52,321 research outputs found
End-to-End Differentiable Proving
We introduce neural networks for end-to-end differentiable proving of queries
to knowledge bases by operating on dense vector representations of symbols.
These neural networks are constructed recursively by taking inspiration from
the backward chaining algorithm as used in Prolog. Specifically, we replace
symbolic unification with a differentiable computation on vector
representations of symbols using a radial basis function kernel, thereby
combining symbolic reasoning with learning subsymbolic vector representations.
By using gradient descent, the resulting neural network can be trained to infer
facts from a given incomplete knowledge base. It learns to (i) place
representations of similar symbols in close proximity in a vector space, (ii)
make use of such similarities to prove queries, (iii) induce logical rules, and
(iv) use provided and induced logical rules for multi-hop reasoning. We
demonstrate that this architecture outperforms ComplEx, a state-of-the-art
neural link prediction model, on three out of four benchmark knowledge bases
while at the same time inducing interpretable function-free first-order logic
rules.Comment: NIPS 2017 camera-ready, NIPS 201
Learning Interpretable Rules for Multi-label Classification
Multi-label classification (MLC) is a supervised learning problem in which,
contrary to standard multiclass classification, an instance can be associated
with several class labels simultaneously. In this chapter, we advocate a
rule-based approach to multi-label classification. Rule learning algorithms are
often employed when one is not only interested in accurate predictions, but
also requires an interpretable theory that can be understood, analyzed, and
qualitatively evaluated by domain experts. Ideally, by revealing patterns and
regularities contained in the data, a rule-based theory yields new insights in
the application domain. Recently, several authors have started to investigate
how rule-based models can be used for modeling multi-label data. Discussing
this task in detail, we highlight some of the problems that make rule learning
considerably more challenging for MLC than for conventional classification.
While mainly focusing on our own previous work, we also provide a short
overview of related work in this area.Comment: Preprint version. To appear in: Explainable and Interpretable Models
in Computer Vision and Machine Learning. The Springer Series on Challenges in
Machine Learning. Springer (2018). See
http://www.ke.tu-darmstadt.de/bibtex/publications/show/3077 for further
informatio
Integration of molecular network data reconstructs Gene Ontology.
Motivation: Recently, a shift was made from using Gene Ontology (GO) to evaluate molecular network data to using these data to construct and evaluate GO. Dutkowski et al. provide the first evidence that a large part of GO can be reconstructed solely from topologies of molecular networks. Motivated by this work, we develop a novel data integration framework that integrates multiple types of molecular network data to reconstruct and update GO. We ask how much of GO can be recovered by integrating various molecular interaction data. Results: We introduce a computational framework for integration of various biological networks using penalized non-negative matrix tri-factorization (PNMTF). It takes all network data in a matrix form and performs simultaneous clustering of genes and GO terms, inducing new relations between genes and GO terms (annotations) and between GO terms themselves. To improve the accuracy of our predicted relations, we extend the integration methodology to include additional topological information represented as the similarity in wiring around non-interacting genes. Surprisingly, by integrating topologies of bakers’ yeasts protein–protein interaction, genetic interaction (GI) and co-expression networks, our method reports as related 96% of GO terms that are directly related in GO. The inclusion of the wiring similarity of non-interacting genes contributes 6% to this large GO term association capture. Furthermore, we use our method to infer new relationships between GO terms solely from the topologies of these networks and validate 44% of our predictions in the literature. In addition, our integration method reproduces 48% of cellular component, 41% of molecular function and 41% of biological process GO terms, outperforming the previous method in the former two domains of GO. Finally, we predict new GO annotations of yeast genes and validate our predictions through GIs profiling. Availability and implementation: Supplementary Tables of new GO term associations and predicted gene annotations are available at http://bio-nets.doc.ic.ac.uk/GO-Reconstruction/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online
Taxonomy Induction using Hypernym Subsequences
We propose a novel, semi-supervised approach towards domain taxonomy
induction from an input vocabulary of seed terms. Unlike all previous
approaches, which typically extract direct hypernym edges for terms, our
approach utilizes a novel probabilistic framework to extract hypernym
subsequences. Taxonomy induction from extracted subsequences is cast as an
instance of the minimumcost flow problem on a carefully designed directed
graph. Through experiments, we demonstrate that our approach outperforms
stateof- the-art taxonomy induction approaches across four languages.
Importantly, we also show that our approach is robust to the presence of noise
in the input vocabulary. To the best of our knowledge, no previous approaches
have been empirically proven to manifest noise-robustness in the input
vocabulary
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