Computational Molecular Biology

Computational Biology is a fairly new subject that arose in response to the computational problems posed by the analysis and the processing of biomolecular sequence and structure data. The field was initiated in the late 60's and early 70's largely by pioneers working in the life sciences. Physicists and mathematicians entered the field in the 70's and 80's, while Computer Science became involved with the new biological problems in the late 1980's. Computational problems have gained further importance in molecular biology through the various genome projects which produce enormous amounts of data. For this bibliography we focus on those areas of computational molecular biology that involve discrete algorithms or discrete optimization. We thus neglect several other areas of computational molecular biology, like most of the literature on the protein folding problem, as well as databases for molecular and genetic data, and genetic mapping algorithms. Due to the availability of review papers and a bibliography this bibliography

Baseband analog front-end and digital back-end for reconfigurable multi-standard terminals

Multimedia applications are driving wireless network operators to add high-speed data services such as Edge (E-GPRS), WCDMA (UMTS) and WLAN (IEEE 802.11a,b,g) to the existing GSM network. This creates the need for multi-mode cellular handsets that support a wide range of communication standards, each with a different RF frequency, signal bandwidth, modulation scheme etc. This in turn generates several design challenges for the analog and digital building blocks of the physical layer. In addition to the above-mentioned protocols, mobile devices often include Bluetooth, GPS, FM-radio and TV services that can work concurrently with data and voice communication. Multi-mode, multi-band, and multi-standard mobile terminals must satisfy all these different requirements. Sharing and/or switching transceiver building blocks in these handsets is mandatory in order to extend battery life and/or reduce cost. Only adaptive circuits that are able to reconfigure themselves within the handover time can meet the design requirements of a single receiver or transmitter covering all the different standards while ensuring seamless inter-interoperability. This paper presents analog and digital base-band circuits that are able to support GSM (with Edge), WCDMA (UMTS), WLAN and Bluetooth using reconfigurable building blocks. The blocks can trade off power consumption for performance on the fly, depending on the standard to be supported and the required QoS (Quality of Service) leve

CryptoKnight:generating and modelling compiled cryptographic primitives

Cryptovirological augmentations present an immediate, incomparable threat. Over the last decade, the substantial proliferation of crypto-ransomware has had widespread consequences for consumers and organisations alike. Established preventive measures perform well, however, the problem has not ceased. Reverse engineering potentially malicious software is a cumbersome task due to platform eccentricities and obfuscated transmutation mechanisms, hence requiring smarter, more efficient detection strategies. The following manuscript presents a novel approach for the classification of cryptographic primitives in compiled binary executables using deep learning. The model blueprint, a Dynamic Convolutional Neural Network (DCNN), is fittingly configured to learn from variable-length control flow diagnostics output from a dynamic trace. To rival the size and variability of equivalent datasets, and to adequately train our model without risking adverse exposure, a methodology for the procedural generation of synthetic cryptographic binaries is defined, using core primitives from OpenSSL with multivariate obfuscation, to draw a vastly scalable distribution. The library, CryptoKnight, rendered an algorithmic pool of AES, RC4, Blowfish, MD5 and RSA to synthesise combinable variants which automatically fed into its core model. Converging at 96% accuracy, CryptoKnight was successfully able to classify the sample pool with minimal loss and correctly identified the algorithm in a real-world crypto-ransomware applicatio

An evaluation of software fault tolerance techniques in real-time safety-critical applications

The usefulness of three software fault tolerance techniques -- n-version programming, recovery blocks, and exception handling is examined within the context of real-time safety-critical environments. The general requirements of such application systems are presented and the techniques evaluated with regard to how well they satisfy these requirements

Exact Covers via Determinants

Given a k-uniform hypergraph on n vertices, partitioned in k equal parts such that every hyperedge includes one vertex from each part, the k-dimensional matching problem asks whether there is a disjoint collection of the hyperedges which covers all vertices. We show it can be solved by a randomized polynomial space algorithm in time O*(2^(n(k-2)/k)). The O*() notation hides factors polynomial in n and k. When we drop the partition constraint and permit arbitrary hyperedges of cardinality k, we obtain the exact cover by k-sets problem. We show it can be solved by a randomized polynomial space algorithm in time O*(c_k^n), where c_3=1.496, c_4=1.642, c_5=1.721, and provide a general bound for larger k. Both results substantially improve on the previous best algorithms for these problems, especially for small k, and follow from the new observation that Lovasz' perfect matching detection via determinants (1979) admits an embedding in the recently proposed inclusion-exclusion counting scheme for set covers, despite its inability to count the perfect matchings