Inductive Programming

Abstract Motivation Although the outbreak of the severe acute respiratory syndrome (SARS) is currently over, it is expected that it will return to attack human beings. A critical challenge to scientists from various disciplines worldwide is to study the specificity of cleavage activity of SARS-related coronavirus (SARS-CoV) and use the knowledge obtained from the study for effective inhibitor design to fight the disease. The most commonly used inductive programming methods for knowledge discovery from data assume that the elements of input patterns are orthogonal to each other. Suppose a sub-sequence is denoted as P2P1P1′P2′, the conventional inductive programming method may result in a rule like ‘if P1 = Q, then the sub-sequence is cleaved, otherwise non-cleaved’. If the site P1 is not orthogonal to the others (for instance, P2, P1′ and P2′), the prediction power of these kind of rules may be limited. Therefore this study is aimed at developing a novel method for constructing non-orthogonal decision trees for mining protease data. Result Eighteen sequences of coronavirus polyprotein were downloaded from NCBI (http://www.ncbi.nlm.nih.gov). Among these sequences, 252 cleavage sites were experimentally determined. These sequences were scanned using a sliding window with size k to generate about 50 000 k-mer sub-sequences (for short, k-mers). The value of k varies from 4 to 12 with a gap of two. The bio-basis function proposed by Thomson et al. is used to transform the k-mers to a high-dimensional numerical space on which an inductive programming method is applied for the purpose of deriving a decision tree for decision-making. The process of this transform is referred to as a bio-mapping. The constructed decision trees select about 10 out of 50 000 k-mers. This small set of selected k-mers is regarded as a set of decisive templates. By doing so, non-orthogonal decision trees are constructed using the selected templates and the prediction accuracy is significantly improved. Availability The program for bio-mapping can be obtained by request to the author. Contact [email protected]

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Semantic programming by example with pre-trained models

Proceedings of the ACM on Programming Languages ◽

10.1145/3485477 ◽

2021 ◽

Vol 5 (OOPSLA) ◽

pp. 1-25

Author(s):

Gust Verbruggen ◽

Vu Le ◽

Sumit Gulwani

Keyword(s):

Syntactic Structure ◽

Language Model ◽

Expressive Power ◽

Language Models ◽

Inductive Synthesis ◽

Inductive Programming ◽

The Given ◽

Learning Language ◽

Semantic Operators

The ability to learn programs from few examples is a powerful technology with disruptive applications in many domains, as it allows users to automate repetitive tasks in an intuitive way. Existing frameworks on inductive synthesis only perform syntactic manipulations, where they rely on the syntactic structure of the given examples and not their meaning. Any semantic manipulations, such as transforming dates, have to be manually encoded by the designer of the inductive programming framework. Recent advances in large language models have shown these models to be very adept at performing semantic transformations of its input by simply providing a few examples of the task at hand. When it comes to syntactic transformations, however, these models are limited in their expressive power. In this paper, we propose a novel framework for integrating inductive synthesis with few-shot learning language models to combine the strength of these two popular technologies. In particular, the inductive synthesis is tasked with breaking down the problem in smaller subproblems, among which those that cannot be solved syntactically are passed to the language model. We formalize three semantic operators that can be integrated with inductive synthesizers. To minimize invoking expensive semantic operators during learning, we introduce a novel deferred query execution algorithm that considers the operators to be oracles during learning. We evaluate our approach in the domain of string transformations: the combination methodology can automate tasks that cannot be handled using either technologies by themselves. Finally, we demonstrate the generality of our approach via a case study in the domain of string profiling.

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