Constraint based and hypothetical reasoning for human and molecular biology languages

语言语法和规则的计算研究是人工智能的一个分支，其最新进展具有实际应用的潜力。最值得注意的是，人类基因组的发现，部分是通过我帮助开发的方法（逻辑语法），突出了将分子生物学问题视为专门的语言问题的潜在好处：DNA可以被视为一种语言，有四个字母（核苷酸A，C，T和G），基因组可以被视为“生命之书”。 拟议的研究旨在通过进一步交织这些领域，扩展我们对人类语言和生命语言的理解。我将探讨潜在的有前途的语言处理方法，特别是HYPROSTRUCTURE，我们的新的逻辑编程语言，它扩展了经典逻辑的可能性，允许用户探索“如果”的情况下，并假设可能的解释使用溯因（不健全的，但有用的推断p作为一个可能的解释q鉴于p意味着q）。 我还将进一步探索一个有前途的新的语言学范式，即属性语法，它允许不完整甚至不正确的输入被解析。研究将继续在我最近开发的解析器，无形中赋予非计算机专家（如语言学家）的描述直接和自动，而有效的，可执行性。语义方面，以及与当前计算语言学理论的关系，将在中期进行审查。从长远来看，这项研究有望为语言学家带来工业上有用的专家系统，甚至可能对语言学理论本身产生影响。 最后，我将继续交叉研究自然语言处理领域与基于知识的系统，重点是知识发现。我最近的研究已经发现了我的方法的有用性，用于解析属性语法应用于知识发现，特别是从互联网上发现的任意文本中提取概念。这有许多有趣的短期潜在副产品，例如应用于系统发育分类。

Recent advances in the computational study of language grammars and rules, a branch of Artificial Intelligence, have the potential for practical, real-world applications. Most notably, the discovery of the human genome, partly through methodologies I helped develop (logic grammars), has highlighted the potential benefits of viewing molecular biology problems as specialized linguistic problems: DNA can be seen as a language with an alphabet of four letters (the nucleotides A, C, T and G), and  the genome can be viewed as the 'book of life'.      The proposed research aims at extending our understanding of not only human languages, but the language of life, by further interleaving these fields. I will explore the potential of promising methodologies for language processing, in particular HYPROLOG, our novel logic programming language which extends the possibilities of classical logic by allowing the user to explore "what if" scenarios, and to hypothesize possible explanations using abduction (the unsound but useful inference of p as a possible explanation for q given that p implies q).      I will also further explore a promising new linguistic paradigm, that of Property Grammars, which allows incomplete and even incorrect input to be parsed. Research will continue on my recently developed parser that invisibly endows descriptions made by non-computer specialists (e.g. linguists) with direct and automatic, while efficient, executability. Semantic aspects, and relation to current computational linguistic theories, will be examined in the medium term. In the long term, this research is expected to result in industrially useful expert systems for linguists, and perhaps even to have an impact on linguistic theory itself.      Finally, I will continue cross-fertilizing the natural language processing field with that of knowledge based systems, focussing on knowledge discovery. My recent research has uncovered the usefulness of my methodology for parsing property grammars as applied to knowledge discovery, in particular, for extracting concepts from arbitrary text found in the internet. This has many interesting short-term potential spin-offs, e.g. applications to phylogenetic classification.