pytorch-tutorial
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Python | Python | |
MIT License | GNU General Public License v3.0 or later |
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pytorch-tutorial
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PyTorch - What does contiguous() do?
I was going through this example of a LSTM language model on github (link).What it does in general is pretty clear to me. But I'm still struggling to understand what calling contiguous() does, which occurs several times in the code.
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How to 'practice' pytorch after finishing its basic tutorial?
I tried to move straight to practicing implementing papers and trying to understand other people's codes but failed miserably. I feel like there was too much of a gap between the basic tutorial and being able to implement ideas into code....hence the question: Is there any resource/way to practice pytorch in general? I did find this and this, but I just wanted to hear what others have gone through to become better at PyTorch up to the point they can build stuff from their own ideas
- [P] Probabilistic Machine Learning: An Introduction, Kevin Murphy's 2021 e-textbook is out
bonito
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miRNA Detection
There is a technology called Nanopore. I’ve never used it myself but the concept was to be able to sequence samples of nucleic acid out in the field. A quick pubmed search indicated that it can detect miRNA, but maybe with some modifications. https://nanoporetech.com Best of luck with it!
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Oxford University Press’s new logo is unfathomably bad
> An unpopular opinion: there are too many other logos that look like the original logo
There are also too many logos that look like the new logo. The first blue circle logos that spring to mind are Blue Circle Cement/Tarmac/Lafarge [1] and Oxford Nanopore [2].
[1]: https://en.wikipedia.org/wiki/Tarmac_(company)
[2]: https://nanoporetech.com/
- PORTABLE DNA SEQUENCER!!!!
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Ask HN: Who is hiring? (May 2022)
Oxford Nanopore Technologies (https://nanoporetech.com/) | Front end developer | Full-time | Oxford | Remote (UK)
Oxford Nanopore Technologies is headquartered at the Oxford Science Park outside Oxford, UK, with satellite offices and commercial presence in many global locations across the US, APAC and Europe. Our DNA/RNA sequencing platform is the only technology that offers real-time analysis (for rapid insights), in fully scalable formats from pocket to population scale. Our goal is to enable the analysis of any living thing, by anyone, anywhere.
Tech stack: Electron, Stencil, React, Typescript, RxJS, GRPC
For more details, please email: [email protected]
- El primer genoma completo de un ser humano abre una nueva era en la ciencia
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Buying artificial membranes
Ok this isn't really my area but I know that there are labs/companies performing these types of electrical current disturbance measurements of membrane-type proteins for both DNA sequencing (https://nanoporetech.com/) and protein sequencing (https://www.nature.com/articles/s41587-019-0401-y).
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ELI5: Why home blood tests do not exist, while we can measure our sugar levels with personal devices at home?
Now nanopore sequencing is solid state and gets much longer reads. https://nanoporetech.com/ and https://en.wikipedia.org/wiki/Nanopore_sequencing
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Raw nanowire sequencer data
Also best of luck with the basecaller, I will say that the latest guppy versions are very good, both in terms of accuracy and speed, as they are GPU accelerated and the best I've seen in accuracy. You may also be interested in Bonito, a tool to generate your own GPU basecalling model or tweak existing models to your data. https://github.com/nanoporetech/bonito.
What are some alternatives?
mixture-of-experts - PyTorch Re-Implementation of "The Sparsely-Gated Mixture-of-Experts Layer" by Noam Shazeer et al. https://arxiv.org/abs/1701.06538
transformers - 🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.
InceptionTime - InceptionTime: Finding AlexNet for Time Series Classification
NanoSim - Nanopore sequence read simulator
Conv-TasNet - A PyTorch implementation of Conv-TasNet described in "TasNet: Surpassing Ideal Time-Frequency Masking for Speech Separation" with Permutation Invariant Training (PIT).
fossa-cli - Fast, portable and reliable dependency analysis for any codebase. Supports license & vulnerability scanning for large monoliths. Language-agnostic; integrates with 20+ build systems.
pytorch-grad-cam - Advanced AI Explainability for computer vision. Support for CNNs, Vision Transformers, Classification, Object detection, Segmentation, Image similarity and more.
yolov5 - YOLOv5 🚀 in PyTorch > ONNX > CoreML > TFLite
BigGAN-PyTorch - The author's officially unofficial PyTorch BigGAN implementation.
pipeline-structural-variation - Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
OpenNMT-py - Open Source Neural Machine Translation and (Large) Language Models in PyTorch
Real-Time-Voice-Cloning - Clone a voice in 5 seconds to generate arbitrary speech in real-time