A multipath analysis of biswapped networks.

Biswapped networks of the form $Bsw(G)$ have recently been proposed as interconnection networks to be implemented as optical transpose interconnection systems. We provide a systematic construction of $\kappa+1$ vertex-disjoint paths joining any two distinct vertices in $Bsw(G)$, where $\kappa\geq 1$ is the connectivity of $G$. In doing so, we obtain an upper bound of $\max\{2\Delta(G)+5,\Delta_\kappa(G)+\Delta(G)+2\}$ on the $(\kappa+1)$-diameter of $Bsw(G)$, where $\Delta(G)$ is the diameter of $G$ and $\Delta_\kappa(G)$ the $\kappa$-diameter. Suppose that we have a deterministic multipath source routing algorithm in an interconnection network $G$ that finds $\kappa$ mutually vertex-disjoint paths in $G$ joining any $2$ distinct vertices and does this in time polynomial in $\Delta_\kappa(G)$, $\Delta(G)$ and $\kappa$ (and independently of the number of vertices of $G$). Our constructions yield an analogous deterministic multipath source routing algorithm in the interconnection network $Bsw(G)$ that finds $\kappa+1$ mutually vertex-disjoint paths joining any $2$ distinct vertices in $Bsw(G)$ so that these paths all have length bounded as above. Moreover, our algorithm has time complexity polynomial in $\Delta_\kappa(G)$, $\Delta(G)$ and $\kappa$. We also show that if $G$ is Hamiltonian then $Bsw(G)$ is Hamiltonian, and that if $G$ is a Cayley graph then $Bsw(G)$ is a Cayley graph

On Characterizing the Data Movement Complexity of Computational DAGs for Parallel Execution

Technology trends are making the cost of data movement increasingly dominant, both in terms of energy and time, over the cost of performing arithmetic operations in computer systems. The fundamental ratio of aggregate data movement bandwidth to the total computational power (also referred to the machine balance parameter) in parallel computer systems is decreasing. It is there- fore of considerable importance to characterize the inherent data movement requirements of parallel algorithms, so that the minimal architectural balance parameters required to support it on future systems can be well understood. In this paper, we develop an extension of the well-known red-blue pebble game to develop lower bounds on the data movement complexity for the parallel execution of computational directed acyclic graphs (CDAGs) on parallel systems. We model multi-node multi-core parallel systems, with the total physical memory distributed across the nodes (that are connected through some interconnection network) and in a multi-level shared cache hierarchy for processors within a node. We also develop new techniques for lower bound characterization of non-homogeneous CDAGs. We demonstrate the use of the methodology by analyzing the CDAGs of several numerical algorithms, to develop lower bounds on data movement for their parallel execution

A Cybernetics Update for Competitive Deep Learning System

A number of recent reports in the peer-reviewed literature have discussed irreproducibility of results in biomedical research. Some of these articles suggest that the inability of independent research laboratories to replicate published results has a negative impact on the development of, and confidence in, the biomedical research enterprise. To get more resilient data and to achieve higher reproducible result, we present an adaptive and learning system reference architecture for smart learning system interface. To get deeper inspiration, we focus our attention on mammalian brain neurophysiology. In fact, from a neurophysiological point of view, neuroscientist LeDoux finds two preferential amygdala pathways in the brain of the laboratory mouse. The low road is a pathway which is able to transmit a signal from a stimulus to the thalamus, and then to the amygdala, which then activates a fast-response in the body. The high road is activated simultaneously. This is a slower road which also includes the cortical parts of the brain, thus creating a conscious impression of what the stimulus is (to develop a rational mechanism of defense for instance). To mimic this biological reality, our main idea is to use a new input node able to bind known information to the unknown one coherently. Then, unknown "environmental noise" or/and local "signal input" information can be aggregated to known "system internal control status" information, to provide a landscape of attractor points, which either fast or slow and deeper system response can computed from. In this way, ideal cybernetics system interaction levels can be matched exactly to practical system modeling interaction styles, with no paradigmatic operational ambiguity and minimal information loss. The present paper is a relevant contribute to classic cybernetics updating towards a new General Theory of Systems, a post-Bertalanffy Systemics

Entropy, Decoherence and Spacetime Splitting

Objects in classical world model are in an "either/or" kind of state. A compass needle cannot point both north and south at the same time. The quantum world, by contrast, is "both/and" and a magnetic atom model has no trouble at pointing both directions at once. When that is the case, physicists say that a quantum object is in a "superposition" of states. In previous paper, we already discussed the major intrinsic limitations of "Science 1.0" arbitrary multi-scale (AMS) modeling and strategies to get better simulation results by "Science 2.0" approach. In 2014, Computational information conservation theory (CICT) has shown that even the most sophisticated instrumentation system is completely unable to reliably discriminate so called "random noise" (RN) from any combinatorically optimized encoded message (OECS, optimized exponential cyclic sequence), called "deterministic noise" (DN) by CICT. Unfortunately, the "probabilistic veil" can be quite opaque computationally, and misplaced precision leads to confusion. The "Science 2.0" paradigm has not yet been completely grasped by many contemporary scientific disciplines and current researchers, so that not all the implications of this big change have been realized hitherto, even less their related, vital applications. Thus, one of the key questions in understanding the quantum-classical transition is what happens to the superposition as you go up that atoms-to-apple scale. Exactly when and how does "both/and" become "either/or"? As an example, we present and discuss the observer space-time splitting case. In other words, we show spacetime mapping to classical system additive representation with entropy generation. It is exactly at this point that "both/and" becomes "either/or" representation by usual Science 1.0 approach. CICT new awareness of a discrete HG (hyperbolic geometry) subspace (reciprocal space) of coded heterogeneous hyperbolic structures, underlying the familiar Q Euclidean (direct space) surface representation can open the way to holographic information geometry (HIG) to recover system lost coherence and to overall system minimum entropy representation

Simulating Evolution’s First Steps

Abstract. We demonstrate a simple artificial chemistry environment in which two small evolutionary transitions from the simplest self-replicators to larger ones are observed. The replicators adapt to increasingly harsh environments, where they must synthesise the components they need for replication. The evolution of a biosynthetic pathway of increasing length is thus achieved, through the use of simple chemical rules for catalytic action.

Dagstuhl News January - December 2002

"Dagstuhl News" is a publication edited especially for the members of the Foundation "Informatikzentrum Schloss Dagstuhl" to thank them for their support. The News give a summary of the scientific work being done in Dagstuhl. Each Dagstuhl Seminar is presented by a small abstract describing the contents and scientific highlights of the seminar as well as the perspectives or challenges of the research topic

Protein Fold Recognition Using Neural Networks

To predict accurately the three-dimensional (3D) structures of proteins from their amino acid sequences alone remains a challenging problem. However, using protein fold recognition tools, it is often possible to achieve good models or at least to gain some more information, to aid scientists in their research. This thesis describes development of TUNE (Threading Using Neural Networks), a fold recognition program using artificial neural network (ANN) models. A new method to generate amino acid substitution matrices is described in chapter two. It uses an ANN to generalise amino acid substitutions observed in protein structure alignments. Matrices for alignment scoring from this approach were compared with classic alignment scoring schemes. From these neural network models, a series of encoding schemes were constructed. These schemes describe the amino acid types with a few numbers. They were generated to replace the orthogonal encoding scheme, so that smaller, faster and more accurate neural network models can be applied on bioinformatic problems. The TUNE model was introduced in chapter four to measure protein sequence-structure compatibility. Given the integrated residue structural environment descriptions, the model predicts probabilities of observing amino acid types in such environments. Using this model, a scoring function to measure the fitness of a residue in a protein structure model can be made for protein threading programs. The model in chapter two was extended by including the residue structural environment descriptions for predictions. A simple protein fold recognition program with a dynamic programming algorithm was developed using this model. The program was then tested in the fourth round of the Critical Assessment of protein Structure Prediction methods (CASP4) and produced reasonably good results