30 research outputs found
Using Answer Set Programming for pattern mining
Serial pattern mining consists in extracting the frequent sequential patterns
from a unique sequence of itemsets. This paper explores the ability of a
declarative language, such as Answer Set Programming (ASP), to solve this issue
efficiently. We propose several ASP implementations of the frequent sequential
pattern mining task: a non-incremental and an incremental resolution. The
results show that the incremental resolution is more efficient than the
non-incremental one, but both ASP programs are less efficient than dedicated
algorithms. Nonetheless, this approach can be seen as a first step toward a
generic framework for sequential pattern mining with constraints.Comment: Intelligence Artificielle Fondamentale (2014
Prefix-Projection Global Constraint for Sequential Pattern Mining
Sequential pattern mining under constraints is a challenging data mining
task. Many efficient ad hoc methods have been developed for mining sequential
patterns, but they are all suffering from a lack of genericity. Recent works
have investigated Constraint Programming (CP) methods, but they are not still
effective because of their encoding. In this paper, we propose a global
constraint based on the projected databases principle which remedies to this
drawback. Experiments show that our approach clearly outperforms CP approaches
and competes well with ad hoc methods on large datasets
Reductions for Frequency-Based Data Mining Problems
Studying the computational complexity of problems is one of the - if not the
- fundamental questions in computer science. Yet, surprisingly little is known
about the computational complexity of many central problems in data mining. In
this paper we study frequency-based problems and propose a new type of
reduction that allows us to compare the complexities of the maximal frequent
pattern mining problems in different domains (e.g. graphs or sequences). Our
results extend those of Kimelfeld and Kolaitis [ACM TODS, 2014] to a broader
range of data mining problems. Our results show that, by allowing constraints
in the pattern space, the complexities of many maximal frequent pattern mining
problems collapse. These problems include maximal frequent subgraphs in
labelled graphs, maximal frequent itemsets, and maximal frequent subsequences
with no repetitions. In addition to theoretical interest, our results might
yield more efficient algorithms for the studied problems.Comment: This is an extended version of a paper of the same title to appear in
the Proceedings of the 17th IEEE International Conference on Data Mining
(ICDM'17
MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences
This paper presents a web service named MAGIIC-PRO, which aims to discover functional signatures of a query protein by sequential pattern mining. Automatic discovery of patterns from unaligned biological sequences is an important problem in molecular biology. MAGIIC-PRO is different from several previously established methods performing similar tasks in two major ways. The first remarkable feature of MAGIIC-PRO is its efficiency in delivering long patterns. With incorporating a new type of gap constraints and some of the state-of-the-art data mining techniques, MAGIIC-PRO usually identifies satisfied patterns within an acceptable response time. The efficiency of MAGIIC-PRO enables the users to quickly discover functional signatures of which the residues are not from only one region of the protein sequences or are only conserved in few members of a protein family. The second remarkable feature of MAGIIC-PRO is its effort in refining the mining results. Considering large flexible gaps improves the completeness of the derived functional signatures. The users can be directly guided to the patterns with as many blocks as that are conserved simultaneously. In this paper, we show by experiments that MAGIIC-PRO is efficient and effective in identifying ligand-binding sites and hot regions in protein–protein interactions directly from sequences. The web service is available at and a mirror site at
DESQ: Frequent Sequence Mining with Subsequence Constraints
Frequent sequence mining methods often make use of constraints to control
which subsequences should be mined. A variety of such subsequence constraints
has been studied in the literature, including length, gap, span,
regular-expression, and hierarchy constraints. In this paper, we show that many
subsequence constraints---including and beyond those considered in the
literature---can be unified in a single framework. A unified treatment allows
researchers to study jointly many types of subsequence constraints (instead of
each one individually) and helps to improve usability of pattern mining systems
for practitioners. In more detail, we propose a set of simple and intuitive
"pattern expressions" to describe subsequence constraints and explore
algorithms for efficiently mining frequent subsequences under such general
constraints. Our algorithms translate pattern expressions to compressed finite
state transducers, which we use as computational model, and simulate these
transducers in a way suitable for frequent sequence mining. Our experimental
study on real-world datasets indicates that our algorithms---although more
general---are competitive to existing state-of-the-art algorithms.Comment: Long version of the paper accepted at the IEEE ICDM 2016 conferenc
Classification with Single Constraint Progressive Mining of Sequential Patterns
Classification based on sequential pattern data has become an important topic to explore. One of research has been carried was the Classify-By-Sequence, CBS. CBS classified data based on sequential patterns obtained from AprioriLike sequential pattern mining. Sequential patterns obtained were called CSP, Classifiable Sequential Patterns. CSP was used as classifier rules or features for the classification task. CBS used AprioriLike algorithm to search for sequential patterns. However, AprioriLike algorithm took a long time to search for them. Moreover, not all sequential patterns were important for the user. In order to get the right and meaningful features for classification, user uses a constraint in sequential pattern mining. Constraint is also expected to reduce the number of sequential patterns that are short and less meaningful to the user. Therefore, we developed CBS_CLASS* with Single Constraint Progressive Mining of Sequential Patterns or Single Constraint PISA or PISA*. CBS_Class* with PISA* was proven to classify data in faster time since it only processed lesser number of sequential patterns but still conform to user’s need. The experiment result showed that compared to CBS_CLASS, CBS_Class* reduced the classification execution time by 89.8%. Moreover, the accuracy of the classification process can still be maintained.
Rank Aggregation for Course Sequence Discovery
In this work, we adapt the rank aggregation framework for the discovery of
optimal course sequences at the university level. Each student provides a
partial ranking of the courses taken throughout his or her undergraduate
career. We compute pairwise rank comparisons between courses based on the order
students typically take them, aggregate the results over the entire student
population, and then obtain a proxy for the rank offset between pairs of
courses. We extract a global ranking of the courses via several state-of-the
art algorithms for ranking with pairwise noisy information, including
SerialRank, Rank Centrality, and the recent SyncRank based on the group
synchronization problem. We test this application of rank aggregation on 15
years of student data from the Department of Mathematics at the University of
California, Los Angeles (UCLA). Furthermore, we experiment with the above
approach on different subsets of the student population conditioned on final
GPA, and highlight several differences in the obtained rankings that uncover
hidden pre-requisites in the Mathematics curriculum
Hierarchies of Weighted Closed Partially-Ordered Patterns for Enhancing Sequential Data Analysis
International audienceDiscovering sequential patterns in sequence databases is an important data mining task. Recently, hierarchies of closed partially-ordered patterns (cpo-patterns), built directly using Relational Concept Analysis (RCA), have been proposed to simplify the interpretation step by highlighting how cpo-patterns relate to each other. However, there are practical cases (e.g. choosing interesting navigation paths in the obtained hierarchies) when these hierarchies are still insufficient for the expert. To address these cases, we propose to extract hierarchies of more informative cpo-patterns, namely weighted cpo-patterns (wcpo-patterns), by extending the RCA-based approach. These wcpo-patterns capture and explicitly show not only the order on itemsets but also their different influence on the analysed sequences. We illustrate how the proposed wcpo-patterns can enhance sequential data analysis on a toy example