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- Bryant, C.H., et al.
(författare)
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Combining Inductive Logic Programming, Active Learning and Robotics to Discover the Function of Genes
- 2001
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- We aim to partially automate some aspects of scientific work, namely the processes of forming hypotheses, devising trials to discriminate between these competing hypotheses, physically performing these trials and then using the results of these trials to converge upon an accurate hypothesis. We have developed ASE-Progol, an Active Learning system which uses Inductive Logic Programming to construct hypothesised first-order theories and uses a CART-like algorithm to select trials for eliminating ILP derived hypotheses. We have developed a novel form of learning curve, which in contrast to the form of learning curve normally used in Active Learning, allows one to compare the costs incurred by different leaning strategies.We plan to combine ASE-Progol with a standard laboratory robot to create a general automated approach to Functional Genomics. As a first step towards this goal, we are using ASE-Progol to rediscover how genes participate in the aromatic amino acid pathway of Saccharomyces cerevisiae. Our approach involves auxotrophic mutant trials. To date, ASE-Progol has conducted such trials in silico. However we describe how they will be performed automatically in vitro by a standard laboratory robot designed for these sorts of liquid handling tasks, namely the Beckman/Coulter Biomek 2000.Although our work to date has been limited to trials conducted in silico, the results have been encouraging. Parts of the model were removed and the ability of ASE-Progol to efficiently recover the performance of the model was measured. The cost of the chemicals consumed in converging upon a hypothesis with an accuracy in the range 46-88% was reduced if trials were selected by ASE-Progol rather than if they were sampled at random (without replacement). To reach an accuracy in the range 46-80%, ASE-Progol incurs five orders of magnitude less experimental costs than random sampling. ASE-Progol requires less time to converge upon a hypothesis with an accuracy in the range 74-87% than if trials are sampled at random (without replacement) or selected using the naive strategy of always choosing the cheapest trial from the set of candidate trials. For example to reach an accuracy of 80%, ASE-Progol requires 4 days while random sampling requires 6 days and the naive strategy requires 10 days.
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| 2. |
- Reiser, Philip G.K., et al.
(författare)
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Developing a Logical Model of Yeast Metabolism
- 2001
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- With the completion of the sequencing of genomes of an increasing number of organisms, the focus of biology is moving to determining the role of these genes (functional genomics). To this end it is useful to view the cell as a biochemical machine: it consumes simple molecules to manufacture more complex ones by chaining together biochemical reactions into long sequences referred to as metabolic pathways. Such metabolic pathways are not linear but often intersect to form a complex network. Genes play a fundamental role in this network by synthesising the enzymes that catalyse biochemical reactions. Although developing a complete model of metabolism is of fundamental importance to biology and medicine, the size and complexity of the network has proven beyond the capacity of human reasoning. This paper presents intermediate results in the Robot Scientist research programme that aims to discover the function of genes in the metabolism of the yeast Saccharomyces cerevisiae. Results include: (1) the first logical model of metabolism; (2) a method to predict phenotype by deductive inference; and (3) a method to infer reactions and gene function by abductive inference. We describe the in vivo experimental set-up which will allow these in silico inferences to be automatically tested by a laboratory robot.
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| 3. |
- von Seggern, J., et al.
(författare)
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Erosion and deposition effects on the vessel wall of TEXTOR-94
- 2001
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Ingår i: Journal of Nuclear Materials. - 0022-3115 .- 1873-4820. ; 290, s. 341-345
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Tidskriftsartikel (refereegranskat)abstract
- Two different sets of long term samples (LTS) were exposed in TEXTOR-94 at the liner with boronized and siliconized wall conditions. Measured erosion/deposition rates of the coating constituents were compared with sputtering rates calculated for pure elements. D-0-fluxes at the LTS locations were determined by the B2-EIRENE code. Over the whole liner, erosion of initial coatings by D-0 is observed. Boron erodes at a rate of 8.4 x 10(13) B cm(-2) s(-1),while silicon erodes at a rate of 5.6 x 10(13) Si cm(-2) s(-1), a factor of 1.5 lower than that of boron. With boronized walls, carbon atoms initially present in the a-C/B:D layers are eroded at a rate of 7.6 x 10(12) C cm(-2) s(-1), at the same time 1.7 x 10(12) (Fe + Cr + Ni) cm(-2) s(-1) are deposited. Compared to boronized conditions where carbon erodes, deposition of carbon (1.7 x 10(13) cm(-2) s(-1)) and of metals (3.8 x 10(12) cm(-2) s(-1) occurred during the Si campaign. Due to long time exposure at high wall temperature (350 degreesC), hydrogenic isotopes desorb; (D + H)/(B + C) and (D + H)/(Si + C) ratios degrade from originally similar to0.4 to similar to0.2.
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