Proceedings of the Workshop on Change of Representation and Problem Reformulation

The proceedings of the third Workshop on Change of representation and Problem Reformulation is presented. In contrast to the first two workshops, this workshop was focused on analytic or knowledge-based approaches, as opposed to statistical or empirical approaches called 'constructive induction'. The organizing committee believes that there is a potential for combining analytic and inductive approaches at a future date. However, it became apparent at the previous two workshops that the communities pursuing these different approaches are currently interested in largely non-overlapping issues. The constructive induction community has been holding its own workshops, principally in conjunction with the machine learning conference. While this workshop is more focused on analytic approaches, the organizing committee has made an effort to include more application domains. We have greatly expanded from the origins in the machine learning community. Participants in this workshop come from the full spectrum of AI application domains including planning, qualitative physics, software engineering, knowledge representation, and machine learning

Proceedings of the Workshop on the lambda-Prolog Programming Language

The expressiveness of logic programs can be greatly increased over first-order Horn clauses through a stronger emphasis on logical connectives and by admitting various forms of higher-order quantification. The logic of hereditary Harrop formulas and the notion of uniform proof have been developed to provide a foundation for more expressive logic programming languages. The λ-Prolog language is actively being developed on top of these foundational considerations. The rich logical foundations of λ-Prolog provides it with declarative approaches to modular programming, hypothetical reasoning, higher-order programming, polymorphic typing, and meta-programming. These aspects of λ-Prolog have made it valuable as a higher-level language for the specification and implementation of programs in numerous areas, including natural language, automated reasoning, program transformation, and databases

QUEER APPALACHIA: TOWARD GEOGRAPHIES OF POSSIBILITY

Stereotypes about Appalachia abound through dubious and reductive representations of the ‘hillbilly’ icon. Sexuality and how it functions in Appalachia is usually cast from the outside as wild, violent, bestial, incestuous and generally base. Movies such as Deliverance and television shows such as The Beverly Hillbillies and The Dukes of Hazard render images of Appalachian sexuality as hyper-sexual, both naive and violent. These images of Appalachian sexual ignorance and violence that permeate popular culture have had problematic and reductive implications for rural gay/trans Appalachian folk. Mainstream gay culture has often used the perceived meanings of these images to circumscribe and foreclose upon the possibility of rural queer life, rendering the rural as monolithically homophobic and impenetrable. This research attempts to destabilize this perspective and critique the impulse for mainstream gay culture to further marginalize rural gay/trans folk in Appalachia. The project reveals the possibility for rural queer life to exist in Appalachia to show not only its presence, but also its varying forms of visibility. To do this, experimental methodologies are employed, drawing on autoethnography that have located my body as an active participant and research object in one particular Appalachian queer geography. By actively participating in a rural queer network, the possibility for Appalachian queer geographies to exist in ways that surpass popular representations emerge in a way that force us to renegotiate our understandings of homophobia and what sets its conditions. This project begins to uncover and theorize the ways in which kinship as a ‘social technology’ mitigates social strangeness and operates as a means for social protection and intimacy within rural queer populations. This research is presented in a way that neither dismisses nor emphasizes homophobic violence, but rather argues the imperative for strong political advocacy that recognizes both the struggles and accomplishments of rural gay/trans folk. Three interlinked approaches are used to highlight these possibilities and foreclosures: the exterior representation of Appalachian sexuality in American metropolitan gay cultures and its politico-cultural effects on rural gay/trans folk, a more nuanced interpretation of homophobia in Appalachia, and how ‘place’ is made through the operation of rural queer networks

Computing a Yeast Tree of Life

This study aimed to compare the results of distinct state-of-the-art phylogenetic tree-building methodologies for a key yeast NGS dataset, with the ultimate goal of establishing a yeast tree of life. Draft genome assemblies of seventy-five species from the Saccharomyces complex, a well-studied group of species of academic and industrial importance, first underwent a stringent quality control process, along with a dataset from an outgroup species. This process uncovered a vast amount of genomic information. New, good quality genome assemblies were introduced for six Saccharomyces complex species and for four strains. Key genomic differences were found in a quality-controlled subset of this dataset including varying genome sizes (8-29Mbp), coding genome proportions (54-77%) and number of genes (4,131-11,243). The total GC content was also found to vary significantly across the dataset, ranging from 31.7% in a Tetrapisispora blattae strain to 52% in a representative of Torulaspora globosa. The core genome of forty Saccharomyces complex species was also identified in this study and it was found that 591 genes with _50% amino-acid sequence identity were present across all strains. Phylogenetic trees were then built from the full 76 species dataset, comprising Maximum Likelihood approaches for a seven-region Multi-Locus Sequence Typing and 1,711 BUSCO gene datasets along with three variations of a recently developed NGS alignment-free approach - Feature Frequency Profiles (FFP). The resulting trees were then compared, with all trees found to be different, though with the BUSCO and FFP 20-letter amino acid trees highly superior to the other approaches. Despite the success of the FFP 20-letter amino acid approach for the Saccharomyces complex dataset, simulation studies confirmed a sequence length bias with the FFP two-letter RY alphabet and a GC bias with the FFP four-letter DNA alphabet approaches. In an effort to overcome the biases within the current FFP approach, a new software tool, jellyphy, was developed. Further development of tools such as this will undoubtedly lead to new methods capable of accurate phylogenetic estimation from yeast NGS datasets