Discovering Knowledge from Local Patterns with Global Constraints

It is well known that local patterns are at the core of a lot of knowledge which may be discovered from data. Nevertheless, use of local patterns is limited by their huge number and computational costs. Several approaches (e.g., condensed representations, pattern set discovery) aim at grouping or synthesizing local patterns to provide a global view of the data. A global pattern is a pattern which is a set or a synthesis of local patterns coming from the data. In this paper, we propose the idea of global constraints to write queries addressing global patterns. A key point is the ability to bias the designing of global patterns according to the expectation of the user. For instance, a global pattern can be oriented towards the search of exceptions or a clustering. It requires to write queries taking into account such biases. Open issues are to design a generic framework to express powerful global constraints and solvers to mine them. We think that global constraints are a promising way to discover relevant global patterns

Unexpected rules using a conceptual distance based on fuzzy ontology

AbstractOne of the major drawbacks of data mining methods is that they generate a notably large number of rules that are often obvious or useless or, occasionally, out of the user’s interest. To address such drawbacks, we propose in this paper an approach that detects a set of unexpected rules in a discovered association rule set. Generally speaking, the proposed approach investigates the discovered association rules using the user’s domain knowledge, which is represented by a fuzzy domain ontology. Next, we rank the discovered rules according to the conceptual distances of the rules

Discovering Unexpected Patterns in Temporal Data Using Temporal Logic

There has been much attention given recently to the task of finding interesting patterns in temporal databases. Since there are so many different approaches to the problem of discovering temporal patterns, we first present a characterization of different discovery tasks and then focus on one task of discovering interesting patterns of events in temporal sequences. Given an (infinite) temporal database or a sequence of events one can, in general, discover an infinite number of temporal patterns in this data. Therefore, it is important to specify some measure of interestingness for discovered patterns and then select only the patterns interesting according to this measure. We present a probabilistic measure of interestingness based on unexpectedness, whereby a pattern P is deemed interesting if the ratio of the actual number of occurrences of P exceeds the expected number of occurrences of P by some user defined threshold. We then make use of a subset of the propositional, linear temporal logic and present an efficient algorithm that discovers unexpected patterns in temporal data. Finally, we apply this algorithm to synthetic data, UNIX operating system calls, and Web logfiles and present the results of these experiments.Information Systems Working Papers Serie

Virus evolution : the emergence of new ideas (and re-emergence of old ones)

Reputed intractable, the question of the origin of viruses has long been neglected. In the modern literature 'Virus evolution' has come to refer to study more akin to population genetics, such as the world-wide scrutiny on new polymorphisms appearing daily in the H5N1 avian flu virus [1], than to the fundamental interrogation: where do viruses come from? This situation is now rapidly changing, due to the coincidence of bold new ideas (and sometimes the revival of old ones), the unexpected features exhibited by recently isolated spectacular viruses [2] (see at URL: www.giantvirus.org), as well as the steady increase of genomic sequences for 'regular' viruses and cellular organisms enhancing the power of comparative genomics [3]. After being considered non-living and relegated in the wings by a majority of biologists, viruses are now pushed back on the center stage: they might have been at the origin of DNA, of the eukaryotic cell, and even of today's partition of biological organisms into 3 domains of life: bacteria, archaea and eukarya. Here, I quickly survey some of the recent discoveries and the new evolutionary thoughts they have prompted, before adding to the confusion with one interrogation of my own: what if we totally missed the true nature of (at least some) viruses?Comment: submitte

No wisdom in the crowd: genome annotation at the time of big data - current status and future prospects

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader