvi', 'harmony', 'scanpy', 'banksy', 'stagate', 'slat'))
+data$method <- factor(data$method, levels = c('decipher', 'scvi', 'harmony', 'scanpy', 'banksy', 'stagate', 'slat'))
 
 # # replace ':' by '-' in all column names
 # data <- data %>% rename_all(~ gsub(":", "__", .))
@@ -98,7 +98,7 @@ ggbarplot(data, x="method", y='run_time', fill='method', color='method', add="me
 
 # %% vscode={"languageId": "r"}
 data <- read_csv('../results/benchmark_results.csv')
-data$method <- factor(data$method, levels = c('spider', 'scvi', 'harmony', 'scanpy', 'banksy', 'stagate', 'slat'))
+data$method <- factor(data$method, levels = c('decipher', 'scvi', 'harmony', 'scanpy', 'banksy', 'stagate', 'slat'))
 data <- data %>% filter(dataset == 'human_brainaging_merfish') %>% filter(method != 'harmony')
 
 head(data)
@@ -144,7 +144,7 @@ p_list[[1]] | p_list[[2]]
 
 # %% vscode={"languageId": "r"}
 data <- read_csv('../results/benchmark_results.csv')
-data$method <- factor(data$method, levels = c('spider', 'scvi', 'harmony', 'scanpy', 'banksy', 'stagate', 'slat'))
+data$method <- factor(data$method, levels = c('decipher', 'scvi', 'harmony', 'scanpy', 'banksy', 'stagate', 'slat'))
 data <- data %>% filter(dataset == 'human_breastcancer_xenium') %>% filter(method != 'harmony')
 
 

benchmark/config/config.yaml

@@ -23,7 +23,7 @@ dataset:
 
 #--------------------------- Benchmark Methods -----------------------------#
 method:
-  - spider
+  - decipher
   # # spatial
   - banksy
   - stagate

benchmark/env/README.md

@@ -8,8 +8,8 @@ mamba create -p ./conda -y -c conda-forge -c rapidsai -c nvidia -c bioconda pyth
 rapids=24.04 cuda-version=11.8 cudnn cutensor cusparselt \
 snakemake==7.32.4 && conda activate ./conda
 
-# spider & scanpy
-# cd /path/to/spider
+# decipher & scanpy
+# cd /path/to/decipher
 pip install '.[dev]'
 install_pyg_dependencies
 

benchmark/env/conda.yaml

@@ -628,7 +628,7 @@ dependencies:
       - seaborn==0.13.2
       - session-info==1.0.0
       - spagcn==1.2.7
-      - spider==0.1.0
+      - decipher==0.1.0
       - stack-data==0.6.3
       - stagate-pyg==1.0.0
       - statsmodels==0.14.2

benchmark/profiles/cls/cls.yaml

@@ -1,5 +1,5 @@
 __default__:
-  jobname: "Spider-{rule}"
+  jobname: "DECIPHER-{rule}"
   output: ".slurm/{rule}.out"
   error: ".slurm/{rule}.err"
   account: gaog_g1
@@ -10,7 +10,7 @@ __default__:
   qos: gaogcns
   gres: ""
 
-run_spider:
+run_decipher:
   partition: gpu_4l
   qos: gaogg4c
   gres: "--gres=gpu:1"
@@ -25,7 +25,7 @@ run_scvi:
   qos: gaogg4c
   gres: "--gres=gpu:1"
 
-search_spider:
+search_decipher:
   partition: gpu_4l
   qos: gaogg4c
   gres: "--gres=gpu:1"

benchmark/profiles/hpc/hpc.yaml

@@ -1,5 +1,5 @@
 __default__:
-  jobname: "Spider-{rule}"
+  jobname: "DECIPHER-{rule}"
   output: ".slurm/{rule}.out"
   error: ".slurm/{rule}.err"
   account: gglab
@@ -9,7 +9,7 @@ __default__:
   n_cpu: "{threads}"
   gres: ""
 
-run_spider:
+run_decipher:
   partition: gpu32,gpu2
   gres: "--gres=gpu:1"
 
@@ -21,6 +21,6 @@ run_scvi:
   partition: gpu32,gpu2
   gres: "--gres=gpu:1"
 
-search_spider:
+search_decipher:
   partition: gpu32,gpu2
   gres: "--gres=gpu:1"

benchmark/workflow/Snakefile

@@ -10,7 +10,7 @@ localrules:
     summary_benchmark,
     summary_hyper_search,
     link_data,
-    # run_spider,
+    # run_decipher,
     # run_scvi,
     # run_stagate,
     # calc_metrics,
@@ -40,7 +40,7 @@ rule summary_hyper_search:
     output:
         "results/hyper_search.csv",
     params:
-        pattern=lambda wildcards: "results/{dataset}/seed:{seed}/search_spider/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/metrics.yaml"
+        pattern=lambda wildcards: "results/{dataset}/seed:{seed}/search_decipher/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/metrics.yaml"
     threads: 1
     script:
         "scripts/summarize.py"

benchmark/workflow/rules/hyper_search.smk

@@ -1,18 +1,18 @@
 
-rule search_spider:
+rule search_decipher:
     input:
         data = "{path}/data.h5ad",
-        script = "workflow/scripts/search_spider.py",
+        script = "workflow/scripts/search_decipher.py",
     output:
-        center_emb = "{path}/search_spider/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/center_emb.npy",
-        nbr_emb = "{path}/search_spider/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/nbr_emb.npy",
-        time = "{path}/search_spider/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/time.yaml",
+        center_emb = "{path}/search_decipher/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/center_emb.npy",
+        nbr_emb = "{path}/search_decipher/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/nbr_emb.npy",
+        time = "{path}/search_decipher/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/time.yaml",
     params:
-        notebook_in = "workflow/scripts/search_spider.ipynb",
-        notebook_out = "{path}/search_spider/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/search_spider.ipynb",
-        work_dir = "{path}/search_spider/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}",
+        notebook_in = "workflow/scripts/search_decipher.ipynb",
+        notebook_out = "{path}/search_decipher/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/search_decipher.ipynb",
+        work_dir = "{path}/search_decipher/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}",
     log:
-        "{path}/search_spider/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/search_spider.log"
+        "{path}/search_decipher/dropout_gex:{dropout_gex}-k:{k}-center_emb_dim:{center_emb_dim}-nbr_emb_dim:{nbr_emb_dim}-epochs:{epochs}-dropout:{dropout}-transformer_layers:{transformer_layers}-temperature_center:{temperature_center}-temperature_nbr:{temperature_nbr}-batch_size:{batch_size}/search_decipher.log"
     threads:8
     resources: gpu=1
     shell:

benchmark/workflow/rules/methods.smk

@@ -1,18 +1,18 @@
 
-rule run_spider:
+rule run_decipher:
     input:
         data = "{path}/data.h5ad",
-        script = "workflow/scripts/run_spider.py",
+        script = "workflow/scripts/run_decipher.py",
     output:
-        center_emb = "{path}/spider/center_emb.npy",
-        nbr_emb = "{path}/spider/nbr_emb.npy",
-        time = "{path}/spider/time.yaml",
+        center_emb = "{path}/decipher/center_emb.npy",
+        nbr_emb = "{path}/decipher/nbr_emb.npy",
+        time = "{path}/decipher/time.yaml",
     params:
-        notebook_in = "workflow/scripts/run_spider.ipynb",
-        notebook_out = "{path}/spider/run_spider.ipynb",
-        work_dir = "{path}/spider",
+        notebook_in = "workflow/scripts/run_decipher.ipynb",
+        notebook_out = "{path}/decipher/run_decipher.ipynb",
+        work_dir = "{path}/decipher",
     log:
-        "{path}/spider/run_spider.log",
+        "{path}/decipher/run_decipher.log",
     threads:8
     resources: gpu=1
     shell: