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ModelZoo
Geneformer_pytorch
Commits
cf2aa107
Commit
cf2aa107
authored
Oct 15, 2024
by
root
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...
@@ -41,7 +41,6 @@ Dockerfile(方式二)
...
@@ -41,7 +41,6 @@ Dockerfile(方式二)
docker build -t geneformer:latest .
docker build -t geneformer:latest .
docker run -dit --shm-size 80g --network=host --name=geneformer --privileged --device=/dev/kfd --device=/dev/dri --group-add video --cap-add=SYS_PTRACE --security-opt seccomp=unconfined -u root -v /opt/hyhal/:/opt/hyhal/:ro geneformer:latest /bin/bash
docker run -dit --shm-size 80g --network=host --name=geneformer --privileged --device=/dev/kfd --device=/dev/dri --group-add video --cap-add=SYS_PTRACE --security-opt seccomp=unconfined -u root -v /opt/hyhal/:/opt/hyhal/:ro geneformer:latest /bin/bash
docker exec -it geneformer /bin/bash
docker exec -it geneformer /bin/bash
```
```
...
@@ -78,12 +77,12 @@ sudo apt-get install git-lfs
...
@@ -78,12 +77,12 @@ sudo apt-get install git-lfs
```
```
##
下载
数据集
## 数据集
下载
```
```
#git clone https://hf-mirror.com/datasets/ctheodoris/Genecorpus-30M
#git clone https://hf-mirror.com/datasets/ctheodoris/Genecorpus-30M
mkdir -p /path/to/
mkdir -p /path/to/
cd /path/to
cd /path/to
git clone http
s
://
hf-mirror.com/dataset
s/ctheodoris/Gene
c
or
pus-30M
git
lfs
clone http://
113.200.138.88:18080/aimodel
s/ctheodoris/Gene
f
or
mer.git
```
```
## geneformer模型下载
## geneformer模型下载
...
@@ -92,15 +91,13 @@ git clone https://hf-mirror.com/datasets/ctheodoris/Genecorpus-30M
...
@@ -92,15 +91,13 @@ git clone https://hf-mirror.com/datasets/ctheodoris/Genecorpus-30M
```
```
cd /path/to
cd /path/to
git clone -b pr146_branch http
s
://
hf-mirror.com
/ctheodoris/Geneformer
git
lfs
clone -b pr146_branch http://
113.200.138.88:18080/aimodels
/ctheodoris/Geneformer
.git
cd Geneformer
cd Geneformer
pip install -e .
pip install -e .
```
```
# 模型训练
# 模型训练
单卡运行 gene classification
单卡运行 gene classification
...
@@ -111,8 +108,25 @@ python train_cell.py
...
@@ -111,8 +108,25 @@ python train_cell.py
详情可以参考 Geneformer/examples/cell_classification.ipynb
详情可以参考 Geneformer/examples/cell_classification.ipynb
# 参考
# 推理
暂无
# 源码仓库及问题反馈
```
http://developer.sourcefind.cn/codes/modelzoo/geneformer.git
```
# 参考资料
```
https://hf-mirror.com/ctheodoris/Geneformer
https://hf-mirror.com/ctheodoris/Geneformer
```
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