Constraint based and hypothetical reasoning for human and molecular biology languages

作为人工智能的一个分支，语言语法和规则的计算研究的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可以被视为一种由四个字母（核苷酸a， C， T和G）组成的字母表的语言，基因组可以被视为“生命之书”。这项研究旨在通过进一步交叉这些领域来扩展我们对人类语言的理解，而且扩展我们对生命语言的理解。我将探索有前途的语言处理方法的潜力，特别是HYPROLOG，我们新颖的逻辑编程语言，它通过允许用户探索“如果”场景来扩展经典逻辑的可能性，并使用溯因法（不合理但有用的推断p作为q的可能解释，假设p暗示q）来假设可能的解释。我还将进一步探索一个有前途的新语言范式，即属性语法，它允许解析不完整甚至不正确的输入。我将继续研究我最近开发的解析器，它无形地赋予非计算机专家（例如语言学家）的描述以直接和自动的，同时高效的可执行性。语义方面，以及与当前计算语言学理论的关系，将在中期进行研究。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，我将继续在自然语言处理领域与基于知识的系统领域进行交叉施肥，重点是知识发现。我最近的研究揭示了我的分析属性语法的方法在知识发现方面的实用性，特别是在从互联网上发现的任意文本中提取概念方面。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.