A knowledge representation meta-model for rule-based modelling of signalling networks

The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their literatures and data are consequently fragmented, distributed and sometimes--at least apparently--inconsistent. This makes it extremely difficult to build significant explanatory models with the result that effects in these systems that are brought about by many interacting factors are poorly understood. The rule-based approach to modelling has shown some promise for the representation of the highly combinatorial systems typically found in signalling where many of the proteins are composed of multiple binding domains, capable of simultaneous interactions, and/or peptide motifs controlled by post-translational modifications. However, the rule-based approach requires highly detailed information about the precise conditions for each and every interaction which is rarely available from any one single source. Rather, these conditions must be painstakingly inferred and curated, by hand, from information contained in many papers--each of which contains only part of the story. In this paper, we introduce a graph-based meta-model, attuned to the representation of cellular signalling networks, which aims to ease this massive cognitive burden on the rule-based curation process. This meta-model is a generalization of that used by Kappa and BNGL which allows for the flexible representation of knowledge at various levels of granularity. In particular, it allows us to deal with information which has either too little, or too much, detail with respect to the strict rule-based meta-model. Our approach provides a basis for the gradual aggregation of fragmented biological knowledge extracted from the literature into an instance of the meta-model from which we can define an automated translation into executable Kappa programs.Comment: In Proceedings DCM 2015, arXiv:1603.0053

Two Algebraic Process Semantics for Contextual Nets

We show that the so-called 'Petri nets are monoids' approach initiated by Meseguer and Montanari can be extended from ordinary place/transition Petri nets to contextual nets by considering suitable non-free monoids of places. The algebraic characterizations of net concurrent computations we provide cover both the collective and the individual token philosophy, uniformly along the two interpretations, and coincide with the classical proposals for place/transition Petri nets in the absence of read-arcs

Strict General Setting for Building Decision Procedures into Theorem Provers

The efficient and flexible incorporating of decision procedures into theorem provers is very important for their successful use. There are several approaches for combining and augmenting of decision procedures; some of them support handling uninterpreted functions, congruence closure, lemma invoking etc. In this paper we present a variant of one general setting for building decision procedures into theorem provers (gs framework [18]). That setting is based on macro inference rules motivated by techniques used in different approaches. The general setting enables a simple describing of different combination/augmentation schemes. In this paper, we further develop and extend this setting by an imposed ordering on the macro inference rules. That ordering leads to a ”strict setting”. It makes implementing and using variants of well-known or new schemes within this framework a very easy task even for a non-expert user. Also, this setting enables easy comparison of different combination/augmentation schemes and combination of their ideas

A User-Centered Concept Mining System for Query and Document Understanding at Tencent

Concepts embody the knowledge of the world and facilitate the cognitive processes of human beings. Mining concepts from web documents and constructing the corresponding taxonomy are core research problems in text understanding and support many downstream tasks such as query analysis, knowledge base construction, recommendation, and search. However, we argue that most prior studies extract formal and overly general concepts from Wikipedia or static web pages, which are not representing the user perspective. In this paper, we describe our experience of implementing and deploying ConcepT in Tencent QQ Browser. It discovers user-centered concepts at the right granularity conforming to user interests, by mining a large amount of user queries and interactive search click logs. The extracted concepts have the proper granularity, are consistent with user language styles and are dynamically updated. We further present our techniques to tag documents with user-centered concepts and to construct a topic-concept-instance taxonomy, which has helped to improve search as well as news feeds recommendation in Tencent QQ Browser. We performed extensive offline evaluation to demonstrate that our approach could extract concepts of higher quality compared to several other existing methods. Our system has been deployed in Tencent QQ Browser. Results from online A/B testing involving a large number of real users suggest that the Impression Efficiency of feeds users increased by 6.01% after incorporating the user-centered concepts into the recommendation framework of Tencent QQ Browser.Comment: Accepted by KDD 201

Follow-up question handling in the IMIX and Ritel systems: A comparative study

One of the basic topics of question answering (QA) dialogue systems is how follow-up questions should be interpreted by a QA system. In this paper, we shall discuss our experience with the IMIX and Ritel systems, for both of which a follow-up question handling scheme has been developed, and corpora have been collected. These two systems are each other's opposites in many respects: IMIX is multimodal, non-factoid, black-box QA, while Ritel is speech, factoid, keyword-based QA. Nevertheless, we will show that they are quite comparable, and that it is fruitful to examine the similarities and differences. We shall look at how the systems are composed, and how real, non-expert, users interact with the systems. We shall also provide comparisons with systems from the literature where possible, and indicate where open issues lie and in what areas existing systems may be improved. We conclude that most systems have a common architecture with a set of common subtasks, in particular detecting follow-up questions and finding referents for them. We characterise these tasks using the typical techniques used for performing them, and data from our corpora. We also identify a special type of follow-up question, the discourse question, which is asked when the user is trying to understand an answer, and propose some basic methods for handling it