Monthly Archives: April 2024

Exploring multilingual programming

Python is a prominent language in the ML and scientific computing space, and for good reason. Python is easy-to-learn and readable, and it offers a vast selection of libraries such as NumPy for numerical computation, Pandas for data manipulation, SciPy for scientific computing, TensorFlow, and PyTorch for deep learning, along with RDKit and Open Babel for cheminformatics. It is understandably an appealing choice for developers and researchers alike. However, a closer look at many common Python libraries reveals their foundations in C++. 

Revisiting C++ Advantages

Many of Python libraries including TensorFlow, PyTorch, and RDKit are all heavily-reliant on C++. C++ allows developers to manage memory and CPU resources more effectively than Python, making it a good choice when handling large volumes of data at a fast pace. A previous post on this blog discusses C++’s speed, its utility in GPU programming through CUDA, and the complexities of managing its libraries. Despite the steeper learning curve and verbosity compared to Python, the performance benefits of C++ are undeniable, especially in contexts where execution speed and memory management are critical.

Rust: A New Contender for High-Performance Computing

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Mounting a remote file system with SSHFS

If you’re working with data stored on a remote server, you might not want to (or even have the space to) copy data to your local file system when you work on it. Instead, we can use SSHFS to mount a remote file system via SSH, allowing us to read and write data on the remote file system without manually copying files.

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Quickly (and lazily) scale your data processing in Python

Do you use pandas for your data processing/wrangling? If you do, and your code involves any data-heavy steps such as data generation, exploding operations, featurization, etc, then it can quickly become inconvenient to test your code.

  • Inconvenient compute times (>tens of minutes). Perhaps fine for a one-off, but over repeated test iterations your efficiency and focus will take a hit.
  • Inconvenient memory usage. Perhaps your dataset is too large for memory, or loads in but then causes an OOM error during a mid-operation memory spike.
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Mapping derivative compounds to parent hits

Whereas it is easy to say in a paper “Given the HT-Sequential-ITC results, 42 led to 113, a substituted decahydro-2,6-methanocyclopropa[f]indene”, it is frequently rather trickier algorithmically figure out which atoms map to which. In Fragmenstein, for the placement route, for example, a lot goes on behind the scenes, yet for some cases human provided mapping may be required. Here I discuss how to get the mapping from Fragmenstein and what goes on behind the scenes.

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Conference Summary: MGMS Adaptive Immune Receptors Meeting 2024

On 5th April 2024, over 60 researchers braved the train strikes and gusty weather to gather at Lady Margaret Hall in Oxford and engage in a day full of scientific talks, posters and discussions on the topic of adaptive immune receptor (AIR) analysis!

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How to write a review paper as a first year PhD student

As a first year PhD student, it is not an uncommon thing to be asked to write a review paper on your subject area. It is both a great way to get acquainted with your research field and to get the background portion of your thesis completed early. However, it can seem like a daunting task to go from knowing almost nothing about your research field to producing something of interest for experts who have spent years studying your subject matter.

In my first year, I was exactly in this position and I found very little online to help guide this process. Thus, here is my reflective look at writing a review paper that will hopefully help someone else in the future.

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How can FemTech help close the gender health gap?

An excellent previous blog post from Sarah [1] describes the gender data gap and touches on the fact that women experience poorer healthcare outcomes. This arises from, amongst other things, the historical exclusion of women from clinical trials and this idea of the ‘male default’, where, for example, drug dosages and diagnostic thresholds are benchmarked against men, or even surgical instruments are designed to fit male hands [2]. I thought I would follow up on Sarah’s blog post and discuss how FemTech can help to close this gender health gap.

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Inverse Vaccines

One of the nice things about OPIG, is that you can talk about something which is outside of your wheelhouse without feeling that the specialists in the group are going to eat your lunch. Last week, I gave an overview of the Hubbell group‘s Nature paper Synthetically glycosylated antigens for the antigen-specific suppression of established immune responses. I am not an immunologist by any stretch of the imagination, but sometimes you come across a piece of really interesting science and just want to say to people: Have you seen this, look at this, it’s really clever!

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Using JAX and Haiku to build a Graph Neural Network

JAX

Last year, I had an opportunity to delve into the world of JAX whilst working at InstaDeep. My first blopig post seems like an ideal time to share some of that knowledge. JAX is an experimental Python library created by Google’s DeepMind for applying accelerated differentiation. JAX can be used to differentiate functions written in NumPy or native Python, just-in-time compile and execute functions on GPUs and TPUs with XLA, and mini-batch repetitious functions with vectorization. Collectively, these qualities place JAX as an ideal candidate for accelerated deep learning research [1].

JAX is inspired by the NumPy API, making usage very familiar for any Python user who has already worked with NumPy [2]. However, unlike NumPy, JAX arrays are immutable; once they are assigned in memory they cannot be changed. As such, JAX includes specific syntax for index manipulation. In the code below, we create a JAX array and change the 1^{st} element to a 4:

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Useful metrics and their meanings

Short and selfish blog here. Probably been done before, but I shall carry on regardless. I am going to review some metrics relevant to our area of Immunoinformatics. In other words, I will try dissect things such as perplexity, logits, pTM, pLDDT and the ABodyBuilder2 confidence score. These numbers can help inform us on the likelihood of predictions, and whether we should have confidence in them.

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