Anthony Gitter

mlf-core: a framework for deterministic machine learning

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This paper dives into sources of non-determinism in machine learning frameworks: https://arxiv.org/abs/2104.07651 It would be a great reference for our paragraph that starts > One specific reproducibility pitfall that is...

The Secrets of Machine Learning: Ten Things You Wish You Had Known Earlier to be More Effective at Data Analysis

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https://arxiv.org/abs/1906.01998 > Despite the widespread usage of machine learning throughout organizations, there are some key principles that are commonly missed. In particular: 1) There are at least four main families...

This commentary covers some pitfalls of deep learning in biology and calls for better benchmarking > Machine learning is a branch of artificial intelligence (AI) involving computer programs that are...

Review all tips for relevance to deep learning and biology

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To keep the scope of this article focused, the tips should be about deep learning in biology. Several tips only pertain to one or the other. I recommend we add...

**Have you checked the [list of proposed tips](https://github.com/Benjamin-Lee/deep-rules/issues?q=is%3Aissue+is%3Aopen+label%3Atip) to see if the tip has already been proposed?** - [x] Yes **Did you add yourself as a [contributor](https://github.com/Benjamin-Lee/deep-rules/blob/master/contributors.md) by making a...

Deep learning in bioinformatics: introduction, application, and perspective in big data era

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https://doi.org/10.1101/563601 This is a (yet another) review article that may be of interest because they provide eight examples of representative deep learning problems in biology: https://github.com/lykaust15/Deep_learning_examples It doesn't look like...

Feature engineering is still (or is no longer) important

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**Have you checked the [list of proposed rules](https://github.com/Benjamin-Lee/deep-rules/issues?q=is%3Aissue+is%3Aopen+label%3Arule) to see if the rule has already been proposed?** - [x] Yes **Did you add yourself as a [contributor](https://github.com/Benjamin-Lee/deep-rules/blob/master/contributors.md) by making a...

A primer on deep learning in genomics

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https://doi.org/10.1038/s41588-018-0295-5 > Deep learning methods are a class of machine learning techniques capable of identifying highly complex patterns in large datasets. Here, we provide a perspective and primer on deep...

Citation Typing Ontology (CiTO) annotation support

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This issue summarizes some of the discussion in a recent [Twitter thread](https://twitter.com/cthoyt/status/1372243571978481666) about options for supporting [CiTO annotations](http://doi.org/10.1186/2041-1480-1-S1-S6) in Manubot. The most promising lead is the [cito lua filter](https://github.com/pandoc/lua-filters/tree/master/cito) for...

Because the manuscript git repository has access to the commit history, it could automatically suggest a list of manuscript authors. Adding authors to the official list in the metadata should...