Refined Genetic Algorithms for Polypeptide Structure Prediction

Accurate and reliable prediction of macromolecular structures has eluded researchers for nearly 40 years. Prediction via energy minimization assumes the native conformation has the globally minimal energy potential. An exhaustive search is impossible since for molecules of normal size, the size of the search space exceeds the size of the universe. Domain knowledge sources, such as the Brookhaven PDB can be mined for constraints to limit the search space. Genetic algorithms (GAs) are stochastic, population based, search algorithms of polynomial (P) time complexity that can produce semi-optimal solutions for problems of nondeterministic polynomial (NP) time complexity such as PSP. Three refined GAs are presented: A farming model parallel hybrid GA (PHGA) preserves the effectiveness of the serial algorithm with substantial speed up. Portability across distributed and MPP platforms is accomplished with the Message Passing Interface (MPI) communications standard. A Real-valved GA system, real-valued Genetic Algorithm, Limited by constraints (REGAL), exploiting domain knowledge. Experiments with the pentapeptide Met-enkephalin have identified conformers with lower energies (CHARMM) than the accepted optimal conformer (Scheraga, et al), -31.98 vs -28.96 kcals/mol. Analysis of exogenous parameters yields additional insight into performance. A parallel version (Para-REGAL), an island model modified to allow different active constraints in the distributed subpopulations and novel concepts of Probability of Migration and Probability of Complete Migration

CAIR: Using Formal Languages to Study Routing, Leaking, and Interception in BGP

The Internet routing protocol BGP expresses topological reachability and policy-based decisions simultaneously in path vectors. A complete view on the Internet backbone routing is given by the collection of all valid routes, which is infeasible to obtain due to information hiding of BGP, the lack of omnipresent collection points, and data complexity. Commonly, graph-based data models are used to represent the Internet topology from a given set of BGP routing tables but fall short of explaining policy contexts. As a consequence, routing anomalies such as route leaks and interception attacks cannot be explained with graphs. In this paper, we use formal languages to represent the global routing system in a rigorous model. Our CAIR framework translates BGP announcements into a finite route language that allows for the incremental construction of minimal route automata. CAIR preserves route diversity, is highly efficient, and well-suited to monitor BGP path changes in real-time. We formally derive implementable search patterns for route leaks and interception attacks. In contrast to the state-of-the-art, we can detect these incidents. In practical experiments, we analyze public BGP data over the last seven years

Accuracy Boosters: Epoch-Driven Mixed-Mantissa Block Floating-Point for DNN Training

The unprecedented growth in DNN model complexity, size and the amount of training data have led to a commensurate increase in demand for computing and a search for minimal encoding. Recent research advocates Hybrid Block Floating-Point (HBFP) as a technique that minimizes silicon provisioning in accelerators by converting the majority of arithmetic operations in training to 8-bit fixed-point. In this paper, we perform a full-scale exploration of the HBFP design space including minimal mantissa encoding, varying block sizes, and mixed mantissa bit-width across layers and epochs. We propose Accuracy Boosters, an epoch-driven mixed-mantissa HBFP that uses 6-bit mantissa only in the last epoch and converts $99.7\%$ of all arithmetic operations in training to 4-bit mantissas. Accuracy Boosters enable reducing silicon provisioning for an HBFP training accelerator by $16.98\times$ as compared to FP32, while preserving or outperforming FP32 accuracy

Shift-Symmetric Configurations in Two-Dimensional Cellular Automata: Irreversibility, Insolvability, and Enumeration

The search for symmetry as an unusual yet profoundly appealing phenomenon, and the origin of regular, repeating configuration patterns have long been a central focus of complexity science and physics. To better grasp and understand symmetry of configurations in decentralized toroidal architectures, we employ group-theoretic methods, which allow us to identify and enumerate these inputs, and argue about irreversible system behaviors with undesired effects on many computational problems. The concept of so-called configuration shift-symmetry is applied to two-dimensional cellular automata as an ideal model of computation. Regardless of the transition function, the results show the universal insolvability of crucial distributed tasks, such as leader election, pattern recognition, hashing, and encryption. By using compact enumeration formulas and bounding the number of shift-symmetric configurations for a given lattice size, we efficiently calculate the probability of a configuration being shift-symmetric for a uniform or density-uniform distribution. Further, we devise an algorithm detecting the presence of shift-symmetry in a configuration. Given the resource constraints, the enumeration and probability formulas can directly help to lower the minimal expected error and provide recommendations for system's size and initialization. Besides cellular automata, the shift-symmetry analysis can be used to study the non-linear behavior in various synchronous rule-based systems that include inference engines, Boolean networks, neural networks, and systolic arrays.Comment: 22 pages, 9 figures, 2 appendice

On the Complexity of Computing Minimal Unsatisfiable LTL formulas

We show that (1) the Minimal False QCNF search-problem (MF-search) and the Minimal Unsatisfiable LTL formula search problem (MU-search) are FPSPACE complete because of the very expressive power of QBF/LTL, (2) we extend the PSPACE-hardness of the MF decision problem to the MU decision problem. As a consequence, we deduce a positive answer to the open question of PSPACE hardness of the inherent Vacuity Checking problem. We even show that the Inherent Non Vacuous formula search problem is also FPSPACE-complete.Comment: Minimal unsatisfiable cores For LTL causes inherent vacuity checking redundancy coverag