|
|
--- |
|
|
library_name: transformers |
|
|
tags: [] |
|
|
--- |
|
|
|
|
|
# Model Card for Phenom CA-MAE-S/16 |
|
|
|
|
|
Channel-agnostic image encoding model designed for microscopy image featurization. |
|
|
The model uses a vision transformer backbone with channelwise cross-attention over patch tokens to create contextualized representations separately for each channel. |
|
|
|
|
|
|
|
|
## Model Details |
|
|
|
|
|
### Model Description |
|
|
|
|
|
This model is a [channel-agnostic masked autoencoder](https://openaccess.thecvf.com/content/CVPR2024/html/Kraus_Masked_Autoencoders_for_Microscopy_are_Scalable_Learners_of_Cellular_Biology_CVPR_2024_paper.html) trained to reconstruct microscopy images over three datasets: |
|
|
1. RxRx3 |
|
|
2. JUMP-CP overexpression |
|
|
3. JUMP-CP gene-knockouts |
|
|
|
|
|
- **Developed, funded, and shared by:** Recursion |
|
|
- **Model type:** Vision transformer CA-MAE |
|
|
- **Image modality:** Optimized for microscopy images from the CellPainting assay |
|
|
- **License:** [More Information Needed] |
|
|
|
|
|
### Model Sources |
|
|
|
|
|
- **Repository:** [https://github.com/recursionpharma/maes_microscopy](https://github.com/recursionpharma/maes_microscopy) |
|
|
- **Paper:** [Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology](https://openaccess.thecvf.com/content/CVPR2024/html/Kraus_Masked_Autoencoders_for_Microscopy_are_Scalable_Learners_of_Cellular_Biology_CVPR_2024_paper.html) |
|
|
|
|
|
## Uses |
|
|
|
|
|
<!-- Address questions around how the model is intended to be used, including the foreseeable users of the model and those affected by the model. --> |
|
|
|
|
|
### Direct Use |
|
|
|
|
|
<!-- This section is for the model use without fine-tuning or plugging into a larger ecosystem/app. --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
### Downstream Use [optional] |
|
|
|
|
|
<!-- This section is for the model use when fine-tuned for a task, or when plugged into a larger ecosystem/app --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
### Out-of-Scope Use |
|
|
|
|
|
<!-- This section addresses misuse, malicious use, and uses that the model will not work well for. --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
## Bias, Risks, and Limitations |
|
|
|
|
|
<!-- This section is meant to convey both technical and sociotechnical limitations. --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
### Recommendations |
|
|
|
|
|
<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. --> |
|
|
|
|
|
Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model. More information needed for further recommendations. |
|
|
|
|
|
## How to Get Started with the Model |
|
|
|
|
|
Use the code below to get started with the model. |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
## Training Details |
|
|
|
|
|
### Training Data |
|
|
|
|
|
<!-- This should link to a Dataset Card, perhaps with a short stub of information on what the training data is all about as well as documentation related to data pre-processing or additional filtering. --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
### Training Procedure |
|
|
|
|
|
<!-- This relates heavily to the Technical Specifications. Content here should link to that section when it is relevant to the training procedure. --> |
|
|
|
|
|
#### Preprocessing [optional] |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
|
|
|
#### Training Hyperparameters |
|
|
|
|
|
- **Training regime:** [More Information Needed] <!--fp32, fp16 mixed precision, bf16 mixed precision, bf16 non-mixed precision, fp16 non-mixed precision, fp8 mixed precision --> |
|
|
|
|
|
#### Speeds, Sizes, Times [optional] |
|
|
|
|
|
<!-- This section provides information about throughput, start/end time, checkpoint size if relevant, etc. --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
## Evaluation |
|
|
|
|
|
<!-- This section describes the evaluation protocols and provides the results. --> |
|
|
|
|
|
### Testing Data, Factors & Metrics |
|
|
|
|
|
#### Testing Data |
|
|
|
|
|
<!-- This should link to a Dataset Card if possible. --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
#### Factors |
|
|
|
|
|
<!-- These are the things the evaluation is disaggregating by, e.g., subpopulations or domains. --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
#### Metrics |
|
|
|
|
|
<!-- These are the evaluation metrics being used, ideally with a description of why. --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
### Results |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
#### Summary |
|
|
|
|
|
|
|
|
|
|
|
## Model Examination [optional] |
|
|
|
|
|
<!-- Relevant interpretability work for the model goes here --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
## Environmental Impact |
|
|
|
|
|
<!-- Total emissions (in grams of CO2eq) and additional considerations, such as electricity usage, go here. Edit the suggested text below accordingly --> |
|
|
|
|
|
Carbon emissions can be estimated using the [Machine Learning Impact calculator](https://mlco2.github.io/impact#compute) presented in [Lacoste et al. (2019)](https://arxiv.org/abs/1910.09700). |
|
|
|
|
|
- **Hardware Type:** [More Information Needed] |
|
|
- **Hours used:** [More Information Needed] |
|
|
- **Cloud Provider:** [More Information Needed] |
|
|
- **Compute Region:** [More Information Needed] |
|
|
- **Carbon Emitted:** [More Information Needed] |
|
|
|
|
|
## Technical Specifications [optional] |
|
|
|
|
|
### Model Architecture and Objective |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
### Compute Infrastructure |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
#### Hardware |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
#### Software |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
## Citation [optional] |
|
|
|
|
|
<!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. --> |
|
|
|
|
|
**BibTeX:** |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
**APA:** |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
## Glossary [optional] |
|
|
|
|
|
<!-- If relevant, include terms and calculations in this section that can help readers understand the model or model card. --> |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
## More Information [optional] |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
## Model Card Authors [optional] |
|
|
|
|
|
[More Information Needed] |
|
|
|
|
|
## Model Card Contact |
|
|
|
|
|
[More Information Needed] |
