We present a new algorithm for Bayesian network structure learning, called Max-Min Hill-Climbing (MMHC). The algorithm combines ideas from local learning, constraint-based, and search-and-score techniques in a principled and effective way. It first reconstructs the skeleton of a Bayesian network and then performs a Bayesian-scoring greedy hill-climbing search to orient the edges. In our extensive empirical evaluation MMHC outperforms on average and in terms of various metrics several prototypical and state-of-the-art algorithms, namely the PC, Sparse Candidate, Three Phase Dependency Analysis, Optimal Reinsertion, Greedy Equivalence Search, and Greedy Search. These are the first empirical results simultaneously comparing most of the major Bayesian network algorithms against each other. MMHC offers certain theoretical advantages, specifically over the Sparse Candidate algorithm, corroborated by our experiments. MMHC and detailed results of our study are publicly available at http://www.dsl-lab.org/supplements/mmhc_paper/mmhc_index.html.

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The max-min hill-climbing Bayesian network structure learning algorithm

Does organic farming reduce environmental impacts?--a meta-analysis of European research.

Bayesian networks (BNs), also known as Bayesian belief networks or Bayes nets, are a kind of probabilistic graphical model that has become very popular to practitioners mainly due to the powerful probability theory involved, which makes them able to deal with a wide range of problems. The goal of this review is to show how BNs are being used in environmental modelling. We are interested in the application of BNs, from January 1990 to December 2010, in the areas of the ISI Web of Knowledge related to Environmental Sciences. It is noted that only the 4.2% of the papers have been published under this item. The different steps that configure modelling via BNs have been revised: aim of the model, data pre-processing, model learning, validation and software. Our literature review indicates that BNs have barely been used for Environmental Science and their potential is, as yet, largely unexploited.

Review: Bayesian networks in environmental modelling

Review: The Transition Handbook: From Oil Dependency to Local Resilience By Rob Hopkins Reviewed by Alex Alkhoury University of Western Ontario, Canada Hopkins, Rob. The Transition Handbook: From Oil Dependency to Local Resilience. White River Junction, VT: Chelsea Green Publishing, 2008. 240 pp. ISBN: 9781900322188. US$24.95, paper. Chlorine-free recycled paper. The intertwined emergencies of peak oil and climate change demand dramatic, urgent action across a range of scales, the magnitude of which can threaten to overwhelm people, particularly those who are just learning about these issues. When problems seem overwhelming it can easily lead to individual inaction and collective inertia, and this is precisely what Rob Hopkins seeks to overcome in The Transition Handbook. His essential goal is to outline a realistic and hopeful vision of post-carbon communities and the practical steps needed to get there. The starting point for Transition is the essential problem now widely understood as ‘peak oil’: as the production of conventional oil declines, its growing scarcity will drive increasingly higher fuel prices with profound implications for industrial economies. Hopkins argues that while climate change exists in the public consciousness as an intangible or, at most, distant fear, the decline of cheap fossil energy is a much more proximate and understandable problem for many – as barrels of oil are easier to visualize than tonnes of [greenhouse] gas (p.40) – and can thus simultaneously spark necessary action on both issues. Hopkins begins by succinctly describing the nature of the problems (what he calls ‘The Head’), then appeals for a rational, composed response (in a section called the 'The Heart'), before digging into the crux of the book, ‘The Hands,’ a discussion of specific, transitional steps and strategies to move beyond economies centred on fossil energy. His 'Twelve Steps of Transition' are underpinned by a clear statement of six core principles, including positive 'visioning', 'inclusion' of all members of the community, 'awareness-raising', 'resilience', using 'psychological insights' to counter the threat of inaction, and focusing on the community level to attain 'credible and appropriate solutions'. For Hopkins, a community's resilience hinges on its ability to produce core goods and services, while only importing what cannot be sourced locally. Building momentum for re-localization depends upon first building a strong foundation of community-level understanding of the issues and rebuilding connections among people. Hopkins provides great, practical detail here, outlining strategies on running successful public meetings, and providing tips on organizing things like empowering re- skilling group events, and how best to obtain publicity for both these and also the launch of a given Transition Initiative. In this, Transition also doubles as a best practices guide for the logistical elements of community organization and activism. This practical and optimistic ‘how to’ dimension is undoubtedly the book’s great objective and strength, and for this it should appeal to those eager to inspire action in their own communities. However, it is not Hopkins' intention to provide a precise, universal plan, but rather a general set of guidelines backed by motivating examples of contemporary re-localization efforts. At times, this does leave difficult questions of scale underdeveloped, with much of the discussion directed at the level of relatively small communities. With a background in permaculture and as the founder of the UK Transition movement, Hopkins is well-positioned to offer both a broader vision and a practical plan for re-localization and self-reliance. His achievement in this book is to give concrete grounds for optimism in a captivating and highly accessible way. In this, it is a particularly useful antidote to those who are concerned but overwhelmed, as well as being a useful starting point into peak oil and transition issues for progressive scholars, students, activists and the general public alike. Alex Alkhoury. , MA Student, Department of Geography, University of Western Ontario, Social Science Centre, London, Ontario N6A 5C2, Canada. Electronic Green Journal, Issue 29, Winter 2009, ISSN:1076-7975

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Review: The Transition Handbook: From Oil Dependency to Local Resilience

BACKGROUND
The health benefits of organic foods are unclear.


PURPOSE
To review evidence comparing the health effects of organic and conventional foods.


DATA SOURCES
MEDLINE (January 1966 to May 2011), EMBASE, CAB Direct, Agricola, TOXNET, Cochrane Library (January 1966 to May 2009), and bibliographies of retrieved articles.


STUDY SELECTION
English-language reports of comparisons of organically and conventionally grown food or of populations consuming these foods.


DATA EXTRACTION
2 independent investigators extracted data on methods, health outcomes, and nutrient and contaminant levels.


DATA SYNTHESIS
17 studies in humans and 223 studies of nutrient and contaminant levels in foods met inclusion criteria. Only 3 of the human studies examined clinical outcomes, finding no significant differences between populations by food type for allergic outcomes (eczema, wheeze, atopic sensitization) or symptomatic Campylobacter infection. Two studies reported significantly lower urinary pesticide levels among children consuming organic versus conventional diets, but studies of biomarker and nutrient levels in serum, urine, breast milk, and semen in adults did not identify clinically meaningful differences. All estimates of differences in nutrient and contaminant levels in foods were highly heterogeneous except for the estimate for phosphorus; phosphorus levels were significantly higher than in conventional produce, although this difference is not clinically significant. The risk for contamination with detectable pesticide residues was lower among organic than conventional produce (risk difference, 30% [CI, -37% to -23%]), but differences in risk for exceeding maximum allowed limits were small. Escherichia coli contamination risk did not differ between organic and conventional produce. Bacterial contamination of retail chicken and pork was common but unrelated to farming method. However, the risk for isolating bacteria resistant to 3 or more antibiotics was higher in conventional than in organic chicken and pork (risk difference, 33% [CI, 21% to 45%]).


LIMITATION
Studies were heterogeneous and limited in number, and publication bias may be present.


CONCLUSION
The published literature lacks strong evidence that organic foods are significantly more nutritious than conventional foods. Consumption of organic foods may reduce exposure to pesticide residues and antibiotic-resistant bacteria.


PRIMARY FUNDING SOURCE
None.

Are organic foods safer or healthier than conventional alternatives? a systematic review

Abstract Increasing concerns about pesticide use and a steadily increasing conversion to organic farming have been major factors driving research in physical and cultural weed control methods in Europe. This article reviews some of the major results achieved with nonchemical methods and strategies, especially adapted for row crops (e.g., corn, sugar beet, onion, leek, and carrot) and small-grain cereals (e.g., barley and wheat). In row crops, intrarow weeds constitute a major challenge, and research has mainly aimed at replacing laborious hand-weeding with mechanization. A number of investigations have focused on optimizing the use of thermal and mechanical weeding methods against intrarow weeds, such as flaming, harrowing, brush weeding, hoeing, torsion weeding, and finger weeding. And new methods are now under investigation such as robotic weeding for row crops with abundant spacing between individual plants and band-steaming for row crops developing dense crop stands. The strategic use of mechanical weed control methods in small-grain cereals has been another area of considerable interest. Weed harrowing and interrow hoeing provide promising results when they are part of a strategy that also involves cultural methods such as fertilizer placement, seed vigor, seed rate, and competitive varieties. Although research in preventive, cultural, and physical methods have improved weed control in row crops and small-grain cereals, effective long-term weed management in low external input and organic systems can only be achieved by tackling the problem in a wider context, i.e., at the cropping system level. Basic principles of this approach, examples of cover crop and intercropping use for weed suppression, and an application in a 2-yr rotation are presented and discussed. Nomenclature: Barley, Hordeum vulgare L.; carrot, Daucus carota L.; corn, Zea mays L.; leek, Allium porrum L.; onion, Allium cepa L.; sugar beet, Beta vulgaris L.; wheat, Triticum aestivum L.

Symposium Integrating physical and cultural methods of weed control— examples from European research

Increasing concerns about pesticide use and a steadily increasing conversion to organic farming have been major factors driving research in physical and cultural weed control methods in Europe. This article reviews some of the major results achieved with nonchemical methods and strategies, especially adapted for row crops (e.g., corn, sugar beet, onion, leek, and carrot) and small-grain cereals (e.g., barley and wheat). In row crops, intrarow weeds constitute a major challenge, and research has mainly aimed at replacing laborious hand-weeding with mechanization. A number of investigations have focused on optimizing the use of thermal and mechanical weeding methods against intrarow weeds, such as flaming, harrowing, brush weeding, hoeing, torsion weeding, and finger weeding. And new methods are now under investigation such as robotic weeding for row crops with abundant spacing between individual plants and band-steaming for row crops developing dense crop stands. The strategic use of mechanical we...

/pdf/integrating-physical-and-cultural-methods-of-weed-control-3zr6386w0j.pdf

Integrating Physical and Cultural Methods of Weed Control – Examples from European Research

Mathematical modelling is a commonly used tool for studying the long-term dynamics of weed populations in agriculture. This was reflected in our review by the large number of scientific papers (134 original publications) and the continuing need to gain an overview over this fast developing field (20 previous review papers were found). In this article, we provide a more comprehensive review than earlier seen, striving to include all relevant publications. Thus, we cover models of the population dynamics of 60 weed species in 40 crops. An online, accompanying database provices an indexed bibliography. Despite the large variation in crops, weeds and geography, the models were surprisingly similar in their approach: structured around the weed life cycle, excluding environmental factors and giving little attention to validation or even documentation of model construction. In addition, their application was similar, limited mostly to strategic decision making. We hope that the overview provided by this review will inspire weed modellers and that it will serve as a basis for discussion and as a frame of reference when we proceed to advance the modelling of weed populations to a new level, developing new approaches and tackling new application domains.

Field weed population dynamics : a review of model approaches and applications

Three field experiments were carried out in organically grown winter wheat in Denmark. The treatments were sowing time (normal or late sowing) and false seedbed, row width (12 cm and 24 cm) and weed control method (untreated, mechanical weed control (weed harrowing at 12 cm supplemented with inter-row hoeing at 24 cm), and herbicide weed control). Weed biomass in mid-summer was greatest on plots sown at the normal sowing time (compared to delayed sowing) and was reduced by mechanical or chemical weed control (compared with untreated plots). Row width alone had no influence on weed biomass, but in the experiment with high weed pressure, the more intensive mechanical weed control used at a row width of 24 cm reduced weed biomass. Normal sowing time tended to give higher yields, but this was only statistically significant in one of the three experiments. Wide rows gave a yield decrease in the experiment with low weed pressure. The effect of weed control on yield was dependent on the weed pressure. At low weed pressure, mechanical weed control caused a yield decrease compared to untreated or herbicide treated. At intermediate weed levels there were no differences, whereas at high weed pressure, mechanical weed control and herbicide treatment caused a yield increase compared to untreated. False seedbeds were shown to contribute to a decrease in the soil seed reserve.

Ilse A. Rasmussen

Papers

Symposium Integrating physical and cultural methods of weed control— examples from European research

Integrating Physical and Cultural Methods of Weed Control – Examples from European Research

Field weed population dynamics : a review of model approaches and applications

The effect of sowing date, stale seedbed, row width and mechanical weed control on weeds and yields of organic winter wheat

Nitrate leaching from organic arable crop rotations is mostly determined by autumn field management