Investigating modularity and transparency within bioinspired connectionist architectures using genetic and epigenetic models

Machine learning algorithms allow computers to deal with incomplete data in tasks such as speech recognition and object detection. Some machine learning algorithms take inspiration from biological systems due to useful properties such as robustness, allowing algorithms to be flexible and domain agnostic. This comes at a cost, resulting in difficulty when one attempts to understand the reasoning behind decisions. This is problematic when such models are applied in realworld situations where accountability, legality, and maintenance are of concern. Artificial gene regulatory networks (AGRNs) are a type of connectionist architecture inspired by gene regulatory mechanisms. AGRNs are of interest within this thesis due to their ability to solve tasks in chaotic dynamical systems despite their relatively small size.The overarching aim of this work was to investigate the properties of connectionist architectures to improve the transparency of their execution. Initially, the evolutionary process and internal structure of AGRNs were investigated. Following this, the creation of an external control layer used to improve the transparency of execution of an external connectionist architecture was attempted.When investigating the evolutionary process of AGRNs, pathways were found that when followed, produced more performant networks in a shorter time frame. Evidence that AGRNs are capable of performing well despite internal interference was found when investigating their modularity, where it was also discovered that they do not develop strict modularity consistently. A control layer inspired by epigenetics that selectively deactivates nodes in trained artificial neural networks (ANNs) was developed; the analysis of its behaviour provided an insight into the internal workings of the ANN

‘Viral’ hunts? A cultural Darwinian analysis of witch persecutions

The theory of Darwinian cultural evolution is gaining currency in many parts of the socio-cultural sciences, but it remains contentious. Critics claim that the theory is either fundamentally mistaken or boils down to a fancy re-description of things we knew all along. We will argue that cultural Darwinism can indeed resolve long-standing socio-cultural puzzles; this is demonstrated through a cultural Darwinian analysis of the European witch persecutions. Two central and unresolved questions concerning witch-hunts will be addressed. From the fifteenth to the seventeenth centuries, a remarkable and highly specific concept of witchcraft was taking shape in Europe. The first question is: who constructed it? With hindsight, we can see that the concept contains many elements that appear to be intelligently designed to ensure the continuation of witch persecutions, such as the witches’ sabbat, the diabolical pact, nightly flight, and torture as a means of interrogation. The second question is: why did beliefs in witchcraft and witch-hunts persist and disseminate, despite the fact that, as many historians have concluded, no one appears to have substantially benefited from them? Historians have convincingly argued that witch-hunts were not inspired by some hidden agenda; persecutors genuinely believed in the threat of witchcraft to their communities. We propose that the apparent ‘design’ exhibited by concepts of witchcraft resulted from a Darwinian process of evolution, in which cultural variants that accidentally enhanced the reproduction of the witch-hunts were selected and accumulated. We argue that witch persecutions form a prime example of a ‘viral’ socio-cultural phenomenon that reproduces ‘selfishly’, even harming the interests of its human hosts

Embodied Robot Models for Interdisciplinary Emotion Research

Due to their complex nature, emotions cannot be properly understood from the perspective of a single discipline. In this paper, I discuss how the use of robots as models is beneficial for interdisciplinary emotion research. Addressing this issue through the lens of my own research, I focus on a critical analysis of embodied robots models of different aspects of emotion, relate them to theories in psychology and neuroscience, and provide representative examples. I discuss concrete ways in which embodied robot models can be used to carry out interdisciplinary emotion research, assessing their contributions: as hypothetical models, and as operational models of specific emotional phenomena, of general emotion principles, and of specific emotion ``dimensions''. I conclude by discussing the advantages of using embodied robot models over other models.Peer reviewe

Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity.

A crisis continues to brew within the pharmaceutical research and development (R&D) enterprise: productivity continues declining as costs rise, despite ongoing, often dramatic scientific and technical advances. To reverse this trend, we offer various suggestions for both the expansion and broader adoption of modeling and simulation (M&S) methods. We suggest strategies and scenarios intended to enable new M&S use cases that directly engage R&D knowledge generation and build actionable mechanistic insight, thereby opening the door to enhanced productivity. What M&S requirements must be satisfied to access and open the door, and begin reversing the productivity decline? Can current methods and tools fulfill the requirements, or are new methods necessary? We draw on the relevant, recent literature to provide and explore answers. In so doing, we identify essential, key roles for agent-based and other methods. We assemble a list of requirements necessary for M&S to meet the diverse needs distilled from a collection of research, review, and opinion articles. We argue that to realize its full potential, M&S should be actualized within a larger information technology framework--a dynamic knowledge repository--wherein models of various types execute, evolve, and increase in accuracy over time. We offer some details of the issues that must be addressed for such a repository to accrue the capabilities needed to reverse the productivity decline

Embodied language learning and cognitive bootstrapping: methods and design principles

Co-development of action, conceptualization and social interaction mutually scaffold and support each other within a virtuous feedback cycle in the development of human language in children. Within this framework, the purpose of this article is to bring together diverse but complementary accounts of research methods that jointly contribute to our understanding of cognitive development and in particular, language acquisition in robots. Thus, we include research pertaining to developmental robotics, cognitive science, psychology, linguistics and neuroscience, as well as practical computer science and engineering. The different studies are not at this stage all connected into a cohesive whole; rather, they are presented to illuminate the need for multiple different approaches that complement each other in the pursuit of understanding cognitive development in robots. Extensive experiments involving the humanoid robot iCub are reported, while human learning relevant to developmental robotics has also contributed useful results. Disparate approaches are brought together via common underlying design principles. Without claiming to model human language acquisition directly, we are nonetheless inspired by analogous development in humans and consequently, our investigations include the parallel co-development of action, conceptualization and social interaction. Though these different approaches need to ultimately be integrated into a coherent, unified body of knowledge, progress is currently also being made by pursuing individual methods

Embodied Language Learning and Cognitive Bootstrapping:Methods and Design Principles

Co-development of action, conceptualization and social interaction mutually scaffold and support each other within a virtuous feedback cycle in the development of human language in children. Within this framework, the purpose of this article is to bring together diverse but complementary accounts of research methods that jointly contribute to our understanding of cognitive development and in particular, language acquisition in robots. Thus, we include research pertaining to developmental robotics, cognitive science, psychology, linguistics and neuroscience, as well as practical computer science and engineering. The different studies are not at this stage all connected into a cohesive whole; rather, they are presented to illuminate the need for multiple different approaches that complement each other in the pursuit of understanding cognitive development in robots. Extensive experiments involving the humanoid robot iCub are reported, while human learning relevant to developmental robotics has also contributed useful results. Disparate approaches are brought together via common underlying design principles. Without claiming to model human language acquisition directly, we are nonetheless inspired by analogous development in humans and consequently, our investigations include the parallel co-development of action, conceptualization and social interaction. Though these different approaches need to ultimately be integrated into a coherent, unified body of knowledge, progress is currently also being made by pursuing individual methods

Pragmatic Frames for Teaching and Learning in Human-Robot interaction: Review and Challenges

Vollmer A-L, Wrede B, Rohlfing KJ, Oudeyer P-Y. Pragmatic Frames for Teaching and Learning in Human-Robot interaction: Review and Challenges. FRONTIERS IN NEUROROBOTICS. 2016;10: 10.One of the big challenges in robotics today is to learn from human users that are inexperienced in interacting with robots but yet are often used to teach skills flexibly to other humans and to children in particular. A potential route toward natural and efficient learning and teaching in Human-Robot Interaction (HRI) is to leverage the social competences of humans and the underlying interactional mechanisms. In this perspective, this article discusses the importance of pragmatic frames as flexible interaction protocols that provide important contextual cues to enable learners to infer new action or language skills and teachers to convey these cues. After defining and discussing the concept of pragmatic frames, grounded in decades of research in developmental psychology, we study a selection of HRI work in the literature which has focused on learning-teaching interaction and analyze the interactional and learning mechanisms that were used in the light of pragmatic frames. This allows us to show that many of the works have already used in practice, but not always explicitly, basic elements of the pragmatic frames machinery. However, we also show that pragmatic frames have so far been used in a very restricted way as compared to how they are used in human-human interaction and argue that this has been an obstacle preventing robust natural multi-task learning and teaching in HRI. In particular, we explain that two central features of human pragmatic frames, mostly absent of existing HRI studies, are that (1) social peers use rich repertoires of frames, potentially combined together, to convey and infer multiple kinds of cues; (2) new frames can be learnt continually, building on existing ones, and guiding the interaction toward higher levels of complexity and expressivity. To conclude, we give an outlook on the future research direction describing the relevant key challenges that need to be solved for leveraging pragmatic frames for robot learning and teaching

Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees

The chemical sciences are producing an unprecedented amount of large, high-dimensional data sets containing chemical structures and associated properties. However, there are currently no algorithms to visualize such data while preserving both global and local features with a sufficient level of detail to allow for human inspection and interpretation. Here, we propose a solution to this problem with a new data visualization method, TMAP, capable of representing data sets of up to millions of data points and arbitrary high dimensionality as a two-dimensional tree (http://tmap.gdb.tools). Visualizations based on TMAP are better suited than t-SNE or UMAP for the exploration and interpretation of large data sets due to their tree-like nature, increased local and global neighborhood and structure preservation, and the transparency of the methods the algorithm is based on. We apply TMAP to the most used chemistry data sets including databases of molecules such as ChEMBL, FDB17, the Natural Products Atlas, DSSTox, as well as to the MoleculeNet benchmark collection of data sets. We also show its broad applicability with further examples from biology, particle physics, and literature.Comment: 33 pages, 14 figures, 1 table, supplementary information include

The road ahead in genetics and genomics

In celebration of the 20th anniversary of Nature Reviews Genetics, we asked 12 leading researchers to reflect on the key challenges and opportunities faced by the field of genetics and genomics. Keeping their particular research area in mind, they take stock of the current state of play and emphasize the work that remains to be done over the next few years so that, ultimately, the benefits of genetic and genomic research can be felt by everyone