Motion Switching with Sensory and Instruction Signals by designing Dynamical Systems using Deep Neural Network

To ensure that a robot is able to accomplish an extensive range of tasks, it is necessary to achieve a flexible combination of multiple behaviors. This is because the design of task motions suited to each situation would become increasingly difficult as the number of situations and the types of tasks performed by them increase. To handle the switching and combination of multiple behaviors, we propose a method to design dynamical systems based on point attractors that accept (i) "instruction signals" for instruction-driven switching. We incorporate the (ii) "instruction phase" to form a point attractor and divide the target task into multiple subtasks. By forming an instruction phase that consists of point attractors, the model embeds a subtask in the form of trajectory dynamics that can be manipulated using sensory and instruction signals. Our model comprises two deep neural networks: a convolutional autoencoder and a multiple time-scale recurrent neural network. In this study, we apply the proposed method to manipulate soft materials. To evaluate our model, we design a cloth-folding task that consists of four subtasks and three patterns of instruction signals, which indicate the direction of motion. The results depict that the robot can perform the required task by combining subtasks based on sensory and instruction signals. And, our model determined the relations among these signals using its internal dynamics.Comment: 8 pages, 6 figures, accepted for publication in RA-L. An accompanied video is available at this https://youtu.be/a73KFtOOB5

Folding, Tiling, and Multidimensional Coding

Folding a sequence $S$ into a multidimensional box is a method that is used to construct multidimensional codes. The well known operation of folding is generalized in a way that the sequence $S$ can be folded into various shapes. The new definition of folding is based on lattice tiling and a direction in the $D$-dimensional grid. There are potentially $\frac{3^D-1}{2}$ different folding operations. Necessary and sufficient conditions that a lattice combined with a direction define a folding are given. The immediate and most impressive application is some new lower bounds on the number of dots in two-dimensional synchronization patterns. This can be also generalized for multidimensional synchronization patterns. We show how folding can be used to construct multidimensional error-correcting codes and to generate multidimensional pseudo-random arrays

Prediction of peptide and protein propensity for amyloid formation

Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of β-sheet, normalized frequency of β-sheet from LG, weights for β-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ΔGº values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation

Connectionist Theory Refinement: Genetically Searching the Space of Network Topologies

An algorithm that learns from a set of examples should ideally be able to exploit the available resources of (a) abundant computing power and (b) domain-specific knowledge to improve its ability to generalize. Connectionist theory-refinement systems, which use background knowledge to select a neural network's topology and initial weights, have proven to be effective at exploiting domain-specific knowledge; however, most do not exploit available computing power. This weakness occurs because they lack the ability to refine the topology of the neural networks they produce, thereby limiting generalization, especially when given impoverished domain theories. We present the REGENT algorithm which uses (a) domain-specific knowledge to help create an initial population of knowledge-based neural networks and (b) genetic operators of crossover and mutation (specifically designed for knowledge-based networks) to continually search for better network topologies. Experiments on three real-world domains indicate that our new algorithm is able to significantly increase generalization compared to a standard connectionist theory-refinement system, as well as our previous algorithm for growing knowledge-based networks.Comment: See http://www.jair.org/ for any accompanying file

Deriving amino acid contact potentials from their frequencies of occurence in proteins: a lattice model study

The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such frequencies and, consequently, to develop a strategy to include in the calculations correlations due to the spatial proximity of the amino acids and to their overall tendency of being conserved in proteins. Making use of a lattice model to describe protein chains and defining a "true" potential, we test these strategies by selecting a database of folding model sequences, deriving the contact potentials from such sequences and comparing them with the "true" potential. Taking into account correlations allows for a markedly better prediction of the interaction potentials

Tensor Networks for Dimensionality Reduction and Large-Scale Optimizations. Part 2 Applications and Future Perspectives

Part 2 of this monograph builds on the introduction to tensor networks and their operations presented in Part 1. It focuses on tensor network models for super-compressed higher-order representation of data/parameters and related cost functions, while providing an outline of their applications in machine learning and data analytics. A particular emphasis is on the tensor train (TT) and Hierarchical Tucker (HT) decompositions, and their physically meaningful interpretations which reflect the scalability of the tensor network approach. Through a graphical approach, we also elucidate how, by virtue of the underlying low-rank tensor approximations and sophisticated contractions of core tensors, tensor networks have the ability to perform distributed computations on otherwise prohibitively large volumes of data/parameters, thereby alleviating or even eliminating the curse of dimensionality. The usefulness of this concept is illustrated over a number of applied areas, including generalized regression and classification (support tensor machines, canonical correlation analysis, higher order partial least squares), generalized eigenvalue decomposition, Riemannian optimization, and in the optimization of deep neural networks. Part 1 and Part 2 of this work can be used either as stand-alone separate texts, or indeed as a conjoint comprehensive review of the exciting field of low-rank tensor networks and tensor decompositions.Comment: 232 page