A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

A binary self-organizing map and its FPGA implementation

A binary Self Organizing Map (SOM) has been designed and implemented on a Field Programmable Gate Array (FPGA) chip. A novel learning algorithm which takes binary inputs and maintains tri-state weights is presented. The binary SOM has the capability of recognizing binary input sequences after training. A novel tri-state rule is used in updating the network weights during the training phase. The rule implementation is highly suited to the FPGA architecture, and allows extremely rapid training. This architecture may be used in real-time for fast pattern clustering and classification of the binary features

Fourth-order flows in surface modelling

This short article is a brief account of the usage of fourth-order curvature flow in surface modelling

Adaptive Relaxed ADMM: Convergence Theory and Practical Implementation

Many modern computer vision and machine learning applications rely on solving difficult optimization problems that involve non-differentiable objective functions and constraints. The alternating direction method of multipliers (ADMM) is a widely used approach to solve such problems. Relaxed ADMM is a generalization of ADMM that often achieves better performance, but its efficiency depends strongly on algorithm parameters that must be chosen by an expert user. We propose an adaptive method that automatically tunes the key algorithm parameters to achieve optimal performance without user oversight. Inspired by recent work on adaptivity, the proposed adaptive relaxed ADMM (ARADMM) is derived by assuming a Barzilai-Borwein style linear gradient. A detailed convergence analysis of ARADMM is provided, and numerical results on several applications demonstrate fast practical convergence.Comment: CVPR 201

The view from elsewhere: perspectives on ALife Modeling

Many artificial life researchers stress the interdisciplinary character of the field. Against such a backdrop, this report reviews and discusses artificial life, as it is depicted in, and as it interfaces with, adjacent disciplines (in particular, philosophy, biology, and linguistics), and in the light of a specific historical example of interdisciplinary research (namely cybernetics) with which artificial life shares many features. This report grew out of a workshop held at the Sixth European Conference on Artificial Life in Prague and features individual contributions from the workshop's eight speakers, plus a section designed to reflect the debates that took place during the workshop's discussion sessions. The major theme that emerged during these sessions was the identity and status of artificial life as a scientific endeavor