16380223
Learning Chomsky-like Grammars for Biological Sequence Families
This paper presents a new method of measuring performance when positives are rare and investigates whether Chomsky-like grammar representations are useful for learning accurate comprehensible predictors of members of biological sequence families. The positive-only learning framework of the Inductive Logic Programming (ILP) system CProgol is used to generate a grammar for recognising a class of proteins known as human neuropeptide precursors (NPPs). As far as these authors are aware, this is both the first biological grammar learnt using ILP and the first real-world scientific application of the positive-only learning framework of CProgol. Performance is measured using both predictive accuracy and a new cost function, em Relative Advantage (RA). The RA results show that searching for NPPs by using our best NPP predictor as a filter is more than 100 times more efficient than randomly selecting proteins for synthesis and testing them for biological activity. The highest RA was achieved by a model which includes grammar-derived features. This RA is significantly higher than the best RA achieved without the use of the grammar-derived features.
27782030
The Applicability to ILP of Results Concerning the Ordering of Binomial Populations
Results obtained in the 1950's on the ordering of k binomial populations are directly applicable to computing the size of data sample required to identify the best amongst k theories in an ILP search. The basic problem considered is that of selecting the best one of k (k ≥= 2) binomial populations on the basis of the observed frequency of 'success' on n observations. In the statistical formulation of the problem the experimenter specifies that he or she would like to guarantee that the probability of correct selection is at least P* (0 ≤ P* < 1) whenever the true difference between the best and second best population is at least d* (0 < d* ≤ 1). The principal result of interest is that for large values of k, the value of n required to meet any fixed specification (d*, P*) is approximately equal to some constant multiple of ln k. Depending on the k, d* and P* specified, this value of n can be substantially lower than that obtained within the corresponding PAC formulation. Applied to the search conducted by an ILP algorithm, the result guarantees with confidence level P*, that the true accuracy of the theory selected will be no more than d* below that of the best theory. In this paper, we review this basic result and test its predictions empirically. We also comment on the relevance to ILP of more recent work in the field.
8863872
The Predictive Toxicology Evaluation Challenge
Can an AI program contribute to scientific discovery? An area where this gauntlet has been thrown is that of understanding the mechanisms of chemical carcinogenesis. One approach is to obtain Structure-Activity Relationships (SARs) relating molecular structure to cancerous activity. Vital to this are the rodent carcinogenicity tests conducted within the US National Toxicology Program by the National Institute of Environmental Health Sciences (NIEHS). This has resulted in a large database of compounds classified as carcinogens or otherwise. The Predictive-Toxicology Evaluation project of the NIEHS provides the opportunity to compare carcinogenicity predictions on previously untested chemicals. This presents a formidable challenge for programs concerned with knowledge discovery. Desirable features of this problem are: (1) involvement in genuine scientific discovery; (2) availability of a large database with expert-certified classifications; (3) strong competition from methods used by chemists; and (4) participation in true blind trials, with results available by next IJCAI. We describe the materials and methods constituting this challenge, and provide some initial benchmarks. These show the Inductive Logic Programming tool Progol to be competitive with current state-of-the-art. The challenge described here is aimed at encouraging AI programs to avail themselves the opportunity of contributing to an enterprise with immediate scientific value.
18104124
A Note on Two Simple Transformations for Improving the Efficiency of an ILP System
Inductive Logic Programming (ILP) systems have had noteworthy successes in extracting comprehensible and accurate models for data drawn from a number of scientific and engineering domains. These results suggest that ILP methods could enhance the model-construction capabilities of software tools being developed for the emerging discipline of "knowledge discovery from databases." One significant concern in the use of ILP for this purpose is that of efficiency. The performance of modern ILP systems is principally affected by two issues: (1) they often have to search through very large numbers of possible rules (usually in the form of definite clauses); (2) they have to score each rule on the data (usually in the form of ground facts) to estimate "goodness". Stochastic and greedy approaches have been proposed to alleviate the complexity arising from each of these issues. While these techniques can result in order-of-magnitude improvements in the worst-case search complexity of an ILP system, they do so at the expense of exactness. As this may be unacceptable in some situations, we examine two methods that result in admissible transformations of clauses examined in a search. While the methods do not alter the size ofthe search space (that is, the number of clauses examined), they can alleviate the theorem-proving effort required to estimate goodness. The first transformation simply involves eliminating literals using a weak test for redundancy. The second involves partitioning the set of literals within a clause into groups that can be executed independently of each other. The efficacy ofthe se transformations are evaluated empirically on a number of well-known ILP datasets. The results suggest that for problems that require the use of highly nondeterminate predicates, the transformations can provide significant gains as the complexity of clauses sought increases.
15982740
Carcinogenesis Predictions Using ILP
Obtaining accurate structural alerts for the causes of chemical cancers is a problem of great scientific and humanitarian value. This paper follows up on earlier research that demonstrated the use of Inductive Logic Programming (ILP) for predictions for the related problem of mutagenic activity amongst nitroaromatic molecules. Here we are concerned with predicting carcinogenic activity in rodent bioassays using data from the U.S. National Toxicology Program conducted by the National Institute of Environmental Health Sciences. The 330 chemicals used here are significantly more diverse than the previous study, and form the basis for obtaining Structure-Activity Relationships (SARs) relating molecular structure to cancerous activity in rodents. We describe the use of the ILP system Progol to obtain SARs from this data. The rules obtained from Progol are comparable in accuracy to those from expert chemists, and more accurate than most state-of-the-art toxicity prediction methods. The rules can also be interpreted to give clues about the biological and chemical mechanisms of carcinogenesis, and make use of those learnt by Progol for mutagenesis. Finally, we present details of, and predictions for, an ongoing international blind trial aimed specifically at comparing prediction methods. This trial provides ILP algorithms an opportunity to participate at the leading-edge of scientific discovery.
2211677
Lattice-Search Runtime Distributions May Be Heavy-Tailed
Recent empirical studies show that runtime distributions of backtrack procedures for solving hard combinatorial problems often have intriguing properties. Unlike standard distributions (such as the normal), such distributions decay slower than exponentially and have "heavy tails". Procedures characterized by heavy-tailed runtime distributions exhibit large variability in efficiency, but a very straightforward method called rapid randomized restarts has been designed to essentially improve their average performance. We show on two experimental domains that heavy-tailed phenomena can be observed in ILP, namely in the search for a clause in the subsumption lattice. We also reformulate the technique of randomized rapid restarts to make it applicable in ILP and show that it can reduce the average search-time.
16475170
Optimal rate-based scheduling on multiprocessors
The PD2 Pfair/ERfair scheduling algorithm is the most efficient known algorithm for optimally scheduling periodic tasks on multiprocessors. In this paper, we prove that PD2 is also optimal for scheduling "rate-based" tasks whose processing steps may be highly jittered. The rate-based task model we consider generalizes the widely-studied sporadic task model.
7812373
Improved bounds on the sample complexity of learning
We present a new general upper bound on the number of examples required to estimate all of the expectations of a set of random variables uniformly well. The quality of the estimates is measured using a variant of the relative error proposed by Haussler and Pollard. We also show that our bound is within a constant factor of the best possible. Our upper bound implies improved bounds on the sample complexity of learning according to Haussler's decision theoretic model.
44926291
Low Discrepancy Sets Yield Approximate Min-Wise Independent Permutation Families
Motivated by a problem of filtering near-duplicate Web documents, Broder, Charikar, Frieze & Mitzenmacher defined the following notion of e-approximate min-wise independent permutation families [2]. A multiset \(\mathcal{F}\) of permutations of {0,1, ... , n–1} is such a family if for all K ⊆ {0,1, ..., n–1} and any x ∈ K, a permutation π chosen uniformly at random form \(\mathcal{F}\) statisfies
5519685
Efficient scheduling of soft real-time applications on multiprocessors
In this paper, we consider fair scheduling of soft real-time applications on multiprocessors using the earliest pseudo deadline first (EPDF) Pfair algorithm. Our main contributions are twofold. First, we establish a condition for ensuring a tardiness of at most one quantum under EPDF. This condition is very liberal and should often hold in practice. Second, we present simulation results involving randomly-generated task sets, including those that do not satisfy our condition. In these experiments, deadline misses were rare, and no misses by more than one quantum ever occurred.
9220714
Extracting Context-Sensitive Models in Inductive Logic Programming
Given domain-specific background knowledge and data in the form of examples, an Inductive Logic Programming (ILP) system extracts models in the data-analytic sense. We view the model-selection step facing an ILP system as a decision problem, the solution of which requires knowledge of the context in which the model is to be deployed. In this paper, "context" will be defined by the current specification of the prior class distribution and the client's preferences concerning errors of classification. Within this restricted setting, we consider the use of an ILP system in situations where: (a) contexts can change regularly. This can arise for example, from changes to class distributions or misclassification costs; and (b) the data are from observational studies. That is, they may not have been collected with any particular context in mind. Some repercussions of these are: (a) any one model may not be the optimal choice forall contexts; and (b) not all the background information provided may be relevant for all contexts. Using results from the analysis of Receiver Operating Characteristic curves, we investigate a technique that can equip an ILP system to reject those models that cannot possibly be optimal in any context. We present empirical results from using the technique to analyse two datasets concerned with the toxicity of chemicals (in particular, their mutagenic and carcinogenic properties). Clients can, and typically do, approach such datasets with quite different requirements. For example, a synthetic chemist would require models with a low rate of commission errors which could be used to direct efficiently the synthesis of new compounds. A toxicologist on the other hand, would prefer models with a low rate of omission errors. This would enable a more complete identification of toxic chemicals at a calculated cost of misidentification of non-toxic cases as toxic. The approach adopted here attempts to obtain a solution that contains models that are optimal for each such user according to the cost function that he or she wishes to apply. In doing so, it also provides one solution to the problem of how the relevance of background predicates is to be assessed in ILP.