cosmx_cxg_lbcl_gene_subset_assay_token

Model Card for Model ID

Kuan Check the new UCE with assay token here: https://huggingface.co/KuanP/cosmx_cxg_lbcl_gene_subset_assay_token ; the training curve looks good; and this model is trained with 5x more sampling rate for cosmx, larger masking ratio (0.2) and assay tokens discriminating cosmx and non-cosmx; you can check the code at this new branch: https://github.com/Kuan-Pang/data_collection_exp/tree/dev-cosmx-mix ; and during inference you will need to specify if the h5ad is from cosmx or not with a hardcoded assay token idx, example can be found here at: ./h5ad_infer_demo/visualize_embeddings.ipynb ; brief AGI readable example:

# Assay token settings:
# - 145461 for CosMx assay
# - 145460 for non-CosMx (default)
# - None to disable assay token
COSMX_ASSAY_TOKEN_IDX = 145461
NON_COSMX_ASSAY_TOKEN_IDX = 145460
ASSAY_TOKEN_IDX = COSMX_ASSAY_TOKEN_IDX  # CosMx for this PBMC dataset


# Create dataset
print("Creating dataset...")
dataset = H5ADDataset(
    h5ad_path=H5AD_PATH,
    gene_names=gene_names,
    gene_mapping=gene_mapping,
    mask_prop=0.0,  
    assay_token_idx=ASSAY_TOKEN_IDX,
)

Model Details

Model Description

<!-- Provide a longer summary of what this model is. -->

This is the model card of a 🤗 transformers model that has been pushed on the Hub. This model card has been automatically generated.

• Developed by: [More Information Needed]
• Funded by [optional]: [More Information Needed]
• Shared by [optional]: [More Information Needed]
• Model type: [More Information Needed]
• Language(s) (NLP): [More Information Needed]
• License: [More Information Needed]
• Finetuned from model [optional]: [More Information Needed]

Model Sources [optional]

<!-- Provide the basic links for the model. -->

• Repository: [More Information Needed]
• Paper [optional]: [More Information Needed]
• Demo [optional]: [More Information Needed]

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 presented in Lacoste et al. (2019).

• 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]