Abstract:
Stochastic methods employing evolutionary algorithms have demonstrated promise in being able to detect and model gene-gene and gene-environment interactions that influence human traits. Here we demonstrate modifications to a neural network algorithm in ATHENA (the Analysis Tool for Heritable and Environmental Network Associations) resulting in clear performance improvements for discovering gene-gene interactions that influence human traits. We employed an alternative tree-based crossover, backpropagation for locally fitting neural network weights, and incorporation of domain knowledge obtainable from publicly accessible biological databases for initializing the search for gene-gene interactions. We tested these modifications in silico using simulated datasets.We show that the alternative tree-based crossover modification resulted in a modest increase in the sensitivity of the ATHENA algorithm for discovering gene-gene interactions. The performance increase was highly statistically significant when backpropagation was used to locally fit NN weights. We also demonstrate that using domain knowledge to initialize the search for gene-gene interactions results in a large performance increase, especially when the search space is larger than the search coverage.We show that a hybrid optimization procedure, alternative crossover strategies, and incorporation of domain knowledge from publicly available biological databases can result in marked increases in sensitivity and performance of the ATHENA algorithm for detecting and modelling gene-gene interactions that influence a complex human trait.The genome-wide association study (GWAS) is a widely used technique in human genetics research to investigate DNA variations associated with common human diseases. The last several decades have ushered in technological advances that have allowed investigators to progress from coarse genomic coverage with linkage maps and candidate gene association studies, to very high resolution associ

Abstract:
"Practice theory" has a long history in philosophy, under various names, but current practice theory is a response to failures of projects of modernity or enlightenment which attempt to reduce science or politics to formulae. Heidegger, Oakeshott, and MacIntyre are each examples of philosophers who turned to practice conceptions. Foucault and Bourdieu made similar turns. Practice accounts come in different forms: some emphasize skill-like individual accomplishments, others emphasize the social character or presupposition-like character of the tacit conditions of activities. The Social Theory of Practices problematized the idea of sameness, the idea that participants in an activity had the same tacit possessions, which undermined the idea that practices were collective objects in which individuals participated. Later critics, such as Schatzki and Rouse, emphasized the normative coherence and character of practice, which has a collective aspect. Pickering and others suggested a notion of practices that was de-mentalized and focused on the objects that were part of the practical activity, which provided for the continuity and sociality of practice without collectivizing its mental content. The discovery of mirror neurons suggested a non-collective mode of transmission of practices. The implications of these developments can be seen in connection with ethics, where the conflict between the ethical and the practical can be understood in terms of the intrinsic conflict between the need to behave successfully and our learned ethical intuitions.

Abstract:
Condensates of spin-1 sodium display rich spin dynamics due to the antiferromagnetic nature of the interactions in this system. We use Faraday rotation spectroscopy to make a continuous and minimally destructive measurement of the dynamics over multiple spin oscillations on a single evolving condensate. This method provides a sharp signature to locate a magnetically tuned separatrix in phase space which depends on the net magnetization. We also observe a phase transition from a two- to a three-component condensate at a low but finite temperature using a Stern-Gerlach imaging technique. This transition should be preserved as a zero-temperature quantum phase transition.

Abstract:
We characterize fluctuations in atom number and spin populations in F=1 sodium spinor condensates. We find that the fluctuations enable a quantitative measure of energy dissipation in the condensate. The time evolution of the population fluctuations shows a maximum. We interpret this as evidence of a dissipation-driven separatrix crossing in phase space. For a given initial state, the critical time to the separatrix crossing is found to depend exponentially on the magnetic field and linearly on condensate density. This crossing is confirmed by tracking the energy of the spinor condensate as well as by Faraday rotation spectroscopy. We also introduce a phenomenological model that describes the observed dissipation with a single coefficient.

Abstract:
Typical quantum communication schemes are such that to achieve perfect decoding the receiver must share a reference frame with the sender. Indeed, if the receiver only possesses a bounded-size quantum token of the sender's reference frame, then the decoding is imperfect, and we can describe this effect as a noisy quantum channel. We seek here to characterize the performance of such schemes, or equivalently, to determine the effective decoherence induced by having a bounded-size reference frame. We assume that the token is prepared in a special state that has particularly nice group-theoretic properties and that is near-optimal for transmitting information about the sender's frame. We present a decoding operation, which can be proven to be near-optimal in this case, and we demonstrate that there are two distinct ways of implementing it (corresponding to two distinct Kraus decompositions). In one, the receiver measures the orientation of the reference frame token and reorients the system appropriately. In the other, the receiver extracts the encoded information from the virtual subsystems that describe the relational degrees of freedom of the system and token. Finally, we provide explicit characterizations of these decoding schemes when the system is a single qubit and for three standard kinds of reference frame: a phase reference, a Cartesian frame (representing an orthogonal triad of spatial directions), and a reference direction (representing a single spatial direction).

Abstract:
We investigate the degradation of reference frames, treated as dynamical quantum systems, and quantify their longevity as a resource for performing tasks in quantum information processing. We adopt an operational measure of a reference frame's longevity, namely, the number of measurements that can be made against it with a certain error tolerance. We investigate two distinct types of reference frame: a reference direction, realized by a spin-j system, and a phase reference, realized by an oscillator mode with bounded energy. For both cases, we show that our measure of longevity increases quadratically with the size of the reference system and is therefore non-additive. For instance, the number of measurements that a directional reference frame consisting of N parallel spins can be put to use scales as N^2. Our results quantify the extent to which microscopic or mesoscopic reference frames may be used for repeated, high-precision measurements, without needing to be reset - a question that is important for some implementations of quantum computing. We illustrate our results using the proposed single-spin measurement scheme of magnetic resonance force microscopy.

Abstract:
We investigate if the degradation of a quantum directional reference frame through repeated use can be modeled as a classical direction undergoing a random walk on a sphere. We demonstrate that the behaviour of the fidelity for a degrading quantum directional reference frame, defined as the average probability of correctly determining the orientation of a test system, can be fit precisely using such a model. Physically, the mechanism for the random walk is the uncontrollable back-action on the reference frame due to its use in a measurement of the direction of another system. However, we find that the magnitude of the step size of this random walk is not given by our classical model and must be determined from the full quantum description.

Abstract:
The initial presentation of multifactor dimensionality reduction (MDR) featured cross-validation to mitigate over-fitting, computationally efficient searches of the epistatic model space, and variable construction with constructive induction to alleviate the curse of dimensionality. However, the method was unable to differentiate association signals arising from true interactions from those due to independent main effects at individual loci. This issue leads to problems in inference and interpretability for the results from MDR and the family-based compliment the MDR-pedigree disequilibrium test (PDT). A suggestion from previous work was to fit regression models post hoc to specifically evaluate the null hypothesis of no interaction for MDR or MDR-PDT models. We demonstrate with simulation that fitting a regression model on the same data as that analyzed by MDR or MDR-PDT is not a valid test of interaction. This is likely to be true for any other procedure that searches for models, and then performs an uncorrected test for interaction. We also show with simulation that when strong main effects are present and the null hypothesis of no interaction is true, that MDR and MDR-PDT reject at far greater than the nominal rate. We also provide a valid regression-based permutation test procedure that specifically tests the null hypothesis of no interaction, and does not reject the null when only main effects are present. The regression-based permutation test implemented here conducts a valid test of interaction after a search for multilocus models, and can be applied to any method that conducts a search to find a multilocus model representing an interaction.