Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study

Peer reviewedPublisher PD

Pen-based Methods For Recognition and Animation of Handwritten Physics Solutions

There has been considerable interest in constructing pen-based intelligent tutoring systems due to the natural interaction metaphor and low cognitive load afforded by pen-based interaction. We believe that pen-based intelligent tutoring systems can be further enhanced by integrating animation techniques. In this work, we explore methods for recognizing and animating sketched physics diagrams. Our methodologies enable an Intelligent Tutoring System (ITS) to understand the scenario and requirements posed by a given problem statement and to couple this knowledge with a computational model of the student\u27s handwritten solution. These pieces of information are used to construct meaningful animations and feedback mechanisms that can highlight errors in student solutions. We have constructed a prototype ITS that can recognize mathematics and diagrams in a handwritten solution and infer implicit relationships among diagram elements, mathematics and annotations such as arrows and dotted lines. We use natural language processing to identify the domain of a given problem, and use this information to select one or more of four domain-specific physics simulators to animate the user\u27s sketched diagram. We enable students to use their answers to guide animation behavior and also describe a novel algorithm for checking recognized student solutions. We provide examples of scenarios that can be modeled using our prototype system and discuss the strengths and weaknesses of our current prototype. Additionally, we present the findings of a user study that aimed to identify animation requirements for physics tutoring systems. We describe a taxonomy for categorizing different types of animations for physics problems and highlight how the taxonomy can be used to define requirements for 50 physics problems chosen from a university textbook. We also present a discussion of 56 handwritten solutions acquired from physics students and describe how suitable animations could be constructed for each of them

Deep Learning for Free-Hand Sketch: A Survey

Free-hand sketches are highly illustrative, and have been widely used by humans to depict objects or stories from ancient times to the present. The recent prevalence of touchscreen devices has made sketch creation a much easier task than ever and consequently made sketch-oriented applications increasingly popular. The progress of deep learning has immensely benefited free-hand sketch research and applications. This paper presents a comprehensive survey of the deep learning techniques oriented at free-hand sketch data, and the applications that they enable. The main contents of this survey include: (i) A discussion of the intrinsic traits and unique challenges of free-hand sketch, to highlight the essential differences between sketch data and other data modalities, e.g., natural photos. (ii) A review of the developments of free-hand sketch research in the deep learning era, by surveying existing datasets, research topics, and the state-of-the-art methods through a detailed taxonomy and experimental evaluation. (iii) Promotion of future work via a discussion of bottlenecks, open problems, and potential research directions for the community.Comment: This paper is accepted by IEEE TPAM

Sketch recognition of digital ink diagrams : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Computer Science at Massey University, Palmerston North, New Zealand

Figures are either re-used with permission, or abstracted with permission from the source article.Sketch recognition of digital ink diagrams is the process of automatically identifying hand-drawn elements in a diagram. This research focuses on the simultaneous grouping and recognition of shapes in digital ink diagrams. In order to recognise a shape, we need to group strokes belonging to a shape, however, strokes cannot be grouped until the shape is identified. Therefore, we treat grouping and recognition as a simultaneous task. Our grouping technique uses spatial proximity to hypothesise shape candidates. Many of the hypothesised shape candidates are invalid, therefore we need a way to reject them. We present a novel rejection technique based on novelty detection. The rejection method uses proximity measures to validate a shape candidate. In addition, we investigate on improving the accuracy of the current shape recogniser by adding extra features. We also present a novel connector recognition system that localises connector heads around recognised shapes. We perform a full comparative study on two datasets. The results show that our approach is significantly more accurate in finding shapes and faster on process diagram compared to Stahovich et al. (2014), which the results show the superiority of our approach in terms of computation time and accuracy. Furthermore, we evaluate our system on two public datasets and compare our results with other approaches reported in the literature that have used these dataset. The results show that our approach is more accurate in finding and recognising the shapes in the FC dataset (by finding and recognising 91.7% of the shapes) compared to the reported results in the literature

Mathematical Modelling and Machine Learning Methods for Bioinformatics and Data Science Applications

Mathematical modeling is routinely used in physical and engineering sciences to help understand complex systems and optimize industrial processes. Mathematical modeling differs from Artificial Intelligence because it does not exclusively use the collected data to describe an industrial phenomenon or process, but it is based on fundamental laws of physics or engineering that lead to systems of equations able to represent all the variables that characterize the process. Conversely, Machine Learning methods require a large amount of data to find solutions, remaining detached from the problem that generated them and trying to infer the behavior of the object, material or process to be examined from observed samples. Mathematics allows us to formulate complex models with effectiveness and creativity, describing nature and physics. Together with the potential of Artificial Intelligence and data collection techniques, a new way of dealing with practical problems is possible. The insertion of the equations deriving from the physical world in the data-driven models can in fact greatly enrich the information content of the sampled data, allowing to simulate very complex phenomena, with drastically reduced calculation times. Combined approaches will constitute a breakthrough in cutting-edge applications, providing precise and reliable tools for the prediction of phenomena in biological macro/microsystems, for biotechnological applications and for medical diagnostics, particularly in the field of precision medicine