Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

A Web Component for Real-Time Collaborative Text Editing

Real-time collaborative software allows physically distinct people to co-operate by working on a shared application state, receiving updates from each other in real-time. The goal of this thesis was to create a developer tool, which would allow web application developers to easily integrate a collaborative text editor into their applications. In order to remain technology agnostic and to utilize the latest web standards, this product was implemented as a web component, a reusable user interface component built with native web browser features. The main challenge in developing a real-time collaboration tool is the handling of concurrent updates, which might conflict with one another. To tackle this issue, many consistency maintenance algorithms have been presented in the academic literature. Most of these techniques are variations of two main approaches: operational transformation and commutative replicated data types. In this thesis, we reviewed some of these methods and chose the GOTO operational transformation algorithm to be implemented in our component. Besides selecting and implementing an appropriate consistency maintenance technique, the contributions of this thesis include the design of an easy-to-use application programming interface (API). Our solution also fulfills some practical requirements of group editors not covered by the consistency maintenance theory, such as session management and cleaning of the message queue. The created web component succeeds in encapsulating the complexity related to concurrency control and handling of joining peers in the client-side implementation, which allows the application logic to remain simplistic. This open-source product enables software developers to add a collaborative text editor to their web applications by broadcasting the updates provided by an event-based API to participating peers

Static analysis of energy consumption for LLVM IR programs

Energy models can be constructed by characterizing the energy consumed by executing each instruction in a processor's instruction set. This can be used to determine how much energy is required to execute a sequence of assembly instructions, without the need to instrument or measure hardware. However, statically analyzing low-level program structures is hard, and the gap between the high-level program structure and the low-level energy models needs to be bridged. We have developed techniques for performing a static analysis on the intermediate compiler representations of a program. Specifically, we target LLVM IR, a representation used by modern compilers, including Clang. Using these techniques we can automatically infer an estimate of the energy consumed when running a function under different platforms, using different compilers. One of the challenges in doing so is that of determining an energy cost of executing LLVM IR program segments, for which we have developed two different approaches. When this information is used in conjunction with our analysis, we are able to infer energy formulae that characterize the energy consumption for a particular program. This approach can be applied to any languages targeting the LLVM toolchain, including C and XC or architectures such as ARM Cortex-M or XMOS xCORE, with a focus towards embedded platforms. Our techniques are validated on these platforms by comparing the static analysis results to the physical measurements taken from the hardware. Static energy consumption estimation enables energy-aware software development, without requiring hardware knowledge

Multi-bits biometric string generation based on the likelyhood ratio

Preserving the privacy of biometric information stored in biometric systems is becoming a key issue. An important element in privacy protecting biometric systems is the quantizer which transforms a normal biometric template into a binary string. In this paper, we present a user-specific quantization method based on a likelihood ratio approach (LQ). The bits generated from every feature are concatenated to form a fixed length binary string that can be hashed to protect its privacy. Experiments are carried out on both fingerprint data (FVC2000) and face data (FRGC). Results show that our proposed quantization method achieves a reasonably good performance in terms of FAR/FRR (when FAR is 10−4, the corresponding FRR are 16.7% and 5.77% for FVC2000 and FRGC, respectively)

A machine vision extension for the Ruby programming language

Dynamically typed scripting languages have become popular in recent years. Although interpreted languages allow for substantial reduction of software development time, they are often rejected due to performance concerns. In this paper we present an extension for the programming language Ruby, called HornetsEye, which facilitates the development of real-time machine vision algorithms within Ruby. Apart from providing integration of crucial libraries for input and output, HornetsEye provides fast native implementations (compiled code) for a generic set of array operators. Different array operators were compared with equivalent implementations in C++. Not only was it possible to achieve comparable real-time performance, but also to exceed the efficiency of the C++ implementation in several cases. Implementations of several algorithms were given to demonstrate how the array operators can be used to create concise implementations.</p