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dlomix-0.0.4
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مشاهده بیشترتوضیحات
Deep Learning for Proteomics
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | dlomix-0.0.4 |
| نام | dlomix |
| نسخه کتابخانه | 0.0.4 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Omar Shouman |
| ایمیل نویسنده | o.shouman@tum.de |
| آدرس صفحه اصلی | https://github.com/wilhelm-lab/dlomix |
| آدرس اینترنتی | https://pypi.org/project/dlomix/ |
| مجوز | - |
# DLOmix
[](https://dlomix.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/wilhelm-lab/dlomix/actions/workflows/build.yaml)
[](https://github.com/wilhelm-lab/dlomix/actions/workflows/pypi.yaml)
**DLOmix** is a python framework for Deep Learning in Proteomics. Initially built ontop of TensorFlow/Keras, support for PyTorch can however be integrated once the main API is established.
## Usage
Experiment a simple retention time prediction use-case using Google Colab [](https://colab.research.google.com/github/wilhelm-lab/dlomix/blob/develop/notebooks/Example_RTModel_Walkthrough_colab.ipynb)
A version that includes experiment tracking with [Weights and Biases](https://www.wandb.ai) is available here [](https://colab.research.google.com/github/wilhelm-lab/dlomix/blob/develop/notebooks/Example_RTModel_Walkthrough_colab-weights-and-biases.ipynb)
**Resources Repository**
More learning resources can be found in the [dlomix-resources](https://github.com/wilhelm-lab/dlomix-resources) repository.
## Installation
Run the following to install:
```bash
$ pip install dlomix
```
**General Overview**
- `data`: structures for modelling the input data, currently based on `tf.Dataset`
- `eval`: classes for evaluating models and reporting results
- `layers`: custom layers used for building models, based on `tf.keras.layers.Layer`
- `losses`: custom losses to be use for training with `model.fit()`
- `models`: common model architectures for the relevant use-cases based on `tf.keras.Model` to allow for using the Keras training API
- `pipelines`: an exemplary high-level pipeline implementation
- `reports`: classes for generating reports related to the different tasks
- `constants.py`: constants and configuration values
- `utils.py`: utility functions
**Use-cases**
- Retention Time Prediction:
- a regression problem where the the retention time of a peptide sequence is to be predicted.
**To-Do**
Functionality:
- [X] integrate prosit
- [ ] extend pipeline for different types of models and backbones
- [ ] extend pipeline to allow for fine-tuning with custom datasets
- [X] add residual plots to reporting, possibly other regression analysis tools
- [X] output reporting results as PDF
- [ ] extend data representation to include modifications
Package structure:
- [X] integrate `deeplc.py` into `models.py`, preferably introduce a package structure (e.g. `models.retention_time`)
- [X] add references for implemented models in the ReadMe
- [ ] introduce a style guide and checking (e.g. PEP)
- [X] plan documentation (sphinx and readthedocs)
## Developing DLOmix
To install dlomix, along with the the tools needed to develop and run tests, run the following command in your virtualenv:
```bash
$ pip install -e .[dev]
```
**References:**
[**Prosit**]
[1] Gessulat, S., Schmidt, T., Zolg, D. P., Samaras, P., Schnatbaum, K., Zerweck, J., ... & Wilhelm, M. (2019). Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nature methods, 16(6), 509-518.
[**DeepLC**]
[2] DeepLC can predict retention times for peptides that carry as-yet unseen modifications
Robbin Bouwmeester, Ralf Gabriels, Niels Hulstaert, Lennart Martens, Sven Degroeve
bioRxiv 2020.03.28.013003; doi: 10.1101/2020.03.28.013003
[3] Bouwmeester, R., Gabriels, R., Hulstaert, N. et al. DeepLC can predict retention times for peptides that carry as-yet unseen modifications. Nat Methods 18, 1363–1369 (2021). https://doi.org/10.1038/s41592-021-01301-5
نیازمندی
| مقدار | نام |
|---|---|
| - | fpdf |
| - | pandas |
| - | numpy |
| - | matplotlib |
| - | scikit-learn |
| - | tensorflow |
| - | pyarrow |
| - | seaborn |
| >=3.7 | pytest |
| - | pytest-cov |
| - | black |
| - | twine |
| - | setuptools |
| - | wheel |
| - | pylint |
نحوه نصب
نصب پکیج whl dlomix-0.0.4:
pip install dlomix-0.0.4.whl
نصب پکیج tar.gz dlomix-0.0.4:
pip install dlomix-0.0.4.tar.gz