Category Archives: How To

How to do things. doh.

Understanding GPU parallelization in deep learning

Deep learning has proven to be the season’s favourite for biology: every other week, an interesting biological problem is solved by clever application of neural networks. Yet, as more challenges get cracked, modern research shifts more and more in the direction of larger models — meaning that increasing computational resources are required for training. Unsurprisingly, NVIDIA, the main manufacturer of GPUs, experienced a significant jump in their stock price earlier this year.

Access to compute is not enough to train good neural networks. As soon as multiple cards enter into play, researchers need to use a completely different paradigm where data and model weights are distributed across different devices — and sometimes even different computers. Though these tools start to be crucial for successful computational biology research, they are generally unknown to researchers. Hence, in this blogpost, I would like to provide a really brief introduction to multi-GPU training.

Continue reading

SSH, the boss-fight level: Jupyter notebooks from compute nodes

Secure shell (SSH) is an essential tool for remote operations. However, not everything with it is smooth-sailing. Especially, when you want to do things like reverse–port-forwarding via a proxy-hump or two a Jupyter notebook to your local machine from a compute node on a no-home container . Even if it sounds less plausible than the exploits on Mr Robot, it actually can work and requires zero social-engineering or sneaking in server rooms to install Raspberry Pis while using a baseball cap as a disguise.

Continue reading

Conference feedback — with a difference

At OPIG Group Meetings, it’s customary to give “Conference Feedback” whenever any of us has recently attended a conference. Typically, people highlight the most interesting talks—either to them or others in the group.

Having just returned from the 6th RSC-BMCS / RSC-CICAG AI in Chemistry Symposium, it was my turn last week. But instead of the usual perspective—of an attendee—I spoke briefly about how to organize a conference.

Continue reading

Deploying a Flask app part I: the gunicorn WSGI server

Last year I wrote a post about deploying Flask apps with Apache/mod_wsgi when your app’s dependencies are installed in a conda environment. The year before, in the dark times, I wrote a post about the black magic invocations required to get multiple apps running stably using mod_wsgi. I’ve since moved away from mod_wsgi entirely and switched to running Flask apps from containers using the gunicorn WSGI server behind an Apache reverse proxy, which has made life immeasurably easier. In this post we’ll cover running a Flask app on localhost using gunicorn; in Part II we’ll run our app as a service using Singularity and deploy it to production using Apache as a HTTP proxy server.

Continue reading

GitHub.dev: Just press “.”

GitHub.dev is an incredibly useful feature in GitHub which allows you to view and edit code directly on the browser as a remote VSCode session.

To access this remote VSCode session, either:

  1. Press “.”
  2. Change “.com” to “.dev” in the URL

This is a great way to quickly explore someone’s code without having to clone it onto your machine or go through the GitHub UI.

Current strategies to predict structures of multiple protein conformational states

Since the release of AlphaFold2 (AF2), the problem of protein structure prediction is widely believed to be solved. Current structure prediction tools, such as AF2, are able to model most proteins with high accuracy. These methods, however, have a major limitation as they have been trained to predict a single structure for a given protein. Proteins are highly dynamic molecules, and their function often depends on transitions between several conformational states. Despite research focusing on the task of predicting the structures of multiple conformations of a protein, currently, no accurate and reliable method is available. In this blog post, I will provide a short overview of the strategies developed for predicting protein conformations. I have grouped these into three sets of related approaches. To conclude, I will also demonstrate how to run one of these strategies on your own.

Continue reading

LightningCLI, my new best friend

If you’ve ever worked on machine learning projects, you’ll know that training models is just one aspect of the process. Code setup, configuration management, and ensuring reproducibility can also take up a lot of time. I’m a big fan of PyTorch Lightning primarily because it hides most of the boilerplate code you usually need, making your code more modular and readable. It even allows you to train your models on multiple GPUs with ease. All of this comes with the minor trade-off of learning an intuitive API, which can be easily extended to tweak any low-level details for those rare cases where the standard API falls short.

However, despite finding PyTorch Lightning incredibly useful, there’s one aspect that has always bothered me: the configuration of the model and training hyperparameters in a flexible and reproducible manner. In my view, the best approach to address this is to use configuration files for the various modules involved. These files can be easily overridden at runtime using command-line arguments or environment variables. To achieve this, I developed my own packages, configfile and argParseFromDoc, which facilitates this process.

But now, there’s a tool within the Lightning suite that offers all these features in a seamlessly integrated package. Allow me to introduce you to LightningCLI. This tool streamlines the process of hyperparameter configuration, making it both flexible and reproducible. With LightningCLI, you get the best of both worlds: the power of PyTorch Lightning and a hassle-free setup.

The core idea here is to write a config file (or several) that contains the required parameters for the trainer, the model and the dataset. This is done as yaml files with the following structure.

trainer:
  logger: true
  ...
model:
  out_dim: 10
  learning_rate: 0.02
data:
  data_dir: ./
  image_size: 256
ckpt_path: null

Where the yaml fields should correspond to the parameters of the PytorchLightning Trainer, and your custom Model and Data classes, that inherit from LightningModule and LightningDataModule. So a full self-contained example could be

import lightning.pytorch as pl
from lightning.pytorch.cli import LightningCLI
class MyModel(pl.LightningModule):
    def __init__(self, out_dim: int, learning_rate: float):
        super().__init__()
        self.save_hyperparameters()
        self.out_dim = out_dim
        self.learning_rate = learning_rate
        self.model = create_my_model(out_dim)
    def training_step(self, batch, batch_idx):
        out = self.model(batch.x)
        loss = self.compute_loss(out, batch.y)
        return loss
class MyDataModule(pl.LightningDataModule):
    def __init__(self, data_dir: str, image_size: int):
        super().__init__()
        self.data_dir = data_dir
        self.image_size = image_size
    def train_dataloader(self):
        return create_dataloader(self.image_size, self.data_dir)

def main():
    cli = LightningCLI(model_class=MyModel, datamodule_class=MyDataModule)
if __name__ == "__main__":
    main()

That can be run easily as

python scrip.py --config config.yaml fit

What is even better is that you can split the configuration into several config files and that the configuration files can refer to Python classes to be instantiated, making this configuration system so flexible that you can literally configure everything you can imagine.

model:
  class_path: model.MyModel2
  init_args:
    learning_rate: 0.2
    loss:
      class_path: torch.nn.CrossEntropyLoss
      init_args:
        reduction: mean

In conclusion, LightningCLI brings the convenience of configuration management, command-line flexibility, and reproducibility to your PyTorch Lightning projects. With simple yet powerful features, it’s a tool that should be part of any machine learning engineer’s toolkit.

The dangers of Conda-Pack and OpenMM

If you are running lots of little jobs in SLURM and want to make use of free nodes that suddenly become available, it is helpful to have a way of rapidly shipping your environments that does not rely on installing conda or rebuilding the environment from scratch every time. This is useful with complex rebuilds where exported .yml files do not always work as expected, even when specifying exact versions and source locations.

In these situations a tool such a conda-pack becomes incredibly useful. Once you have perfected the house of cards that is your conda environment, you can use conda-pack to save that exact state as a tar.gz file.

conda-pack -n my_precious_env -o my_precious_env.tar.gz

This can provide you with a backup to be used when you accidentally delete conda from your system, or if you irreparable corrupt the environment and cannot roll back to the point in time when everything worked. These tar.gz files can also be copied to distant locations by the use of rsync or scp, unpacked, sourced and used without installing conda…

Continue reading

What can you do with the OPIG Immunoinformatics Suite? v3.0

OPIG’s growing immunoinformatics team continues to develop and openly distribute a wide variety of databases and software packages for antibody/nanobody/T-cell receptor analysis. Below is a summary of all the latest updates (follows on from v1.0 and v2.0).

Continue reading

Exploring the Observed Antibody Space (OAS)

The Observed Antibody Space (OAS) [1,2] is an amazing resource for investigating observed antibodies or as a resource for training antibody specific models, however; its size (over 2.4 billion unpaired and 1.5 million paired antibody sequences as of June 2023) can make it painful to work with. Additionally, OAS is extremely information rich, having nearly 100 columns for each antibody heavy or light chain, further complicating how to handle the data. 

From spending a lot of time working with OAS, I wanted to share a few tricks and insights, which I hope will reduce the pain and increase the joy of working with OAS!

Continue reading