A robust elicitation algorithm for discovering DNA motifs using fuzzy self-organizing maps

Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering

Understanding binding cores is of fundamental importance in deciphering Protein-DNA (TF-TFBS) binding and gene regulation. Limited by expensive experiments, it is promising to discover them with variations directly from sequence data. Although existing computational methods have produced satisfactory results, they are one-to-one mappings with no site-specific information on residue/nucleotide variations, where these variations in binding cores may impact binding specificity. This study presents a new representation for modeling binding cores by incorporating variations and an algorithm to discover them from only sequence data. Our algorithm takes protein and DNA sequences from TRANSFAC (a Protein-DNA Binding Database) as input; discovers from both sets of sequences conserved regions in Aligned Pattern Clusters (APCs); associates them as Protein-DNA Co-Occurring APCs; ranks the Protein-DNA Co-Occurring APCs according to their co-occurrence, and among the top ones, finds three-dimensional structures to support each binding core candidate. If successful, candidates are verified as binding cores. Otherwise, homology modeling is applied to their close matches in PDB to attain new chemically feasible binding cores. Our algorithm obtains binding cores with higher precision and much faster runtime ( ≥ 1,600x) than that of its contemporaries, discovering candidates that do not co-occur as one-to-one associated patterns in the raw data.

AVAILABILITY

http://www.pami.uwaterloo.ca/~ealee/files/tcbbPnDna2015/Release.zip.

Power Quality Analysis Using a Hybrid Model of the Fuzzy Min-Max Neural Network and Clustering Tree

A hybrid intelligent model comprising a modified fuzzy min-max (FMM) clustering neural network and a modified clustering tree (CT) is developed. A review of clustering models with rule extraction capabilities is presented. The hybrid FMM-CT model is explained. We first use several benchmark problems to illustrate the cluster evolution patterns from the proposed modifications in FMM. Then, we employ a case study with real data related to power quality monitoring to assess the usefulness of FMM-CT. The results are compared with those from other clustering models. More importantly, we extract explanatory rules from FMM-CT to justify its predictions. The empirical findings indicate the usefulness of the proposed model in tackling data clustering and power quality monitoring problems under different environments.

Adaptive Portfolio Optimization for Multiple Electricity Markets Participation

The increase of distributed energy resources, mainly based on renewable sources, requires new solutions that are able to deal with this type of resources' particular characteristics (namely, the renewable energy sources intermittent nature). The smart grid concept is increasing its consensus as the most suitable solution to facilitate the small players' participation in electric power negotiations while improving energy efficiency. The opportunity for players' participation in multiple energy negotiation environments (smart grid negotiation in addition to the already implemented market types, such as day-ahead spot markets, balancing markets, intraday negotiations, bilateral contracts, forward and futures negotiations, and among other) requires players to take suitable decisions on whether to, and how to participate in each market type. This paper proposes a portfolio optimization methodology, which provides the best investment profile for a market player, considering different market opportunities. The amount of power that each supported player should negotiate in each available market type in order to maximize its profits, considers the prices that are expected to be achieved in each market, in different contexts. The price forecasts are performed using artificial neural networks, providing a specific database with the expected prices in the different market types, at each time. This database is then used as input by an evolutionary particle swarm optimization process, which originates the most advantage participation portfolio for the market player. The proposed approach is tested and validated with simulations performed in multiagent simulator of competitive electricity markets, using real electricity markets data from the Iberian operator-MIBEL.

A Further Study on Mining DNA Motifs Using Fuzzy Self-Organizing Maps

Self-organizing map (SOM)-based motif mining, despite being a promising approach for problem solving, mostly fails to offer a consistent interpretation of clusters with respect to the mixed composition of signal and noise in the nodes. The main reason behind this shortcoming comes from the similarity metrics used in data assignment, specially designed with the biological interpretation for this domain, which are not meant to consider the inevitable noise mixture in the clusters. This limits the explicability of the majority of clusters that are supposedly noise dominated, degrading the overall system clarity in motif discovery. This paper aims to improve the explicability aspect of learning process by introducing a composite similarity function (CSF) that is specially designed for the k -mer-to-cluster similarity measure with respect to the degree of motif properties and embedded noise in the cluster. Our proposed motif finding algorithm in this paper is built on our previous work robust elicitation algorithms for discovering (READ) [1] and termed READ Deoxyribonucleic acid motifs using CSFs (READ(csf)), which performs slightly better than READ and shows some remarkable improvements over SOM-based SOMBRERO and SOMEA tools in terms of F-measure on the testing data sets. A real data set containing multiple motifs is used to explore the potential of the READ(csf) for more challenging biological data mining tasks. Visual comparisons with the verified logos extracted from JASPAR database demonstrate that our algorithm is promising to discover multiple motifs simultaneously.