Mining frequent biological sequences based on bitmap without candidate sequence generation

Biological sequences carry a lot of important genetic information of organisms. Furthermore, there is an inheritance law related to protein function and structure which is useful for applications such as disease prediction. Frequent sequence mining is a core technique for association rule discovery, but existing algorithms suffer from low efficiency or poor error rate because biological sequences differ from general sequences with more characteristics. In this paper, an algorithm for mining Frequent Biological Sequence based on Bitmap, FBSB, is proposed. FBSB uses bitmaps as the simple data structure and transforms each row into a quicksort list QS-list for sequence growth. For the continuity and accuracy requirement of biological sequence mining, tested sequences used during the mining process of FBSB are real ones instead of generated candidates, and all the frequent sequences can be mined without any errors. Comparing with other algorithms, the experimental results show that FBSB can achieve a better performance on both run time and scalability

Colossal Trajectory Mining: A unifying approach to mine behavioral mobility patterns

Spatio-temporal mobility patterns are at the core of strategic applications such as urban planning and monitoring. Depending on the strength of spatio-temporal constraints, different mobility patterns can be defined. While existing approaches work well in the extraction of groups of objects sharing fine-grained paths, the huge volume of large-scale data asks for coarse-grained solutions. In this paper, we introduce Colossal Trajectory Mining (CTM) to efficiently extract heterogeneous mobility patterns out of a multidimensional space that, along with space and time dimensions, can consider additional trajectory features (e.g., means of transport or activity) to characterize behavioral mobility patterns. The algorithm is natively designed in a distributed fashion, and the experimental evaluation shows its scalability with respect to the involved features and the cardinality of the trajectory dataset

Complexity, BioComplexity, the Connectionist Conjecture and Ontology of Complexity\ud

This paper develops and integrates major ideas and concepts on complexity and biocomplexity - the connectionist conjecture, universal ontology of complexity, irreducible complexity of totality & inherent randomness, perpetual evolution of information, emergence of criticality and equivalence of symmetry & complexity. This paper introduces the Connectionist Conjecture which states that the one and only representation of Totality is the connectionist one i.e. in terms of nodes and edges. This paper also introduces an idea of Universal Ontology of Complexity and develops concepts in that direction. The paper also develops ideas and concepts on the perpetual evolution of information, irreducibility and computability of totality, all in the context of the Connectionist Conjecture. The paper indicates that the control and communication are the prime functionals that are responsible for the symmetry and complexity of complex phenomenon. The paper takes the stand that the phenomenon of life (including its evolution) is probably the nearest to what we can describe with the term “complexity”. The paper also assumes that signaling and communication within the living world and of the living world with the environment creates the connectionist structure of the biocomplexity. With life and its evolution as the substrate, the paper develops ideas towards the ontology of complexity. The paper introduces new complexity theoretic interpretations of fundamental biomolecular parameters. The paper also develops ideas on the methodology to determine the complexity of “true” complex phenomena.\u

ARM-AMO: An Efficient Association Rule Mining Algorithm Based on Animal Migration Optimization

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI linkAssociation rule mining (ARM) aims to find out association rules that satisfy predefined minimum support and confidence from a given database. However, in many cases ARM generates extremely large number of association rules, which are impossible for end users to comprehend or validate, thereby limiting the usefulness of data mining results. In this paper, we propose a new mining algorithm based on Animal Migration Optimization (AMO), called ARM-AMO, to reduce the number of association rules. It is based on the idea that rules which are not of high support and unnecessary are deleted from the data. Firstly, Apriori algorithm is applied to generate frequent itemsets and association rules. Then, AMO is used to reduce the number of association rules with a new fitness function that incorporates frequent rules. It is observed from the experiments that, in comparison with the other relevant techniques, ARM-AMO greatly reduces the computational time for frequent item set generation, memory for association rule generation, and the number of rules generated

ARM-AMO: An Efficient Association Rule Mining Algorithm Based on Animal Migration Optimization

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI linkAssociation rule mining (ARM) aims to find out association rules that satisfy predefined minimum support and confidence from a given database. However, in many cases ARM generates extremely large number of association rules, which are impossible for end users to comprehend or validate, thereby limiting the usefulness of data mining results. In this paper, we propose a new mining algorithm based on Animal Migration Optimization (AMO), called ARM-AMO, to reduce the number of association rules. It is based on the idea that rules which are not of high support and unnecessary are deleted from the data. Firstly, Apriori algorithm is applied to generate frequent itemsets and association rules. Then, AMO is used to reduce the number of association rules with a new fitness function that incorporates frequent rules. It is observed from the experiments that, in comparison with the other relevant techniques, ARM-AMO greatly reduces the computational time for frequent item set generation, memory for association rule generation, and the number of rules generated

The Density of States of hole-doped Manganites: A Scanning Tunneling Microscopy/Spectroscopy study

Variable temperature scanning tunneling microscopy/spectroscopy studies on single crystals and epitaxial thin films of hole-doped manganites, which show colossal magnetoresistance, have been done. We have investigated the variation of the density of states, at and near the Fermi energy ($E_f$), as a function of temperature. Simple calculations have been carried out, to find out the effect of temperature on the tunneling spectra and extract the variation of density of states with temperature, from the observed data. We also report here, atomic resolution images, on the single crystals and larger range images showing the growth patterns on thin films. Our investigation shows unambiguously that there is a rapid variation in density of states for temperatures near the Curie temperature ($T_c$). While for temperatures below $T_c$, a finite DOS is observed at $E_f$, for temperatures near $T_c$ a hard gap opens up in the density of states near $E_f$. For temperatures much higher than $T_c$, this gap most likely gives way to a soft gap. The observed hard gap for temperatures near $T_c$, is somewhat higher than the transport gap for all the materials. For different materials, we find that the magnitude of the hard gap decreases as the $T_c$ of the material increases and eventually, for materials with a $T_c$ close to 400 K, the value of the gap approaches zero.Comment: 9 pages RevTeX, 12 postscript figures, 1 table included in text, submitted to Physical Review