4,635 research outputs found
TopologyNet: Topology based deep convolutional neural networks for biomolecular property predictions
Although deep learning approaches have had tremendous success in image, video
and audio processing, computer vision, and speech recognition, their
applications to three-dimensional (3D) biomolecular structural data sets have
been hindered by the entangled geometric complexity and biological complexity.
We introduce topology, i.e., element specific persistent homology (ESPH), to
untangle geometric complexity and biological complexity. ESPH represents 3D
complex geometry by one-dimensional (1D) topological invariants and retains
crucial biological information via a multichannel image representation. It is
able to reveal hidden structure-function relationships in biomolecules. We
further integrate ESPH and convolutional neural networks to construct a
multichannel topological neural network (TopologyNet) for the predictions of
protein-ligand binding affinities and protein stability changes upon mutation.
To overcome the limitations to deep learning arising from small and noisy
training sets, we present a multitask topological convolutional neural network
(MT-TCNN). We demonstrate that the present TopologyNet architectures outperform
other state-of-the-art methods in the predictions of protein-ligand binding
affinities, globular protein mutation impacts, and membrane protein mutation
impacts.Comment: 20 pages, 8 figures, 5 table
EIGEN: Ecologically-Inspired GENetic Approach for Neural Network Structure Searching from Scratch
Designing the structure of neural networks is considered one of the most
challenging tasks in deep learning, especially when there is few prior
knowledge about the task domain. In this paper, we propose an
Ecologically-Inspired GENetic (EIGEN) approach that uses the concept of
succession, extinction, mimicry, and gene duplication to search neural network
structure from scratch with poorly initialized simple network and few
constraints forced during the evolution, as we assume no prior knowledge about
the task domain. Specifically, we first use primary succession to rapidly
evolve a population of poorly initialized neural network structures into a more
diverse population, followed by a secondary succession stage for fine-grained
searching based on the networks from the primary succession. Extinction is
applied in both stages to reduce computational cost. Mimicry is employed during
the entire evolution process to help the inferior networks imitate the behavior
of a superior network and gene duplication is utilized to duplicate the learned
blocks of novel structures, both of which help to find better network
structures. Experimental results show that our proposed approach can achieve
similar or better performance compared to the existing genetic approaches with
dramatically reduced computation cost. For example, the network discovered by
our approach on CIFAR-100 dataset achieves 78.1% test accuracy under 120 GPU
hours, compared to 77.0% test accuracy in more than 65, 536 GPU hours in [35].Comment: CVPR 201
Neuroevolution on the Edge of Chaos
Echo state networks represent a special type of recurrent neural networks.
Recent papers stated that the echo state networks maximize their computational
performance on the transition between order and chaos, the so-called edge of
chaos. This work confirms this statement in a comprehensive set of experiments.
Furthermore, the echo state networks are compared to networks evolved via
neuroevolution. The evolved networks outperform the echo state networks,
however, the evolution consumes significant computational resources. It is
demonstrated that echo state networks with local connections combine the best
of both worlds, the simplicity of random echo state networks and the
performance of evolved networks. Finally, it is shown that evolution tends to
stay close to the ordered side of the edge of chaos.Comment: To appear in Proceedings of the Genetic and Evolutionary Computation
Conference 2017 (GECCO '17
Evolution and development of complex computational systems using the paradigm of metabolic computing in Epigenetic Tracking
Epigenetic Tracking (ET) is an Artificial Embryology system which allows for
the evolution and development of large complex structures built from artificial
cells. In terms of the number of cells, the complexity of the bodies generated
with ET is comparable with the complexity of biological organisms. We have
previously used ET to simulate the growth of multicellular bodies with
arbitrary 3-dimensional shapes which perform computation using the paradigm of
"metabolic computing". In this paper we investigate the memory capacity of such
computational structures and analyse the trade-off between shape and
computation. We now plan to build on these foundations to create a
biologically-inspired model in which the encoding of the phenotype is efficient
(in terms of the compactness of the genome) and evolvable in tasks involving
non-trivial computation, robust to damage and capable of self-maintenance and
self-repair.Comment: In Proceedings Wivace 2013, arXiv:1309.712
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