3,444 research outputs found
A Review on Biological Inspired Computation in Cryptology
Cryptology is a field that concerned with cryptography and cryptanalysis. Cryptography, which is a key technology in providing a secure transmission of information, is a study of designing strong cryptographic algorithms, while cryptanalysis is a study of breaking the cipher. Recently biological approaches provide inspiration in solving problems from various fields. This paper reviews major works in the application of biological inspired computational (BIC) paradigm in cryptology. The paper focuses on three BIC approaches, namely, genetic algorithm (GA), artificial neural network (ANN) and artificial immune system (AIS). The findings show that the research on applications of biological approaches in cryptology is minimal as compared to other fields. To date only ANN and GA have been used in cryptanalysis and design of cryptographic primitives and protocols. Based on similarities that AIS has with ANN and GA, this paper provides insights for potential application of AIS in cryptology for further research
Analyzing analytical methods: The case of phonology in neural models of spoken language
Given the fast development of analysis techniques for NLP and speech
processing systems, few systematic studies have been conducted to compare the
strengths and weaknesses of each method. As a step in this direction we study
the case of representations of phonology in neural network models of spoken
language. We use two commonly applied analytical techniques, diagnostic
classifiers and representational similarity analysis, to quantify to what
extent neural activation patterns encode phonemes and phoneme sequences. We
manipulate two factors that can affect the outcome of analysis. First, we
investigate the role of learning by comparing neural activations extracted from
trained versus randomly-initialized models. Second, we examine the temporal
scope of the activations by probing both local activations corresponding to a
few milliseconds of the speech signal, and global activations pooled over the
whole utterance. We conclude that reporting analysis results with randomly
initialized models is crucial, and that global-scope methods tend to yield more
consistent results and we recommend their use as a complement to local-scope
diagnostic methods.Comment: ACL 202
Progressive growing of self-organized hierarchical representations for exploration
Designing agent that can autonomously discover and learn a diversity of
structures and skills in unknown changing environments is key for lifelong
machine learning. A central challenge is how to learn incrementally
representations in order to progressively build a map of the discovered
structures and re-use it to further explore. To address this challenge, we
identify and target several key functionalities. First, we aim to build lasting
representations and avoid catastrophic forgetting throughout the exploration
process. Secondly we aim to learn a diversity of representations allowing to
discover a "diversity of diversity" of structures (and associated skills) in
complex high-dimensional environments. Thirdly, we target representations that
can structure the agent discoveries in a coarse-to-fine manner. Finally, we
target the reuse of such representations to drive exploration toward an
"interesting" type of diversity, for instance leveraging human guidance.
Current approaches in state representation learning rely generally on
monolithic architectures which do not enable all these functionalities.
Therefore, we present a novel technique to progressively construct a Hierarchy
of Observation Latent Models for Exploration Stratification, called HOLMES.
This technique couples the use of a dynamic modular model architecture for
representation learning with intrinsically-motivated goal exploration processes
(IMGEPs). The paper shows results in the domain of automated discovery of
diverse self-organized patterns, considering as testbed the experimental
framework from Reinke et al. (2019)
Affective Man-Machine Interface: Unveiling human emotions through biosignals
As is known for centuries, humans exhibit an electrical profile. This profile is altered through various psychological and physiological processes, which can be measured through biosignals; e.g., electromyography (EMG) and electrodermal activity (EDA). These biosignals can reveal our emotions and, as such, can serve as an advanced man-machine interface (MMI) for empathic consumer products. However, such a MMI requires the correct classification of biosignals to emotion classes. This chapter starts with an introduction on biosignals for emotion detection. Next, a state-of-the-art review is presented on automatic emotion classification. Moreover, guidelines are presented for affective MMI. Subsequently, a research is presented that explores the use of EDA and three facial EMG signals to determine neutral, positive, negative, and mixed emotions, using recordings of 21 people. A range of techniques is tested, which resulted in a generic framework for automated emotion classification with up to 61.31% correct classification of the four emotion classes, without the need of personal profiles. Among various other directives for future research, the results emphasize the need for parallel processing of multiple biosignals
Scalable Distributed DNN Training using TensorFlow and CUDA-Aware MPI: Characterization, Designs, and Performance Evaluation
TensorFlow has been the most widely adopted Machine/Deep Learning framework.
However, little exists in the literature that provides a thorough understanding
of the capabilities which TensorFlow offers for the distributed training of
large ML/DL models that need computation and communication at scale. Most
commonly used distributed training approaches for TF can be categorized as
follows: 1) Google Remote Procedure Call (gRPC), 2) gRPC+X: X=(InfiniBand
Verbs, Message Passing Interface, and GPUDirect RDMA), and 3) No-gRPC: Baidu
Allreduce with MPI, Horovod with MPI, and Horovod with NVIDIA NCCL. In this
paper, we provide an in-depth performance characterization and analysis of
these distributed training approaches on various GPU clusters including the Piz
Daint system (6 on Top500). We perform experiments to gain novel insights along
the following vectors: 1) Application-level scalability of DNN training, 2)
Effect of Batch Size on scaling efficiency, 3) Impact of the MPI library used
for no-gRPC approaches, and 4) Type and size of DNN architectures. Based on
these experiments, we present two key insights: 1) Overall, No-gRPC designs
achieve better performance compared to gRPC-based approaches for most
configurations, and 2) The performance of No-gRPC is heavily influenced by the
gradient aggregation using Allreduce. Finally, we propose a truly CUDA-Aware
MPI Allreduce design that exploits CUDA kernels and pointer caching to perform
large reductions efficiently. Our proposed designs offer 5-17X better
performance than NCCL2 for small and medium messages, and reduces latency by
29% for large messages. The proposed optimizations help Horovod-MPI to achieve
approximately 90% scaling efficiency for ResNet-50 training on 64 GPUs.
Further, Horovod-MPI achieves 1.8X and 3.2X higher throughput than the native
gRPC method for ResNet-50 and MobileNet, respectively, on the Piz Daint
cluster.Comment: 10 pages, 9 figures, submitted to IEEE IPDPS 2019 for peer-revie
NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features
UNLABELLED: β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC=0.50, Qtotal=82.1%, sensitivity=75.6%, PPV=68.8% and AUC=0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17-0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. CONCLUSION: The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences
A generic method for assignment of reliability scores applied to solvent accessibility predictions
<p>Abstract</p> <p>Background</p> <p>Estimation of the reliability of specific real value predictions is nontrivial and the efficacy of this is often questionable. It is important to know if you can trust a given prediction and therefore the best methods associate a prediction with a reliability score or index. For discrete qualitative predictions, the reliability is conventionally estimated as the difference between output scores of selected classes. Such an approach is not feasible for methods that predict a biological feature as a single real value rather than a classification. As a solution to this challenge, we have implemented a method that predicts the relative surface accessibility of an amino acid and simultaneously predicts the reliability for each prediction, in the form of a Z-score.</p> <p>Results</p> <p>An ensemble of artificial neural networks has been trained on a set of experimentally solved protein structures to predict the relative exposure of the amino acids. The method assigns a reliability score to each surface accessibility prediction as an inherent part of the training process. This is in contrast to the most commonly used procedures where reliabilities are obtained by post-processing the output.</p> <p>Conclusion</p> <p>The performance of the neural networks was evaluated on a commonly used set of sequences known as the CB513 set. An overall Pearson's correlation coefficient of 0.72 was obtained, which is comparable to the performance of the currently best public available method, Real-SPINE. Both methods associate a reliability score with the individual predictions. However, our implementation of reliability scores in the form of a Z-score is shown to be the more informative measure for discriminating good predictions from bad ones in the entire range from completely buried to fully exposed amino acids. This is evident when comparing the Pearson's correlation coefficient for the upper 20% of predictions sorted according to reliability. For this subset, values of 0.79 and 0.74 are obtained using our and the compared method, respectively. This tendency is true for any selected subset.</p
Assessing the representation of seen and unseen contents in human brains and deep artificial networks
119 p.The functional scope of unconscious visual information processing and its implementation in the human brain remains a highly contested issue in cognitive neuroscience. The influential global workspace and higher-order theories predict that unconscious visual processing is restricted to representations in the visual cortex, which are not read-out further by frontoparietal areas. The present thesis employs fMRI and computational approaches to develop a high-precision, within-subject framework in order to define the properties of the brain representations of unconscious content associated with null perceptual sensitivity. Machine learning models were used to read-out multivariate unconscious content from fMRI signals throughout the ventral visual pathway, and model-based representational similarity analysis examined the properties of both conscious and unconscious representations. Finally, feedforward convolutional neural network (FCNN) models were used to simulate the fMRI results, namely, to probe the existence of informative representations of visual objects with null perceptual sensitivity in artificial networks. The results show that even when human observers display null perceptual sensitivity at a behavioral level, there are neural representations of unconscious content widely distributed throughout the cortex, and these are not only contained in visual regions but also extend to higher-order regions in the ventral visual pathway, parietal and even prefrontal areas. The computational simulations with different FCNN models trained to perform the same visual task with noisy images demonstrated that even when the FCNN models failed to classify the category of the noisy images, the hidden representation of the FCNN models contained an informative representation that allowed for decoding of the image class. The implications of the results for models of visual consciousness are discusse
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