Predicting protein functions with message passing algorithms

Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most relevant issues has recently become that of correctly and reliably predicting the functions of observed but still functionally undetermined proteins starting from information coming from the network of co-observed proteins of known functions. Method: The method proposed in this article is based on a message passing algorithm known as Belief Propagation, which takes as input the network of proteins physical interactions and a catalog of known proteins functions, and returns the probabilities for each unclassified protein of having one chosen function. The implementation of the algorithm allows for fast on-line analysis, and can be easily generalized to more complex graph topologies taking into account hyper-graphs, {\em i.e.} complexes of more than two interacting proteins.Comment: 12 pages, 9 eps figures, 1 additional html tabl

Alien Registration- Letovsky, Ethel (Caribou, Aroostook County)

https://digitalmaine.com/alien_docs/26136/thumbnail.jp

Conncetionist Variable-Binding By Optimization

Symbolic AI systems based on logical or frame languages can easily perform inferencesthat are still beyond the capability of most connectionist networks. This paper presents a strategy for implementing in connectionist networks the basic mechanisms of variable binding, dynamic frzune allocation and equality that underlie many of the types of inferences commonly handled by frame systems, including inheritance, subsumption and abductive inference. The paper describes a scheme for translating frame definitions in a simple frame language into objective functions whose minima correspond to partial deductive closures of the legaJ inferences. The resulting constrained optimization problem can be viewed as a specification for a connectionist network

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes

COMBREX (http://combrex.bu.edu) is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids.National Institute of General Medical Sciences (U.S.) (Go grant 1RC2GM092602-01

Environmental Protection and Economic Development: The Case of the Huaihe River Basin Cleanup Plan

The case examines efforts by the Chinese government and local authorities to restore the Huiahe River, a 1,000 kilometer waterway which runs through four provinces in eastern China. The river basin, covering an area of some 270,000 square kilometers, is home to almost 150 million people and represents one of the most important areas of agricultural output in China. As a result of rapid economic development, the river has, over the past twenty years, become seriously polluted. This has had dire consequences for industries that depend on the river, notably agriculture and fishing. As well, the limited groundwater supplies in eastern China have meant that surface water has always been an important source of supply for residential and industrial uses. The pollution of the Huaihe has therefore had serious public health consequences. In mid-1995, the Chinese government formally adopted an ambitious plan to restore the water quality in the river. The case is based on material gathered from secondary sources, supplemented by interviews conducted with government officials and company managers in Beijing and Anhui province in China. The case begins with an overview of the impact of economic growth on the Chinese environment, and the steps which China has taken to address its growing environmental challenges. The case then focuses on the plan as proposed by the Chinese Research Academy of Environmental Sciences (CRAES). The case goes on to describe some of the early implementation measures taken as part of the plan, in particular the forced closure of hundreds of small factories that have sprung up along the banks of the river. The case outlines the various stakeholders affected by the plan and its ultimate success or failure. These include local residents and businesses, various Chinese government ministries, multilateral lending agencies and international suppliers of anti-pollution technologies. The ultimate success of the plan is, at the time of this writing, not known. Future issues and questions that will affect the plan's success are then described. These include resistance by some elements of the Chinese government concerned about foreign debts incurred to finance the cleanup plan; local officials who may not wish to sacrifice short-term economic growth for environmental protection; and businesses concerned about the financial burden of having to install new clean technologies.http://deepblue.lib.umich.edu/bitstream/2027.42/39536/3/wp147.pd

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes

COMBREX (http://combrex.bu.edu) is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids.National Institute of General Medical Sciences (U.S.) (Go grant 1RC2GM092602-01

Environmental Protection and Economic Development: The Case of the Huaihe River Basin Cleanup Plan

The case examines efforts by the Chinese government and local authorities to restore the Huiahe River, a 1,000 kilometer waterway which runs through four provinces in eastern China. The river basin, covering an area of some 270,000 square kilometers, is home to almost 150 million people and represents one of the most important areas of agricultural output in China. As a result of rapid economic development, the river has, over the past twenty years, become seriously polluted. This has had dire consequences for industries that depend on the river, notably agriculture and fishing. As well, the limited groundwater supplies in eastern China have meant that surface water has always been an important source of supply for residential and industrial uses. The pollution of the Huaihe has therefore had serious public health consequences. In mid-1995, the Chinese government formally adopted an ambitious plan to restore the water quality in the river. The case is based on material gathered from secondary sources, supplemented by interviews conducted with government officials and company managers in Beijing and Anhui province in China. The case begins with an overview of the impact of economic growth on the Chinese environment, and the steps which China has taken to address its growing environmental challenges. The case then focuses on the plan as proposed by the Chinese Research Academy of Environmental Sciences (CRAES). The case goes on to describe some of the early implementation measures taken as part of the plan, in particular the forced closure of hundreds of small factories that have sprung up along the banks of the river. The case outlines the various stakeholders affected by the plan and its ultimate success or failure. These include local residents and businesses, various Chinese government ministries, multilateral lending agencies and international suppliers of anti-pollution technologies. The ultimate success of the plan is, at the time of this writing, not known. Future issues and questions that will affect the plan's success are then described. These include resistance by some elements of the Chinese government concerned about foreign debts incurred to finance the cleanup plan; local officials who may not wish to sacrifice short-term economic growth for environmental protection; and businesses concerned about the financial burden of having to install new clean technologies.

Long-term trends in aquatic ecosystem bioassessment metrics are not influenced by sampling method: empirical evidence from the Niobrara River

Choosing an aquatic invertebrate sampling method for biomonitoring depends upon study goals, resources, and ecosystem conditions. In this study, we compared two methods that are widely used in stream ecology, but have not been directly compared: Hester–Dendy (HD) and Hess sampling. Hester–Dendy sampling uses artificial substrate that invertebrates colonize over a specific period of time. In contrast, Hess samplers surround a fixed area of natural substrate with a net. To compare approaches, we combined 5 years of simultaneous HD and Hess data collection (2010–2014) from the Niobrara River with a 14-year (1996–2009) historical HD data set for the same study sites. We used this full 19-year data set to assess how ecosystem health has changed in the Niobrara River over time, while also testing the influence of HD versus Hess data (2010–2014) on historical trends (1996–2009). Our results showed that HD samples are more taxonomically variable and bias bioassessment metrics because they collect more sensitive taxa versus Hess sampling. However, when combined with the 1996–2009 HD data set, both recent HD and Hess data sets recovered the same trend of declining ecosystem health in the Niobrara River. These results provide empirical evidence that even when historical HD data are combined with recent Hess data, long-term bioassessment trends remain unchanged despite more accurate perspectives of invertebrate assemblages being collected

Expert Programming Knowledge: a Schema-Based Approach

The topic of this chapter is the role of expert programming knowledge in the understanding activity. In the "schema-based approach", the role of semantic structures is emphasized whereas, in the "control-flow approach", the role of syntactic structures is emphasized. Data which support schema-based models of understanding are presented. Data which are more consistent with the "control-flow approach" allow to discuss the limits of the former kind of models