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Register a new userGenetic Architect: Discovering Genomic Structure with Learned Neural Architectures
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Added by
Sasha Targ
Publication date
2016
fields
Informatics Engineering
and research's language is
English
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Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design architectures to suit it. As such, architectures that fit the structure of genomics should be learned not prescribed. Here, we develop a novel search algorithm, applicable across domains, that discovers an optimal architecture which simultaneously learns general genomic patterns and identifies the most important sequence motifs in predicting functional genomic outcomes. The architectures we find using this algorithm succeed at using only RNA expression data to predict gene regulatory structure, learn human-interpretable visualizations of key sequence motifs, and surpass state-of-the-art results on benchmark genomics challenges.
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Neural Architecture Search (NAS) is a laborious process. Prior work on automated NAS targets mainly on improving accuracy, but lacks consideration of computational resource use. We propose the Resource-Efficient Neural Architect (RENA), an efficient resource-constrained NAS using reinforcement learning with network embedding. RENA uses a policy network to process the network embeddings to generate new configurations. We demonstrate RENA on image recognition and keyword spotting (KWS) problems. RENA can find novel architectures that achieve high performance even with tight resource constraints. For CIFAR10, it achieves 2.95% test error when compute intensity is greater than 100 FLOPs/byte, and 3.87% test error when model size is less than 3M parameters. For Google Speech Commands Dataset, RENA achieves the state-of-the-art accuracy without resource constraints, and it outperforms the optimized architectures with tight resource constraints.
Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA sequence signals and give insights as to why TFs bind to certain locations. In this paper, we propose a toolkit called the Deep Motif Dashboard (DeMo Dashboard) which provides a suite of visualization strategies to extract motifs, or sequence patterns from deep neural network models for TFBS classification. We demonstrate how to visualize and understand three important DNN models: convolutional, recurrent, and convolutional-recurrent networks. Our first visualization method is finding a test sequences saliency map which uses first-order derivatives to describe the importance of each nucleotide in making the final prediction. Second, considering recurrent models make predictions in a temporal manner (from one end of a TFBS sequence to the other), we introduce temporal output scores, indicating the prediction score of a model over time for a sequential input. Lastly, a class-specific visualization strategy finds the optimal input sequence for a given TFBS positive class via stochastic gradient optimization. Our experimental results indicate that a convolutional-recurrent architecture performs the best among the three architectures. The visualization techniques indicate that CNN-RNN makes predictions by modeling both motifs as well as dependencies among them.
Manifold learning methods are an invaluable tool in todays world of increasingly huge datasets. Manifold learning algorithms can discover a much lower-dimensional representation (embedding) of a high-dimensional dataset through non-linear transformations that preserve the most important structure of the original data. State-of-the-art manifold learning methods directly optimise an embedding without mapping between the original space and the discovered embedded space. This makes interpretability - a key requirement in exploratory data analysis - nearly impossible. Recently, genetic programming has emerged as a very promising approach to manifold learning by evolving functional mappings from the original space to an embedding. However, genetic programming-based manifold learning has struggled to match the performance of other approaches. In this work, we propose a new approach to using genetic programming for manifold learning, which preserves local topology. This is expected to significantly improve performance on tasks where local neighbourhood structure (topology) is paramount. We compare our proposed approach with various baseline manifold learning methods and find that it often outperforms other methods, including a clear improvement over previous genetic programming approaches. These results are particularly promising, given the potential interpretability and reusability of the evolved mappings.
Biological evolution has distilled the experiences of many learners into the general learning algorithms of humans. Our novel meta reinforcement learning algorithm MetaGenRL is inspired by this process. MetaGenRL distills the experiences of many complex agents to meta-learn a low-complexity neural objective function that decides how future individuals will learn. Unlike recent meta-RL algorithms, MetaGenRL can generalize to new environments that are entirely different from those used for meta-training. In some cases, it even outperforms human-engineered RL algorithms. MetaGenRL uses off-policy second-order gradients during meta-training that greatly increase its sample efficiency.
The backpropagation of error algorithm (BP) is impossible to implement in a real brain. The recent success of deep networks in machine learning and AI, however, has inspired proposals for understanding how the brain might learn across multiple layers, and hence how it might approximate BP. As of yet, none of these proposals have been rigorously evaluated on tasks where BP-guided deep learning has proved critical, or in architectures more structured than simple fully-connected networks. Here we present results on scaling up biologically motivated models of deep learning on datasets which need deep networks with appropriate architectures to achieve good performance. We present results on the MNIST, CIFAR-10, and ImageNet datasets and explore variants of target-propagation (TP) and feedback alignment (FA) algorithms, and explore performance in both fully- and locally-connected architectures. We also introduce weight-transport-free variants of difference target propagation (DTP) modified to remove backpropagation from the penultimate layer. Many of these algorithms perform well for MNIST, but for CIFAR and ImageNet we find that TP and FA variants perform significantly worse than BP, especially for networks composed of locally connected units, opening questions about whether new architectures and algorithms are required to scale these approaches. Our results and implementation details help establish baselines for biologically motivated deep learning schemes going forward.
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