An incremental approach to automated protein localisation

Tscherepanow M, Jensen N, Kummert F. An incremental approach to automated protein localisation. BMC Bioinformatics. 2008;9(1): 445.Background: The subcellular localisation of proteins in intact living cells is an important means for gaining information about protein functions. Even dynamic processes can be captured, which can barely be predicted based on amino acid sequences. Besides increasing our knowledge about intracellular processes, this information facilitates the development of innovative therapies and new diagnostic methods. In order to perform such a localisation, the proteins under analysis are usually fused with a fluorescent protein. So, they can be observed by means of a fluorescence microscope and analysed. In recent years, several automated methods have been proposed for performing such analyses. Here, two different types of approaches can be distinguished: techniques which enable the recognition of a fixed set of protein locations and methods that identify new ones. To our knowledge, a combination of both approaches – i.e. a technique, which enables supervised learning using a known set of protein locations and is able to identify and incorporate new protein locations afterwards – has not been presented yet. Furthermore, associated problems, e.g. the recognition of cells to be analysed, have usually been neglected. Results: We introduce a novel approach to automated protein localisation in living cells. In contrast to well-known techniques, the protein localisation technique presented in this article aims at combining the two types of approaches described above: After an automatic identification of unknown protein locations, a potential user is enabled to incorporate them into the pre-trained system. An incremental neural network allows the classification of a fixed set of protein location as well as the detection, clustering and incorporation of additional patterns that occur during an experiment. Here, the proposed technique achieves promising results with respect to both tasks. In addition, the protein localisation procedure has been adapted to an existing cell recognition approach. Therefore, it is especially well-suited for high-throughput investigations where user interactions have to be avoided. Conclusion: We have shown that several aspects required for developing an automatic protein localisation technique – namely the recognition of cells, the classification of protein distribution patterns into a set of learnt protein locations, and the detection and learning of new locations – can be combined successfully. So, the proposed method constitutes a crucial step to render image-based protein localisation techniques amenable to large-scale experiments

Automated Adaptation Strategies for Stream Learning

Automation of machine learning model development is increasingly becoming an established research area. While automated model selection and automated data pre-processing have been studied in depth, there is, however, a gap concerning automated model adaptation strategies when multiple strategies are available. Manually developing an adaptation strategy can be time consuming and costly. In this paper we address this issue by proposing the use of flexible adaptive mechanism deployment for automated development of adaptation strategies. Experimental results after using the proposed strategies with five adaptive algorithms on 36 datasets confirm their viability. These strategies achieve better or comparable performance to the custom adaptation strategies and the repeated deployment of any single adaptive mechanism

ART-based Fusion of Multi-Modal Information for Mobile Robots

Berghöfer E, Schulze D, Tscherepanow M, Wachsmuth S. ART-based Fusion of Multi-Modal Information for Mobile Robots. In: Iliadis L, Jayne C, eds. Proceedings of the International Conference on Engineering Applications of Neural Networks (EANN). IFIP Advances in Information and Communication Technology. Vol 363. Berlin: Springer; 2011: 1-10.Robots operating in complex environments shared with humans are confronted with numerous problems. One important problem is the identification of obstacles and interaction partners. In order to reach this goal, it can be beneficial to use data from multiple available sources, which need to be processed appropriately. Furthermore, such environments are not static. Therefore, the robot needs to learn novel objects. In this paper, we propose a method for learning and identifying obstacles based on multi-modal information. As this approach is based on Adaptive Resonance Theory networks, it is inherently capable of incremental online learning

Adaptive crossover memetic differential harmony search for optimizing document clustering

An Adaptive Crossover Memetic Differential Harmony Search (ACMDHS) method was developed for optimizing document clustering in this paper. Due to the complexity of the documents available today, the allocation of the centroid of the document clusters and finding the optimum clusters in the search space are more complex to deal with. One of the possible enhancements on the document clustering is the use of Harmony Search (HS) algorithm to optimize the search. As HS is highly dependent on its control parameters, a differential version of HS was introduced. In the modified version of HS, the Band Width parameter (BW) has been replaced by another pitch adjustment technique due to the sensitivity of the BW parameter. Thus, the Differential Evolution (DE) mutation was used instead. In this paper the DE crossover was also used with the Differential HS for further search space exploitation, the produced global search is named Crossover DHS (CDHS). Moreover, DE crossover (Cr) and mutation (F) probabilities are dynamically tuned through generations. The Memetic optimization was used to enhance the local search capability of CDHS. The proposed ACMDHS was compared to other document clustering techniques using HS, DHS, and K-means methods. It was also compared to its other two variants which are the Memetic DHS (MDHS) and the Crossover Memetic Differential Harmony Search (CMDHS). Moreover, two state-of-the-art clustering methods were also considered in comparisons, the Chaotic Gradient Artificial Bee Colony (CGABC) and the Differential Evolution Memetic Clustering (DEMC). From the experimental results, it was shown that CMDHS variant (the non-adaptive version of ACMDHS) and ACMDHS were highly competitive while both CMDHS and ACMDHS were superior to all other methods

Computational intelligence algorithms analysis for smart grid cyber security

The cyber attack risks are threatening the smart grid security. Malicious worm could spread from meter to meter to take out power in a simulated attack. The North American Electric Reliability Corporation (NERC) has thus developed several iterations of cyber security standards. According to the NERC cyber standards CIP-002-2 requirements, in this paper, we present cyber security risk analysis using computational intelligence methods and review on core methods, such as in risk assessment HHM, IIM, RFRM algorithms, fault analysis FTA, ETA, FMEA, FMECA algorithms, fuzzy sets, intrusion detection systems, artificial neural networks and artificial immune systems. Through the analysis of the core computational intelligence algorithms used in the smart grid cyber security in power system network security lab, we clearly defined existing smart grid research challenges