Specific-to-General Learning for Temporal Events with Application to Learning Event Definitions from Video

We develop, analyze, and evaluate a novel, supervised, specific-to-general learner for a simple temporal logic and use the resulting algorithm to learn visual event definitions from video sequences. First, we introduce a simple, propositional, temporal, event-description language called AMA that is sufficiently expressive to represent many events yet sufficiently restrictive to support learning. We then give algorithms, along with lower and upper complexity bounds, for the subsumption and generalization problems for AMA formulas. We present a positive-examples--only specific-to-general learning method based on these algorithms. We also present a polynomial-time--computable ``syntactic'' subsumption test that implies semantic subsumption without being equivalent to it. A generalization algorithm based on syntactic subsumption can be used in place of semantic generalization to improve the asymptotic complexity of the resulting learning algorithm. Finally, we apply this algorithm to the task of learning relational event definitions from video and show that it yields definitions that are competitive with hand-coded ones

AN ECONOMIC EVALUATION OF SOYBEAN STINK BUG CONTROL ALTERNATIVES FOR THE SOUTHEASTERN UNITED STATES

Methyl parathion or Penncap M (an encapsulated methyl parathion) are used extensively throughout the United States for controlling stink bug pests in soybeans, Glycine Max (L.) Merrill. However, this insecticide is highly toxic to mammals, birds, and non-target arthropods, and thus is less environmentally sound than other insecticides. For environmental and human health considerations, investigating alternative insecticides for control is desired. For this investigation, research based on field experimental data from Florida, Georgia, and Louisiana during the 1988 and 1989 growing seasons were employed. Results indicate that alternative, currently available, and less toxic insecticides may reduce producer costs, increase yield, and improve soybean quality. These alternative insecticides include Scout (tralomethrin), Karate (lambda-cyhalothrin), Orthene (acephate), and Baythroid (cyfluthrin). In terms of improved profits these alternative insecticides may dominate methyl parathion or encapsulated methyl parathion.Crop Production/Industries,

Extreme State Aggregation Beyond MDPs

We consider a Reinforcement Learning setup where an agent interacts with an environment in observation-reward-action cycles without any (esp.\ MDP) assumptions on the environment. State aggregation and more generally feature reinforcement learning is concerned with mapping histories/raw-states to reduced/aggregated states. The idea behind both is that the resulting reduced process (approximately) forms a small stationary finite-state MDP, which can then be efficiently solved or learnt. We considerably generalize existing aggregation results by showing that even if the reduced process is not an MDP, the (q-)value functions and (optimal) policies of an associated MDP with same state-space size solve the original problem, as long as the solution can approximately be represented as a function of the reduced states. This implies an upper bound on the required state space size that holds uniformly for all RL problems. It may also explain why RL algorithms designed for MDPs sometimes perform well beyond MDPs.Comment: 28 LaTeX pages. 8 Theorem

Multi-objective Robust Strategy Synthesis for Interval Markov Decision Processes

Interval Markov decision processes (IMDPs) generalise classical MDPs by having interval-valued transition probabilities. They provide a powerful modelling tool for probabilistic systems with an additional variation or uncertainty that prevents the knowledge of the exact transition probabilities. In this paper, we consider the problem of multi-objective robust strategy synthesis for interval MDPs, where the aim is to find a robust strategy that guarantees the satisfaction of multiple properties at the same time in face of the transition probability uncertainty. We first show that this problem is PSPACE-hard. Then, we provide a value iteration-based decision algorithm to approximate the Pareto set of achievable points. We finally demonstrate the practical effectiveness of our proposed approaches by applying them on several case studies using a prototypical tool.Comment: This article is a full version of a paper accepted to the Conference on Quantitative Evaluation of SysTems (QEST) 201

ASRP: the Arabidopsis Small RNA Project Database

Eukaryotes produce functionally diverse classes of small RNAs (20–25 nt). These include microRNAs (miRNAs), which act as regulatory factors during growth and development, and short-interfering RNAs (siRNAs), which function in several epigenetic and post-transcriptional silencing systems. The Arabidopsis Small RNA Project (ASRP) seeks to characterize and functionally analyze the major classes of endogenous small RNAs in plants. The ASRP database provides a repository for sequences of small RNAs cloned from various Arabidopsis genotypes and tissues. Version 3.0 of the database contains 1920 unique sequences, with tools to assist in miRNA and siRNA identification and analysis. The comprehensive database is publicly available through a web interface at http://asrp.cgrb.oregonstate.edu

Study of the Germination Dynamics for Plants using Advanced Image Processing Algorithms

Study of the Germination Dynamics for Plants using Advanced Image Processing Algorithm

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants with defects in three RNA-dependent RNA polymerase (RDR) and four Dicer-like (DCL) genes. The profiling involved direct analysis using a multiplexed, parallel-sequencing strategy. Small RNA-generating loci, especially those producing predominantly 24-nt siRNAs, were found to be highly correlated with repetitive elements across the genome. These were found to be largely RDR2- and DCL3-dependent, although alternative DCL activities were detected on a widespread level in the absence of DCL3. In contrast, no evidence for RDR2-alternative activities was detected. Analysis of RDR2- and DCL3-dependent small RNA accumulation patterns in and around protein-coding genes revealed that upstream gene regulatory sequences systematically lack siRNA-generating activities. Further, expression profiling suggested that relatively few genes, proximal to abundant 24-nt siRNAs, are regulated directly by RDR2- and DCL3-dependent silencing. We conclude that the widespread accumulation patterns for RDR2- and DCL3-dependent siRNAs throughout the Arabidopsis genome largely reflect mechanisms to silence highly repeated sequences

The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases

Background: Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequence databases. However, this is usually not an easy task for the average bench scientist. Results: We present the Personal Sequence Database (PSD), a suite of tools to create and maintain small- to medium-sized web-accessible sequence databases. All interactions with PSD tools occur via the internet with a web browser. Users may define sequence groups within their database that can be maintained privately or published to the web for public use. A sequence group can be downloaded, browsed, searched by keyword or searched for sequence similarities using BLAST. Publishing a sequence group extends these capabilities to colleagues and collaborators. In addition to being able to manage their own sequence databases, users can enroll sequences in BLASTAgent, a BLAST hit tracking system, to monitor NCBI databases for new entries displaying a specified level of nucleotide or amino acid similarity. Conclusion: The PSD offers a valuable set of resources unavailable elsewhere. In addition to managing sequence data and BLAST search results, it facilitates data sharing with colleagues, collaborators and public users. The PSD is hosted by the authors and is available at http:// bioinfo.cgrb.oregonstate.edu/psd/

An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6

<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas fluorescens </it>is a genetically and physiologically diverse species of bacteria present in many habitats and in association with plants. This species of bacteria produces a large array of secondary metabolites with potential as natural products. <it>P. fluorescens </it>isolate WH6 produces Germination-Arrest Factor (GAF), a predicted small peptide or amino acid analog with herbicidal activity that specifically inhibits germination of seeds of graminaceous species.</p> <p>Results</p> <p>We used a hybrid next-generation sequencing approach to develop a high-quality draft genome sequence for <it>P. fluorescens </it>WH6. We employed automated, manual, and experimental methods to further improve the draft genome sequence. From this assembly of 6.27 megabases, we predicted 5876 genes, of which 3115 were core to <it>P. fluorescens </it>and 1567 were unique to WH6. Comparative genomic studies of WH6 revealed high similarity in synteny and orthology of genes with <it>P. fluorescens </it>SBW25. A phylogenomic study also placed WH6 in the same lineage as SBW25. In a previous non-saturating mutagenesis screen we identified two genes necessary for GAF activity in WH6. Mapping of their flanking sequences revealed genes that encode a candidate anti-sigma factor and an aminotransferase. Finally, we discovered several candidate virulence and host-association mechanisms, one of which appears to be a complete type III secretion system.</p> <p>Conclusions</p> <p>The improved high-quality draft genome sequence of WH6 contributes towards resolving the <it>P. fluorescens </it>species, providing additional impetus for establishing two separate lineages in <it>P. fluorescens</it>. Despite the high levels of orthology and synteny to SBW25, WH6 still had a substantial number of unique genes and represents another source for the discovery of genes with implications in affecting plant growth and health. Two genes are demonstrably necessary for GAF and further characterization of their proteins is important for developing natural products as control measure against grassy weeds. Finally, WH6 is the first isolate of <it>P. fluorescens </it>reported to encode a complete T3SS. This gives us the opportunity to explore the role of what has traditionally been thought of as a virulence mechanism for non-pathogenic interactions with plants.</p

GPs are from Mars, Administrators are from Venus: The Role of Misaligned Occupational Dispositions in Inhibiting Mandated Role Change

Research on mandated occupational role change focuses on jurisdictional conflict to explain change failure. Our study of the English National Health Service highlights the role of occupational dispositions in shaping how mandated role change is implemented by members of multiple occupational groups. We find that tension stemming from misaligned dispositions may emerge as members of different occupations interact during their role change implementation efforts. Depending on dispositional responses to tension, change may fail as members of the different occupations avoid interactions. This suggests that effective role change can be elusive even in the initial absence of conflicting occupational interests