Exploring ant-based algorithms for gene expression data analysis

Objective: Recently, much research has been proposed using nature inspired algorithms to perform complex machine learning tasks. Ant colony optimization (ACO) is one such algorithm based on swarm intelligence and is derived from a model inspired by the collective foraging behavior of ants. Taking advantage of the ACO in traits such as self-organization and robustness, this paper investigates ant-based algorithms for gene expression data clustering and associative classification. Methods and material: An ant-based clustering (Ant-C) and an ant-based association rule mining (Ant-ARM) algorithms are proposed for gene expression data analysis. The proposed algorithms make use of the natural behavior of ants such as cooperation and adaptation to allow for a flexible robust search for a good candidate solution. Results: Ant-C has been tested on the three datasets selected from the Stanford Genomic Resource Database and achieved relatively high accuracy compared to other classical clustering methods. Ant-ARM has been tested on the acute lymphoblastic leukemia (ALL)/acute myeloid leukemia (AML) dataset and generated about 30 classification rules with high accuracy. Conclusions: Ant-C can generate optimal number of clusters without incorporating any other algorithms such as K-means or agglomerative hierarchical clustering. For associative classification, while a few of the well-known algorithms such as Apriori, FP-growth and Magnum Opus are unable to mine any association rules from the ALL/AML dataset within a reasonable period of time, Ant-ARM is able to extract associative classification rules.

Quantifying the complexity of chaos in multibasin multidimensional dynamics of molecular systems

The simulated classical dynamics of a small molecule exhibiting self-organizing behavior via a fast transition between two states is analyzed by calculation of the statistical complexity of the system. It is shown that the complexity of molecular descriptors such as atom coordinates and dihedral angles have different values before and after the transition. This provides a new tool to identify metastable states during molecular self-organization. The highly concerted collective motion of the molecule is revealed. Low-dimensional subspaces dynamics is found sensitive to the processes in the whole, high-dimensional phase space of the system. © 2004 Wiley Periodicals, Inc.

Adaptive Control and Multi-agent Interface for Infotelecommunication Systems of New Generation

Problems for intellectualisation for man-machine interface and methods of self-organization for network control in multi-agent infotelecommunication systems have been discussed. Architecture and principles for construction of network and neural agents for telecommunication systems of new generation have been suggested. Methods for adaptive and multi-agent routing for information flows by requests of external agents- users of global telecommunication systems and computer networks have been described.

Static, dynamic, and adaptive heterogeneity in distributed smart camera networks

We study heterogeneity among nodes in self-organizing smart camera networks, which use strategies based on social and economic knowledge to target communication activity efficiently. We compare homogeneous configurations, when cameras use the same strategy, with heterogeneous configurations, when cameras use different strategies. Our first contribution is to establish that static heterogeneity leads to new outcomes that are more efficient than those possible with homogeneity. Next, two forms of dynamic heterogeneity are investigated: nonadaptive mixed strategies and adaptive strategies, which learn online. Our second contribution is to show that mixed strategies offer Pareto efficiency consistently comparable with the most efficient static heterogeneous configurations. Since the particular configuration required for high Pareto efficiency in a scenario will not be known in advance, our third contribution is to show how decentralized online learning can lead to more efficient outcomes than the homogeneous case. In some cases, outcomes from online learning were more efficient than all other evaluated configuration types. Our fourth contribution is to show that online learning typically leads to outcomes more evenly spread over the objective space. Our results provide insight into the relationship between static, dynamic, and adaptive heterogeneity, suggesting that all have a key role in achieving efficient self-organization.

The thermodynamics and statistical mechanics of protein folding

The physics of self-organization and complexity is manifested on a variety of biological scales, from large ecosystems to the molecular level. Protein molecules exhibit characteristics of complex systems in terms of their structure, dynamics, and function. Proteins have the extraordinary ability to fold to a specific functional three-dimensional shape, starting from a random coil, in a biologically relevant time. How they accomplish this is one of the secrets of life. In this work, theoretical research into understanding this remarkable behavior is discussed. Thermodynamic and statistical mechanical tools are used in order to investigate the protein folding dynamics and stability. Theoretical analyses of the results from computer simulation of the dynamics of a four-helix bundle show that the excluded volume entropic effects are very important in protein dynamics and crucial for protein stability. The dramatic effects of changing the size of sidechains imply that a strategic placement of amino acid residues with a particular size may be an important consideration in protein engineering. Another investigation deals with modeling protein structural transitions as a phase transition. Using finite size scaling theory, the nature of unfolding transition of a four-helix bundle protein was investigated and critical exponents for the transition were calculated for various hydrophobic strengths in the core. It is found that the order of the transition changes from first to higher order as the strength of the hydrophobic interaction in the core region is significantly increased. Finally, a detailed kinetic and thermodynamic analysis was carried out in a model two-helix bundle. The connection between the structural free-energy landscape and folding kinetics was quantified. I show how simple protein engineering, by changing the hydropathy of a small number of amino acids, can enhance protein folding by significantly changing the free energy landscape so that kinetic traps are removed. The results have general applicability in protein engineering as well as understanding the underlying physical mechanisms of protein folding. ^

Mode-locking via dissipative Faraday instability

Emergence of coherent structures and patterns at the nonlinear stage of modulation instability of a uniform state is an inherent feature of many biological, physical and engineering systems. There are several well-studied classical modulation instabilities, such as Benjamin-Feir, Turing and Faraday instability, which play a critical role in the self-organization of energy and matter in non-equilibrium physical, chemical and biological systems. Here we experimentally demonstrate the dissipative Faraday instability induced by spatially periodic zig-zag modulation of a dissipative parameter of the system - spectrally dependent losses - achieving generation of temporal patterns and high-harmonic mode-locking in a fibre laser. We demonstrate features of this instability that distinguish it from both the Benjamin-Feir and the purely dispersive Faraday instability. Our results open the possibilities for new designs of mode-locked lasers and can be extended to other fields of physics and engineering.

Emergence of additional visible range photoluminescence due to aggregation of cyanine dye:astraphloxin on carbon nanotubes dispersed with anionic surfactant

Self-organization of organic molecules with carbon nanomaterials leads to formation of functionalized molecular nano-complexes with advanced features. We present a study of physical and chemical properties of carbon nanotube-surfactant-indocarbocyanine dye (astraphloxin) in water focusing on aggregation of the dye and resonant energy transfer from the dye to the nanotubes. Self-assembly of astraphloxin is evidenced in absorbance and photoluminescence depending dramatically on the concentrations of both the dye and surfactant in the mixtures. We observed an appearance of new photoluminescence peaks in visible range from the dye aggregates. The aggregates characterized with red shifted photoluminescence peaks at 595, 635 and 675 nm are formed mainly due to the presence of surfactant at the premicellar concentration. The energy transfer from the dye to the nanotubes amplifying near-infrared photoluminescence from the nanotubes is not affected by the aggregation of astraphloxin molecules providing important knowledge for further development of advanced molecular nano-complexes. The aggregation with the turned-on peaks and the energy transfer with amplified photoluminescence create powerful tools of visualization and/or detection of the nanotubes in visible and near-infrared spectral range, respectively, boosting its possible applications in sensors, energy generation/storage, and healthcare.

Collective excitability, synchronization, and array-enhanced coherence resonance in a population of lasers with a saturable absorber

In this article we present a numerical study of the collective dynamics in a population of coupled semiconductor lasers with a saturable absorber, operating in the excitable regime under the action of additive noise. We demonstrate that temporal and intensity synchronization takes place in a broad region of the parameter space and for various array sizes. The synchronization is robust and occurs even for a set of nonidentical coupled lasers. The cooperative nature of the system results in a self-organization process which enhances the coherence of the single element of the population too and can have broad impact for detection purposes, for building all-optical simulators of neural networks and in the field of photonics-based computation.

Reconfiguring the contours of statehood and the rights of the peoples of disappearing states

Many of the elements that have traditionally supported state level normative self-organization, most notably territory, are being actively undermined by rising sea levels, flooding, desertification, amongst other climate change effects. As more and more states come to be redefined as â disappearingâ , that is, states losing their territories to the natural environment through no specific fault of their own, a question arises as to how displaced communities will be assisted in their desire (and right) to continue to practice principles of self-determination and self-government? What is clear is that the international community can no longer continue with the fiction of a unified or unchanging model of the liberal democratic state. Instead, alternative ontological models of sovereign community are required, as is a re-imagining of how statehood might be re-constituted in the future in response to deepening ecological problems. The international community must now begin to address the immanent nature of threats posed to disappearing states and consider how a model of statehood that does not privilege territory as a fixed component of state identity could be operationalized. This paper considers how a democratic reform of statehood might proceed and resettlement agreements for displaced communities determined. The transition to an era of peaceful sovereign relations under deteriorating global climate conditions and growing natural resource scarcity, it argues, will require a significant extension of established traditions of democratic compromise, human rights solidarity and cosmopolitan justice.

Instantaneous photoinduced patterning of an azopolymer colloidal nanosphere assembly

Colloidal azopolymer nanospheres assembled on a glass substrate were exposed to a single collimated laser beam. The combination of photo-fluidic elongation of the spherical colloids and light induced self-organization of the azopolymer film allows the quasiinstantaneous growth of a large amplitude surface relief grating. Pre-structuration of the sample with the nanosphere assembly supports faster creation of the spontaneous pattern. Confinement into the nanospheres provides exceptionally large modulation amplitude of the spontaneous relief. The method is amenable to any kind of photoactive azo-materials.

Of Marx and Makers: an Historical Perspective on Generative Justice

In Marxist frameworks “distributive justice” depends on extracting value through a centralized state. Many new social movements—peer to peer economy, maker activism, community agriculture, queer ecology, etc.—take the opposite approach, keeping value in its unalienated form and allowing it to freely circulate from the bottom up. Unlike Marxism, there is no general theory for bottom-up, unalienated value circulation. This paper examines the concept of “generative justice” through an historical contrast between Marx’s writings and the indigenous cultures that he drew upon. Marx erroneously concluded that while indigenous cultures had unalienated forms of production, only centralized value extraction could allow the productivity needed for a high quality of life. To the contrary, indigenous cultures now provide a robust model for the “gift economy” that underpins open source technological production, agroecology, and restorative approaches to civil rights. Expanding Marx’s concept of unalienated labor value to include unalienated ecological (nonhuman) value, as well as the domain of freedom in speech, sexual orientation, spirituality and other forms of “expressive” value, we arrive at an historically informed perspective for generative justice. 

Cultivating Subjectivities: The Class Politics of Convivial Labor in the Interstitial Spaces of Neoliberal Neglect

Thesis (Ph.D.)--University of Washington, 2016-08

Resilience of small-scale societies: a view from drylands

To gain insights on long-term social-ecological resilience, we examined adaptive responses of small-scale societies to dryland-related hazards in different regions and chronological periods, spanning from the mid-Holocene to the present. Based on evidence from Africa (Sahara and Sahel), Asia (south margin of the Thar desert), and Europe (South Spain), we discuss key traits and coping practices of small-scale societies that are potentially relevant for building resilience. The selected case studies illustrate four main coping mechanisms: mobility and migration, storage, commoning, and collective action driven by religious beliefs. Ultimately, the study of resilience in the context of drylands emphasizes the importance of adaptive traits and practices that are distinctive of small-scale societies: a strong social-ecological coupling, a solid body of traditional ecological knowledge, and a high degree of internal cohesion and self-organization.

Global teacher für die Weltgesellschaft!? Theoretische Überlegungen zu den Kompetenzen von Lehrkräften, um Globales Lernen kompetenzorientiert zu unterrichten

In diesem Aufsatz werden historisch-systematische Anregungen zur Debatte um Kompetenz und Kompetenzen im Kontext bildungs- und professionstheoretischer Überlegungen angeboten. Dies ist der Ausgangspunkt für ein Nachdenken über angestrebte Kompetenzen Globalen Lernens sowie Kompetenzfelder des Global Teachers, um einen kompetenzorientierten Umgang damit zu ermöglichen. (DIPF/Orig.)

Integrating Environmental Justice and Social-Ecological Resilience for Successful Adaptation to Climate Change: Lessons from African American Communities on the Eastern Shore of the Chesapeake Bay

This research concerns the conceptual and empirical relationship between environmental justice and social-ecological resilience as it relates to climate change vulnerability and adaptation. Two primary questions guided this work. First, what is the level of resilience and adaptive capacity for social-ecological systems that are characterized by environmental injustice in the face of climate change? And second, what is the role of an environmental justice approach in developing adaptation policies that will promote social-ecological resilience? These questions were investigated in three African American communities that are particularly vulnerable to flooding from sea-level rise on the Eastern Shore of the Chesapeake Bay. Using qualitative and quantitative methods, I found that in all three communities, religious faith and the church, rootedness in the landscape, and race relations were highly salient to community experience. The degree to which these common aspects of the communities have imparted adaptive capacity has changed over time. Importantly, a given social-ecological factor does not have the same effect on vulnerability in all communities; however, in all communities political isolation decreases adaptive capacity and increases vulnerability. This political isolation is at least partly due to procedural injustice, which occurs for a number of interrelated reasons. This research further revealed that while all stakeholders (policymakers, environmentalists, and African American community members) generally agree that justice needs to be increased on the Eastern Shore, stakeholder groups disagree about what a justice approach to adaptation would look like. When brought together at a workshop, however, these stakeholders were able to identify numerous challenges and opportunities for increasing justice. Resilience was assessed by the presence of four resilience factors: living with uncertainty, nurturing diversity, combining different types of knowledge, and creating opportunities for self-organization. Overall, these communities seem to have low resilience; however, there is potential for resilience to increase. Finally, I argue that the use of resilience theory for environmental justice communities is limited by the great breadth and depth of knowledge required to evaluate the state of the social-ecological system, the complexities of simultaneously promoting resilience at both the regional and local scale, and the lack of attention to issues of justice.