scholarly journals Tiling Nussinov’s RNA folding loop nest with a space-time approach

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Marek Palkowski ◽  
Wlodzimierz Bielecki
Keyword(s):  
Electronics ◽  
2021 ◽  
Vol 10 (18) ◽  
pp. 2233
Author(s):  
Wlodzimierz Bielecki ◽  
Marek Palkowski

We present a new space-time loop tiling approach and demonstrate its application for the generation of parallel tiled code of enhanced locality for three dynamic programming algorithms. The technique envisages that, for each loop nest statement, sub-spaces are first generated so that the intersection of them results in space tiles. Space tiles can be enumerated in lexicographical order or in parallel by using the wave-front technique. Then, within each space tile, time slices are formed, which are enumerated in lexicographical order. Target tiles are represented with multiple time slices within each space tile. We explain the basic idea of space-time loop tiling and then illustrate it by means of an example. Then, we present a formal algorithm and prove its correctness. The algorithm is implemented in the publicly available TRACO compiler. Experimental results demonstrate that parallel codes generated by means of the presented approach outperform closely related manually generated ones or those generated by using affine transformations. The main advantage of code generated by means of the presented approach is its enhanced locality due to splitting each larger space tile into multiple smaller tiles represented with time slices.


2002 ◽  
Author(s):  
J. B. Kennedy
Keyword(s):  

Author(s):  
Roger Penrose ◽  
Wolfgang Rindler
Keyword(s):  

2018 ◽  
Vol 77 (4) ◽  
pp. 173-184
Author(s):  
Wenxing Yang ◽  
Ying Sun

Abstract. The causal role of a unidirectional orthography in shaping speakers’ mental representations of time seems to be well established by many psychological experiments. However, the question of whether bidirectional writing systems in some languages can also produce such an impact on temporal cognition remains unresolved. To address this issue, the present study focused on Japanese and Taiwanese, both of which have a similar mix of texts written horizontally from left to right (HLR) and vertically from top to bottom (VTB). Two experiments were performed which recruited Japanese and Taiwanese speakers as participants. Experiment 1 used an explicit temporal arrangement design, and Experiment 2 measured implicit space-time associations in participants along the horizontal (left/right) and the vertical (up/down) axis. Converging evidence gathered from the two experiments demonstrate that neither Japanese speakers nor Taiwanese speakers aligned their vertical representations of time with the VTB writing orientation. Along the horizontal axis, only Japanese speakers encoded elapsing time into a left-to-right linear layout, which was commensurate with the HLR writing direction. Therefore, two distinct writing orientations of a language could not bring about two coexisting mental time lines. Possible theoretical implications underlying the findings are discussed.


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