PASS: a simple classifier system for data analysis

Let x be a vector of predictors and y a scalar response associated with it. Consider the regression problem of inferring the relantionship between predictors and response on the basis of a sample of observed pairs (x,y). This is a familiar problem for which a variety of methods are available. This paper describes a new method based on the classifier system approach to problem solving. Classifier systems provide a rich framework for learning and induction, and they have been suc:cessfully applied in the artificial intelligence literature for some time. The present method emiches the simplest classifier system architecture with some new heuristic and explores its potential in a purely inferential context. A prototype called PASS (Predictive Adaptative Sequential System) has been built to test these ideas empirically. Preliminary Monte Carlo experiments indicate that PASS is able to discover the structure imposed on the data in a wide array of cases

Relatedness Measures to Aid the Transfer of Building Blocks among Multiple Tasks

Multitask Learning is a learning paradigm that deals with multiple different tasks in parallel and transfers knowledge among them. XOF, a Learning Classifier System using tree-based programs to encode building blocks (meta-features), constructs and collects features with rich discriminative information for classification tasks in an observed list. This paper seeks to facilitate the automation of feature transferring in between tasks by utilising the observed list. We hypothesise that the best discriminative features of a classification task carry its characteristics. Therefore, the relatedness between any two tasks can be estimated by comparing their most appropriate patterns. We propose a multiple-XOF system, called mXOF, that can dynamically adapt feature transfer among XOFs. This system utilises the observed list to estimate the task relatedness. This method enables the automation of transferring features. In terms of knowledge discovery, the resemblance estimation provides insightful relations among multiple data. We experimented mXOF on various scenarios, e.g. representative Hierarchical Boolean problems, classification of distinct classes in the UCI Zoo dataset, and unrelated tasks, to validate its abilities of automatic knowledge-transfer and estimating task relatedness. Results show that mXOF can estimate the relatedness reasonably between multiple tasks to aid the learning performance with the dynamic feature transferring.Comment: accepted by The Genetic and Evolutionary Computation Conference (GECCO 2020

KACST Arabic Text Classification Project: Overview and Preliminary Results

Electronically formatted Arabic free-texts can be found in abundance these days on the World Wide Web, often linked to commercial enterprises and/or government organizations. Vast tracts of knowledge and relations lie hidden within these texts, knowledge that can be exploited once the correct intelligent tools have been identified and applied. For example, text mining may help with text classification and categorization. Text classification aims to automatically assign text to a predefined category based on identifiable linguistic features. Such a process has different useful applications including, but not restricted to, E-Mail spam detection, web pages content filtering, and automatic message routing. In this paper an overview of King Abdulaziz City for Science and Technology (KACST) Arabic Text Classification Project will be illustrated along with some preliminary results. This project will contribute to the better understanding and elaboration of Arabic text classification techniques

Automatic categorization of diverse experimental information in the bioscience literature

Background: Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. Results: We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions: Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort

Robust Subgraph Generation Improves Abstract Meaning Representation Parsing

The Abstract Meaning Representation (AMR) is a representation for open-domain rich semantics, with potential use in fields like event extraction and machine translation. Node generation, typically done using a simple dictionary lookup, is currently an important limiting factor in AMR parsing. We propose a small set of actions that derive AMR subgraphs by transformations on spans of text, which allows for more robust learning of this stage. Our set of construction actions generalize better than the previous approach, and can be learned with a simple classifier. We improve on the previous state-of-the-art result for AMR parsing, boosting end-to-end performance by 3 F$_1$ on both the LDC2013E117 and LDC2014T12 datasets.Comment: To appear in ACL 201

On the emergence and evolution of artificial cell signaling networks

This PhD project is concerned with the evolution of Cell Signaling Networks (CSNs) in silico. CSNs are complex biochemical networks responsible for the coordination of cellular activities. We are investigating the possibility to build an evolutionary simulation platform that would allow the spontaneous emergence and evolution of Artificial Cell Signaling Networks (ACSNs). From a practical point of view, realizing and evolving ACSNs may provide novel computational paradigms for a variety of application areas. This work may also contribute to the biological understanding of the origins and evolution of real CSNs