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Charles Siegel

Publications and source records attributed to Charles Siegel.

17 recordsLinked to original sources
arXiv2019

Recombination of Artificial Neural Networks

We propose a genetic algorithm (GA) for hyperparameter optimization of artificial neural networks which includes chromosomal crossover as well as a decoupling of parameters (i.e., weights and biases) from hyperparameters (e.g., learning rate, weight decay, and dropout) during sexual reproduction. Children are produced from three parents; two contributing hyperparameters and one contributing the parameters. Our version of population-based training (PBT) combines traditional gradient-based approaches such as stochastic gradient descent (SGD) with our GA to optimize both parameters and hyperparameters across SGD epochs. Our improvements over traditional PBT provide an increased speed of adaptation and a greater ability to shed deleterious genes from the population. Our methods improve final accuracy as well as time to fixed accuracy on a wide range of deep neural network architectures including convolutional neural networks, recurrent neural networks, dense neural networks, and capsule networks.

cs.NE↗
arXiv2018

Multimodal Deep Neural Networks using Both Engineered and Learned Representations for Biodegradability Prediction

Deep learning algorithms excel at extracting patterns from raw data, and with large datasets, they have been very successful in computer vision and natural language applications. However, in other domains, large datasets on which to learn representations from may not exist. In this work, we develop a novel multimodal CNN-MLP neural network architecture that utilizes both domain-specific feature engineering as well as learned representations from raw data. We illustrate the effectiveness of such network designs in the chemical sciences, for predicting biodegradability. DeepBioD, a multimodal CNN-MLP network is more accurate than either standalone network designs, and achieves an error classification rate of 0.125 that is 27% lower than the current state-of-the-art. Thus, our work indicates that combining traditional feature engineering with representation learning can be effective, particularly in situations where labeled data is limited.

cs.LG↗
arXiv2018

ColdRoute: Effective Routing of Cold Questions in Stack Exchange Sites

Routing questions in Community Question Answer services (CQAs) such as Stack Exchange sites is a well-studied problem. Yet, cold-start -- a phenomena observed when a new question is posted is not well addressed by existing approaches. Additionally, cold questions posted by new askers present significant challenges to state-of-the-art approaches. We propose ColdRoute to address these challenges. ColdRoute is able to handle the task of routing cold questions posted by new or existing askers to matching experts. Specifically, we use Factorization Machines on the one-hot encoding of critical features such as question tags and compare our approach to well-studied techniques such as CQARank and semantic matching (LDA, BoW, and Doc2Vec). Using data from eight stack exchange sites, we are able to improve upon the routing metrics (Precision$@1$, Accuracy, MRR) over the state-of-the-art models such as semantic matching by $159.5\%$,$31.84\%$, and $40.36\%$ for cold questions posted by existing askers, and $123.1\%$, $27.03\%$, and $34.81\%$ for cold questions posted by new askers respectively.

cs.AI↗
arXiv2018

How Much Chemistry Does a Deep Neural Network Need to Know to Make Accurate Predictions?

The meteoric rise of deep learning models in computer vision research, having achieved human-level accuracy in image recognition tasks is firm evidence of the impact of representation learning of deep neural networks. In the chemistry domain, recent advances have also led to the development of similar CNN models, such as Chemception, that is trained to predict chemical properties using images of molecular drawings. In this work, we investigate the effects of systematically removing and adding localized domain-specific information to the image channels of the training data. By augmenting images with only 3 additional basic information, and without introducing any architectural changes, we demonstrate that an augmented Chemception (AugChemception) outperforms the original model in the prediction of toxicity, activity, and solvation free energy. Then, by altering the information content in the images, and examining the resulting model's performance, we also identify two distinct learning patterns in predicting toxicity/activity as compared to solvation free energy. These patterns suggest that Chemception is learning about its tasks in the manner that is consistent with established knowledge. Thus, our work demonstrates that advanced chemical knowledge is not a pre-requisite for deep learning models to accurately predict complex chemical properties.

stat.ML↗
arXiv2018

SMILES2Vec: An Interpretable General-Purpose Deep Neural Network for Predicting Chemical Properties

Chemical databases store information in text representations, and the SMILES format is a universal standard used in many cheminformatics software. Encoded in each SMILES string is structural information that can be used to predict complex chemical properties. In this work, we develop SMILES2vec, a deep RNN that automatically learns features from SMILES to predict chemical properties, without the need for additional explicit feature engineering. Using Bayesian optimization methods to tune the network architecture, we show that an optimized SMILES2vec model can serve as a general-purpose neural network for predicting distinct chemical properties including toxicity, activity, solubility and solvation energy, while also outperforming contemporary MLP neural networks that uses engineered features. Furthermore, we demonstrate proof-of-concept of interpretability by developing an explanation mask that localizes on the most important characters used in making a prediction. When tested on the solubility dataset, it identified specific parts of a chemical that is consistent with established first-principles knowledge with an accuracy of 88%. Our work demonstrates that neural networks can learn technically accurate chemical concept and provide state-of-the-art accuracy, making interpretable deep neural networks a useful tool of relevance to the chemical industry.

stat.ML↗
arXiv2018

Using Rule-Based Labels for Weak Supervised Learning: A ChemNet for Transferable Chemical Property Prediction

With access to large datasets, deep neural networks (DNN) have achieved human-level accuracy in image and speech recognition tasks. However, in chemistry, data is inherently small and fragmented. In this work, we develop an approach of using rule-based knowledge for training ChemNet, a transferable and generalizable deep neural network for chemical property prediction that learns in a weak-supervised manner from large unlabeled chemical databases. When coupled with transfer learning approaches to predict other smaller datasets for chemical properties that it was not originally trained on, we show that ChemNet's accuracy outperforms contemporary DNN models that were trained using conventional supervised learning. Furthermore, we demonstrate that the ChemNet pre-training approach is equally effective on both CNN (Chemception) and RNN (SMILES2vec) models, indicating that this approach is network architecture agnostic and is effective across multiple data modalities. Our results indicate a pre-trained ChemNet that incorporates chemistry domain knowledge, enables the development of generalizable neural networks for more accurate prediction of novel chemical properties.

stat.ML↗
arXiv2018

GossipGraD: Scalable Deep Learning using Gossip Communication based Asynchronous Gradient Descent

In this paper, we present GossipGraD - a gossip communication protocol based Stochastic Gradient Descent (SGD) algorithm for scaling Deep Learning (DL) algorithms on large-scale systems. The salient features of GossipGraD are: 1) reduction in overall communication complexity from Θ(log(p)) for p compute nodes in well-studied SGD to O(1), 2) model diffusion such that compute nodes exchange their updates (gradients) indirectly after every log(p) steps, 3) rotation of communication partners for facilitating direct diffusion of gradients, 4) asynchronous distributed shuffle of samples during the feedforward phase in SGD to prevent over-fitting, 5) asynchronous communication of gradients for further reducing the communication cost of SGD and GossipGraD. We implement GossipGraD for GPU and CPU clusters and use NVIDIA GPUs (Pascal P100) connected with InfiniBand, and Intel Knights Landing (KNL) connected with Aries network. We evaluate GossipGraD using well-studied dataset ImageNet-1K (~250GB), and widely studied neural network topologies such as GoogLeNet and ResNet50 (current winner of ImageNet Large Scale Visualization Research Challenge (ILSVRC)). Our performance evaluation using both KNL and Pascal GPUs indicates that GossipGraD can achieve perfect efficiency for these datasets and their associated neural network topologies. Specifically, for ResNet50, GossipGraD is able to achieve ~100% compute efficiency using 128 NVIDIA Pascal P100 GPUs - while matching the top-1 classification accuracy published in literature.

cs.DC↗
arXiv2017

What does fault tolerant Deep Learning need from MPI?

Deep Learning (DL) algorithms have become the de facto Machine Learning (ML) algorithm for large scale data analysis. DL algorithms are computationally expensive - even distributed DL implementations which use MPI require days of training (model learning) time on commonly studied datasets. Long running DL applications become susceptible to faults - requiring development of a fault tolerant system infrastructure, in addition to fault tolerant DL algorithms. This raises an important question: What is needed from MPI for de- signing fault tolerant DL implementations? In this paper, we address this problem for permanent faults. We motivate the need for a fault tolerant MPI specification by an in-depth consideration of recent innovations in DL algorithms and their properties, which drive the need for specific fault tolerance features. We present an in-depth discussion on the suitability of different parallelism types (model, data and hybrid); a need (or lack thereof) for check-pointing of any critical data structures; and most importantly, consideration for several fault tolerance proposals (user-level fault mitigation (ULFM), Reinit) in MPI and their applicability to fault tolerant DL implementations. We leverage a distributed memory implementation of Caffe, currently available under the Machine Learning Toolkit for Extreme Scale (MaTEx). We implement our approaches by ex- tending MaTEx-Caffe for using ULFM-based implementation. Our evaluation using the ImageNet dataset and AlexNet, and GoogLeNet neural network topologies demonstrates the effectiveness of the proposed fault tolerant DL implementation using OpenMPI based ULFM.

cs.DC↗
arXiv2017

Distributed TensorFlow with MPI

Machine Learning and Data Mining (MLDM) algorithms are becoming increasingly important in analyzing large volume of data generated by simulations, experiments and mobile devices. With increasing data volume, distributed memory systems (such as tightly connected supercomputers or cloud computing systems) are becoming important in designing in-memory and massively parallel MLDM algorithms. Yet, the majority of open source MLDM software is limited to sequential execution with a few supporting multi-core/many-core execution. In this paper, we extend recently proposed Google TensorFlow for execution on large scale clusters using Message Passing Interface (MPI). Our approach requires minimal changes to the TensorFlow runtime -- making the proposed implementation generic and readily usable to increasingly large users of TensorFlow. We evaluate our implementation using an InfiniBand cluster and several well knowndatasets. Our evaluation indicates the efficiency of our proposed implementation.

cs.DC↗
arXiv2017

Chemception: A Deep Neural Network with Minimal Chemistry Knowledge Matches the Performance of Expert-developed QSAR/QSPR Models

In the last few years, we have seen the transformative impact of deep learning in many applications, particularly in speech recognition and computer vision. Inspired by Google's Inception-ResNet deep convolutional neural network (CNN) for image classification, we have developed "Chemception", a deep CNN for the prediction of chemical properties, using just the images of 2D drawings of molecules. We develop Chemception without providing any additional explicit chemistry knowledge, such as basic concepts like periodicity, or advanced features like molecular descriptors and fingerprints. We then show how Chemception can serve as a general-purpose neural network architecture for predicting toxicity, activity, and solvation properties when trained on a modest database of 600 to 40,000 compounds. When compared to multi-layer perceptron (MLP) deep neural networks trained with ECFP fingerprints, Chemception slightly outperforms in activity and solvation prediction and slightly underperforms in toxicity prediction. Having matched the performance of expert-developed QSAR/QSPR deep learning models, our work demonstrates the plausibility of using deep neural networks to assist in computational chemistry research, where the feature engineering process is performed primarily by a deep learning algorithm.

stat.ML↗
arXiv2017

User-transparent Distributed TensorFlow

Deep Learning (DL) algorithms have become the {\em de facto} choice for data analysis. Several DL implementations -- primarily limited to a single compute node -- such as Caffe, TensorFlow, Theano and Torch have become readily available. Distributed DL implementations capable of execution on large scale systems are becoming important to address the computational needs of large data produced by scientific simulations and experiments. Yet, the adoption of distributed DL implementations faces significant impediments: 1) most implementations require DL analysts to modify their code significantly -- which is a show-stopper, 2) several distributed DL implementations are geared towards cloud computing systems -- which is inadequate for execution on massively parallel systems such as supercomputers. This work addresses each of these problems. We provide a distributed memory DL implementation by incorporating required changes in the TensorFlow runtime itself. This dramatically reduces the entry barrier for using a distributed TensorFlow implementation. We use Message Passing Interface (MPI) -- which provides performance portability, especially since MPI specific changes are abstracted from users. Lastly -- and arguably most importantly -- we make our implementation available for broader use, under the umbrella of Machine Learning Toolkit for Extreme Scale (MaTEx) at {\texttt http://hpc.pnl.gov/matex}. We refer to our implementation as MaTEx-TensorFlow.

cs.DC↗
arXiv2016

Adaptive Neuron Apoptosis for Accelerating Deep Learning on Large Scale Systems

We present novel techniques to accelerate the convergence of Deep Learning algorithms by conducting low overhead removal of redundant neurons -- apoptosis of neurons -- which do not contribute to model learning, during the training phase itself. We provide in-depth theoretical underpinnings of our heuristics (bounding accuracy loss and handling apoptosis of several neuron types), and present the methods to conduct adaptive neuron apoptosis. Specifically, we are able to improve the training time for several datasets by 2-3x, while reducing the number of parameters by up to 30x (4-5x on average) on datasets such as ImageNet classification. For the Higgs Boson dataset, our implementation improves the accuracy (measured by Area Under Curve (AUC)) for classification from 0.88/1 to 0.94/1, while reducing the number of parameters by 3x in comparison to existing literature. The proposed methods achieve a 2.44x speedup in comparison to the default (no apoptosis) algorithm.

cs.NE↗
arXiv2014

Strongly Cyclic Coverings of Cyclic Curves

In this note, we introduce the notion of an unramified strongly cyclic covering for a cyclic curve, a class that has similar properties to, and contains, unramified double covers of hyperelliptic curves. We determine several of their basic properties, extending the theorems in \cite{MR2217998} to this larger class. In particular, we will write down equations for smooth affine models, determine when they are isomorphic, and discuss the curves that they are ramified cyclic covers of.

math.AG↗
arXiv2014

The Moduli of Klein Covers of Curves

We study the moduli space ${V}_4\mathcal{M}_{g}$ of Klein four covers of genus $g$ curves and its natural compactification. This requires the construction of a related space which has a choice of basis for the Klein four group. This space has the interesting property that the two components intersect along a component of the boundary. Further, we carry out a detailed analysis of the boundary, determining components, degrees of the components over their images in $\overline{\mathcal{M}_g}$, and computing the canonical divisor of $\overline{{V}_4\mathcal{M}_{g}}$.

math.AG↗
arXiv2013

The Schottky problem in genus five

In this paper, we present a solution to the Schottky problem in the spirit of Schottky and Jung for genus five curves. To do so, we exploit natural incidence structures on the fibers of several maps to reduce all questions to statements about the Prym map for genus six curves. This allows us to find all components of the big Schottky locus and thus, to show that the small Schottky locus introduced by Donagi is irreducible.

math.AG↗
arXiv2008

Improved Error Bounds for Dirichlet-to-Neumann Absorbing Boundaries

It has long been known how to construct radiation boundary conditions for the time dependent wave equation. Although arguments suggesting that they are accurate have been given, it is only recently that rigorous error bounds have been proved. Previous estimates show that the error caused by these methods behaves like epsilon C exp(gamma t) for any gamma > 0. We improve these results and show that the error behaves like epsilon t^2.

math.NA↗