2,506 research outputs found
Learning Edge Representations via Low-Rank Asymmetric Projections
We propose a new method for embedding graphs while preserving directed edge
information. Learning such continuous-space vector representations (or
embeddings) of nodes in a graph is an important first step for using network
information (from social networks, user-item graphs, knowledge bases, etc.) in
many machine learning tasks.
Unlike previous work, we (1) explicitly model an edge as a function of node
embeddings, and we (2) propose a novel objective, the "graph likelihood", which
contrasts information from sampled random walks with non-existent edges.
Individually, both of these contributions improve the learned representations,
especially when there are memory constraints on the total size of the
embeddings. When combined, our contributions enable us to significantly improve
the state-of-the-art by learning more concise representations that better
preserve the graph structure.
We evaluate our method on a variety of link-prediction task including social
networks, collaboration networks, and protein interactions, showing that our
proposed method learn representations with error reductions of up to 76% and
55%, on directed and undirected graphs. In addition, we show that the
representations learned by our method are quite space efficient, producing
embeddings which have higher structure-preserving accuracy but are 10 times
smaller
Investigating the biological relevance in trained embedding representations of protein sequences
As genome sequencing is becoming faster and cheaper, an abundance of DNA and protein sequence data is available. However, experimental annotation of structural or functional information develops at a much slower pace. Therefore, machine learning techniques have been widely adopted to make accurate predictions on unseen sequence data. In recent years, deep learning has been gaining popularity, as it allows for effective end-to-end learning. One consideration for its application on sequence data is the choice for a suitable and effective sequence representation strategy. In this paper, we investigate the significance of three common encoding schemes on the multi-label prediction problem of Gene Ontology (GO) term annotation, namely a one-hot encoding, an ad-hoc trainable embedding, and pre-trained protein vectors, using different hyper-parameters. We found that traditional unigram one-hot encodings achieved very good results, only slightly outperformed by unigram ad-hoc trainable embeddings and bigram pre-trained embeddings (by at most 3%for the F maxscore), suggesting the exploration of different encoding strategies to be potentially beneficial. Most interestingly, when analyzing and visualizing the trained embeddings, we found that biologically relevant (dis)similarities between amino acid n-grams were implicitly learned, which were consistent with their physiochemical properties
Machine learning-guided directed evolution for protein engineering
Machine learning (ML)-guided directed evolution is a new paradigm for
biological design that enables optimization of complex functions. ML methods
use data to predict how sequence maps to function without requiring a detailed
model of the underlying physics or biological pathways. To demonstrate
ML-guided directed evolution, we introduce the steps required to build ML
sequence-function models and use them to guide engineering, making
recommendations at each stage. This review covers basic concepts relevant to
using ML for protein engineering as well as the current literature and
applications of this new engineering paradigm. ML methods accelerate directed
evolution by learning from information contained in all measured variants and
using that information to select sequences that are likely to be improved. We
then provide two case studies that demonstrate the ML-guided directed evolution
process. We also look to future opportunities where ML will enable discovery of
new protein functions and uncover the relationship between protein sequence and
function.Comment: Made significant revisions to focus on aspects most relevant to
applying machine learning to speed up directed evolutio
LASAGNE: Locality And Structure Aware Graph Node Embedding
In this work we propose Lasagne, a methodology to learn locality and
structure aware graph node embeddings in an unsupervised way. In particular, we
show that the performance of existing random-walk based approaches depends
strongly on the structural properties of the graph, e.g., the size of the
graph, whether the graph has a flat or upward-sloping Network Community Profile
(NCP), whether the graph is expander-like, whether the classes of interest are
more k-core-like or more peripheral, etc. For larger graphs with flat NCPs that
are strongly expander-like, existing methods lead to random walks that expand
rapidly, touching many dissimilar nodes, thereby leading to lower-quality
vector representations that are less useful for downstream tasks. Rather than
relying on global random walks or neighbors within fixed hop distances, Lasagne
exploits strongly local Approximate Personalized PageRank stationary
distributions to more precisely engineer local information into node
embeddings. This leads, in particular, to more meaningful and more useful
vector representations of nodes in poorly-structured graphs. We show that
Lasagne leads to significant improvement in downstream multi-label
classification for larger graphs with flat NCPs, that it is comparable for
smaller graphs with upward-sloping NCPs, and that is comparable to existing
methods for link prediction tasks
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