University of Konstanz
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Free Energy Projective Simulation (FEPS) : Active inference with interpretability
No full textIn the last decade, the free energy principle (FEP) and active inference (AIF) have achieved many successes connecting conceptual models of learning and cognition to mathematical models of perception and action. This effort is driven by a multidisciplinary interest in understanding aspects of self-organizing complex adaptive systems, including elements of agency. Various reinforcement learning (RL) models performing active inference have been proposed and trained on standard RL tasks using deep neural networks. Recent work has focused on improving such agents’ performance in complex environments by incorporating the latest machine learning techniques. In this paper, we build upon these techniques. Within the constraints imposed by the FEP and AIF, we attempt to model agents in an interpretable way without deep neural networks by introducing Free Energy Projective Simulation (FEPS). Using internal rewards only, FEPS agents build a representation of their partially observable environments with which they interact. Following AIF, the policy to achieve a given task is derived from this world model by minimizing the expected free energy. Leveraging the interpretability of the model, techniques are introduced to deal with long-term goals and reduce prediction errors caused by erroneous hidden state estimation. We test the FEPS model on two RL environments inspired from behavioral biology: a timed response task and a navigation task in a partially observable grid. Our results show that FEPS agents fully resolve the ambiguity of both environments by appropriately contextualizing their observations based on prediction accuracy only. In addition, they infer optimal policies flexibly for any target observation in the environment.publishe
The need for epigenotoxicity testing
No full textWhile the genome codes for all proteins an organism can express, only certain sets of proteins are expressed in defined cell types. A cell’s phenotype is influenced by the life-stage, exposure to signal molecules, as well as the exposome, i.e., external influences including physical stressors or chemicals from food, the environment or microorganisms. The interplay between genetics and these expo-sures is termed gene x environment interaction (GxE). Epigenetics contributes to GxE by modifying the accessibility of genes and thus their ability to be translated to proteins. Epigenetic mechanisms include DNA methylation, histone modifications, non-coding RNAs, and changes in local DNA packaging. As genetics and the exposome often jointly contribute to disease, understanding epi-genetics may enable a better understanding of many human pathologies. Often, epigenetics will retain the memory of exposure, which changes an organism’s susceptibility to subsequent, other exposures. This concept may allow new insights into mixture toxicity, especially when the exposures do not take place at the same time. Knowledge on epigenetic processes provides a basis for novel drugs that modify cell phenotypes (e.g., in cancer or neurodegenerative disease). Here, we provide an overview of the role of epigenetics in toxicology, and we call for a systematic assessment of epi-genetic changes as part of investigative, and possibly regulatory, toxicity assessments. We propose tools and strategies for using human-relevant models, biomarkers, and AI to better predict who may be at risk. Ultimately, adding epigenetics to toxicology will help us create safer products and protect vulnerable individuals and future generations.publishe
Macromolecular crystallography
No full textCrystallography provides structural evidence of macromolecules in atomic detail. However, the atomic structure is not the direct outcome of the experiment. Diffraction data need to be processed and the phase problem must be solved to visualize the map from which an atomic model of the macromolecule is interpreted and iteratively improved. Despite this complex process from sample to scientific answer, crystallography is widely accessible in biochemical and biological research. Easy access to the experimental set-ups, free software for academic use and complimentary analytical computing, supported by automation and expert assistance, makes crystallography available to non-crystallographers. This Primer offers a practical and rational introduction to macromolecular crystallography, whether to engage directly or to critically assess results, with a focus on understanding the diffraction data, solving the phase problem, building and refining the atomic model, and interpreting the resulting atomic structure. We provide an overview of what crystallography can achieve, the key decisions and trade-offs involved, and how to evaluate outcomes effectively.publishe
Optimal transitions between nonequilibrium steady states
No full textThe optimal control of finite-time processes on the microscale is of significant theoretical and practical interest, particularly for the energy-efficient operation of nanomachines. While previous studies have primarily focused on transitions between equilibrium states, many biologically and technologically relevant processes occur far from equilibrium. In such nonequilibrium settings, memory, a ubiquitous feature in realistic systems, plays an intricate role, as any driving necessarily excites internal memory modes. This motivates a deeper exploration of optimal control strategies in nonequilibrium regimes. Here, we combine experiments, theory, and computational methods to investigate the transition of a colloidal particle confined in an optical trap between two nonequilibrium steady states (NESS). We identify optimal control protocols that minimize the thermodynamic work during the finite-time transition between two NESS. We compare optimal protocols in viscous and viscoelastic fluid environments, which are common in realistic technical and biological processes and introduce memory due to a delayed response. Regardless of the presence of memory effects, optimal protocols consistently balance energy extraction with dissipation minimization. In the presence of memory, optimal control is achieved if the protocol matches the time response of the environment. These findings offer key insights for designing optimal control strategies for finite-time, nonequilibrium processes in complex environments.publishe
Designing Fluid Interaction for Immersive Analytics using Hybrid User Interfaces in Mixed Reality
No full textImmersive mixed reality environments are gradually becoming part of our everyday life. Yet, their sole reliance on spatial interaction paradigms presents inherent limitations for their broader applicability. One proposition, which is the focus of this dissertation, is to form a hybrid user interface by complementing mixed reality head-worn devices with familiar everyday devices, such as smartphones, tablets, and desktop computers. Although the concept of hybrid user interfaces has persisted for decades, no coherent delineation has emerged, leading to a distinct lack of consistent terminologies and design principles.
To take a step towards understanding the potential of hybrid user interfaces in general, this dissertation explores their potential for fluid interaction in immersive analytics. Hybrid interfaces are especially well-suited for immersive analytics, where the benefits of immersive 3D visualization must be balanced with the precision and familiarity of 2D interaction. Thus, this dissertation addressed the overarching research goal of: How can hybrid user interfaces support fluid interaction in immersive analytics workflows?
The first part of this dissertation addresses the foundational gap in prior literature. It introduces the concept of complementary interfaces to generally describe meaningful device combinations. It then contextualizes the concept of hybrid user interfaces within the current research landscape, thereby extracting key dimensions for describing and classifying hybrid user interfaces.
The second part presents the design and empirical evaluation of four hybrid user interface exemplars, each providing a unique perspective on the overarching research goal. The exemplars explore different design principles of hybrid user interfaces, such as enabling seamless transitions between devices, applying effective task allocation across heterogeneous environments, or creating novel interaction techniques enabled through such meaningful device combinations. The evaluation of each prototype contributes context-specific design insights and research implications that are synthesized into broader principles.
Overall, this dissertation revisits and contextualizes the fragmented concept of hybrid user interfaces within the current research landscape, providing design guidelines for achieving fluid interaction. While immersive analytics provides a fitting use case, the resulting guidelines extend to a wider range of scenarios, thus providing a foundation for the future of hybrid user interfaces.publishe
The role of methodological conditions and model interpretation in the adsorption of a nanomaterial on a volcanic soil
No full textpublishe
Species-specific retention vs. recovery of coral thermal tolerance following nursery propagation
No full textThermal screening of coral source material is likely crucial to enhancing long-term restoration success under ocean warming. It is unclear, however, whether reef-based donor colonies retain their thermal tolerance in a nursery environment. Here, we used CBASS acute thermal assays to compare standardized thermal tolerance thresholds (ED50s) of donor colonies from Acropora cytherea and Acropora florida from two sites in Pulau Lang Tengah, Malaysia to their ‘nursery propagules’ reared in a common garden coral nursery over 365 days. CBASS assays of reef-based donors and their nursery counterparts were conducted in parallel and over two seasons to assess retention of thermal tolerance following nursery rearing. After 6 months, average ED50s of A. cytherea nursery corals were significantly lower compared to their reef-based donor colonies, but such difference disappeared after 365 days. By comparison, no such differences were measurable for A. florida and thermal tolerances were retained. Further, we did not observe trade-offs between growth and thermal thresholds for either species. Based on our findings, in situ thermal tolerance differences are likely adaptive and, consequently, either retained or recovered in longer-term restoration settings. Our findings further imply that thermal screening should be conducted prior to nursery propagation to avoid selection based on long-term acclimation artifacts.publishe
Future of coral bleaching research
No full textCoral bleaching is the largest global threat to coral reef ecosystem persistence this century. Advancing our understanding of coral bleaching and developing solutions to protect corals and the reefs they support are critical. In the present article, we, the US National Science Foundation–funded Coral Bleaching Research Coordination Network, outline future directions for coral bleaching research. Specifically, we address the need for embedded inclusiveness, codevelopment, and capacity building as a foundation for excellence in coral bleaching research and the critical role of coral-bleaching science in shaping policy. We outline a path for research innovation and technology and propose the formation of an international coral bleaching consortium that, in coordination with existing multinational organizations, could be a hub for planning, coordinating, and integrating global-scale coral bleaching research, innovation, and mitigation strategies. This proposed strategy for future coral bleaching research could facilitate a step-function change in how we address the coral bleaching crisis.publishe
Adults’ Involvement in Social Pretend Play in the Context of Early Childhood Education
No full textEducational positions on adult involvement in social pretend play vary. Some view it as an interference that could disrupt children's play (e.g., Korat et al., 2002), while others believe that adult involvement could enhance the quality or complexity of children's play, leading to improved learning and social development (e.g., Bodrova et al., 2013; Weisberg et al., 2013). The role that adults take on during play matters. Research suggests that less involved behaviour, such as running back and forth or being unavailable is negatively related to children’s engagement in play (Singer et al., 2014). On the other hand, taking a more active role as a co-player or play leader has been shown to increase children's social interactions with peers and their level of social play (Gaviria-Loaiza et al., 2017). We conducted a controlled intervention study with a pre-, post-test, and follow-up design on pretend play tutoring and children’s social development. The study sample consisted of 27 Swiss play groups with N=215 three- to four-year-old children, who were randomly assigned to one of three experimental conditions: Pretend play tutoring, provision of role play material, or usual interaction. The results showed that taking an active role in children's pretend play improved the quality of their play compared to solely providing play materials or usual interaction. This ultimately enhanced children's social competencies (Kalkusch et al., 2020; Jaggy et al., 2023). Implications for the design of child-centered learning environments that encourage peer interactions and social development are discussed.).publishe