Low Data Drug Discovery with One-shot Learning Low Data Drug Discovery with One-shot Learning
Paper summary The goal of one-shot learning tasks is to design a learning structure that can perform a new task (or, more canonically, add a new class to an existing task) using only one a small number of examples of the new task or class. So, as an example: you'd want to be able to take one positive and one negative example of a given task and correctly classify subsequent points as either positive or negative. A common way of achieving this, and the way that the paper builds on, is to learn a parametrized function projecting both your labeled points (your "support set") and your unlabeled point (your "query") into an embedding space, and then assigning a class to your query according to how close it is to the support set points associated with each label. The hope is that, in the course of training on different but similar tasks, you've learned a metric space where nearby things tend to be of similar classes. This method is called a "matching network". This paper has the specific objective of using such one-shot methods for drug discovery, and evaluates on tasks drawn from that domain, but most of the mechanics of the paper can be understood without reference to molecular dat in particular. In the simplest version of such a network, the query and support set points are embedded unconditionally - meaning that the query would be embedded in the same way regardless of the values in the support set, and that each point in the support set would be embedded without knowledge of each other. However, given how little data we're giving our model to work with, it might be valuable to allow our query embedder (f(x)) and support set embedder (g(x)) to depend on the values within the support set. Prior work had achieved this by: 1) Creating initial f'(x) and g'(x) query and support embedders. 2) Concatenating the embedded support points g'(x) into a single vector and running a bidirectional LSTM over the concatenation, which results in a representation g(x) of each input that incorporates information from g'(x_i) for all other x_i (albeit in a way that imposes a concatenation ordering that may not correspond to a meaningful order) 3) Calculating f(x) of your embedding point by using an attention mechanism to combine f'(x) with the contextualized embeddings g(x) The authors of the current paper argue that this approach is suboptimal because of the artificially imposed ordering, and because it calculated g(x) prior to f(x) using asymmetrical model structures (though it's not super clear why this latter point is a problem). Instead, they propose a somewhat elaborate and difficult-to-follow attention based mechanism. As best as I can understand, this is what they're suggesting: https://i.imgur.com/4DLWh8H.png 1) Update the query embedding f(x) by calculating an attention distribution over the vector current embeddings of support set points (here referred to as bolded <r>), pooling downward to a single aggregate embedding vector r, and then using a LSTM that takes in that aggregate vector and the prior update to generate a new update. This update, dz, is added to the existing query embedding estimate to get a new one 2) Update the vector of support set embeddings by iteratively calculating an attention mapping between the vector of current support set embeddings and the original features g'(S), and using that attention mapping to create a new <r>, which, similar to the above, is fed into an LSTM to calculate the next update. Since the model is evaluated on molecular tasks, all of the embedding functions are structured as graph convolutions. Other than the obvious fact that attention is a great way of aggregating information in an order-independent way, the authors give disappointingly little justification of why they would expect their method to work meaningfully better than past approaches. Empirically, they do find that it performs slightly better than prior contextualized matching networks on held out tasks of predicting toxicity and side effects with only a small number from the held out task. However, neither this paper's new method nor previous one-shot learning work is able to perform very well on the challenging MUV dataset, where held-out binding tasks involve structurally dissimilar molecules from those seen during training, suggesting that whatever generalization this method is able to achieve doesn't quite rise to the task of making inferences based on molecules with different structures.
Low Data Drug Discovery with One-shot Learning
Altae-Tran, Han and Ramsundar, Bharath and Pappu, Aneesh S. and Pande, Vijay S.
arXiv e-Print archive - 2016 via Local Bibsonomy
Keywords: dblp

Summary by CodyWild 1 month ago
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