S4 Computations for chaos(p), quant(p), and class(p) constraints - PLOS
Recommend Documents
... Coastguard Agency; MMO â Marine Management Organisation; MoD â. Ministry of Defence; TCE â The Crown Estate; UK DEAL â now UK Oil and Gas Data.
S3 Computations for ELFP. A convex bounded polytope can be equivalently defined either as the convex hull of a set of points. (V-representation) or as the ...
No of Exonic. SNPs. BWA. Samtools. 1391002. 60215. 7746. GATK. 610524. -. 25766. Freebayes. 22530966. 224211. 145248. Bambino. 199482. 43389.
Page 1. S4 Fig. (mAU). 250 -. 15 - anti-αSyn. A. B. 9 10 11 15. 9 10 11 15. 100 -. C. D anti-VAMP2. - +. αSyn Agg. Free VAMP2. Bound VAMP2. - +. αSyn Agg.
S4 Fig. pLenti-CMV. pLenti-CMV-MSANTD3. pBABE. pBABE-KRAS(V12). A. B. 0. 10. 20. 30. 40. 50. 60. 70. Foci per plate. pLenti-CMV. pLenti-CMV-. MSANTD3.
S4 Fig. Routine metabolic rate and maximum metabolic rate of copper and blue rockfish. (A,B). Routine metabolic rate was measured as the oxygen ...
Figure S4. 3D models of selected domains in the Drosophila genome. Superimposed 3D structures for selected models in cluster #1 for each of the 50 modeled.
103. 104. 105. 106. 107. 108. InlP sum of intensity (A.U.). 103. 104. 105. 106. 107. 108. A. LRR5 sum of intensity (A.U.). All proteins. Afadin. X=Y. S4 Figure.
S4 Fig. Phospho-proteins measured by Luminex. Proteins were measured from the distal colons of control and naïve T-treated animals and those treated for 2 ...
CON B. CON IO. PKD1 B PKD1 IO. 0. 5. 10. 15. M. M. P. -1. 3. /1. 8. S. rR. N. A. shCon. shPRKD1. IL-1+OSM -. +. -. +. **. ***. MMP1. MMP13. MMP-1 gene ...
Figure S4. Correlation matrix of the measured phenotypes. The Pearson correlation coefficient was calculated for each phenotype pair where the.
Table S4. Marker-trait association P-values in the severe U.K. subset (126 families) â Adapted from Harold et al. [17]. P-Value for Trait3. Marker1. Gene.
S4 Table: Comparison of the sensitivity and specificity of RISC (HIV-uninfected) in our. Malawian study population (ALL) with that of the South African RISC ...
S4 Text: Reanalysis of MA fitness data. Although crossing over with vg occurred in
S4 Table. Cis-regulatory elements involved in diurnal and circadian regulation identified in StBBX promoters. Gene name. Site. Name. Organism Position Strand.
S4 Computations for chaos(p), quant(p), and class(p) constraints - PLOS
S4 Computations for chaos(p), quant(p), and class(p) constraints. The Allconstr polytopes for the three constraints are obtained by concatenating the ELFP ...
Dzhafarov and Kujala S4
1
Computations for
chaos(p), quant(p),
and
class(p)
constraints
The Allconstr polytopes for the three constraints are obtained by concatenating the ELFP equations and inequalities with the constraint inequalities. Then, the volumes are computed by using the lrs program as described above. For Fitconstr polytopes, we observe rst that they are convex. This follows from
denote the vertices of the 4D convex polytope dened by
denotes the (convex) cross-section of the ELFP set formed with
p = p(i) .
constr and ELFPp(i) Fitconstr is convex
It follows that
as the intersection of convex sets. Following the logic of this observation, we have implemented a general program for eliminating variables from a system of linear equations and inequalities so that the resulting system is satised for exactly those values for which there exist such values of the eliminated variables for which the original system is satised. This program together with steps to ensure that the resulting representation is minimal was used to nd all the Fit sets shown in the main text. Finding the forcing sets is more dicult as they are generally not convex. We characterize them using the equation
Forcechaos − Forceconstr = {ε : (∃p : (p, ε) ∈ ELFP ∧ ¬constr (p))} . This equation provides an algorithm: for each inequality in
constr,
(S4.2)
form the conjunction of the ELFP
inequalities with the negation of the inequality. Then project this conjunction to the of these projections over all inequalities in
constr is the set Forcechaos − Forceconstr .
ε 4-space.
The union
We have implemented
a general program that takes as input a representation of a polytope, a list of additional constraints, and a list of variables to eliminate. It then outputs a representation of the dierence of the polytope and the set represented by the additional constraints projected to the remaining (not eliminated) variables. This representation consists of a list of linear systems whose disjunction characterizes the resulting set. In all our computations it turned out that all the linear systems in the disjunction were the same, and so the sets
Forcechaos − Forceconstr
are in fact convex in these cases.
The computations of Equi sets require no elaboration. Remark 1. There is the practical problem that the negation of a
≤
-inequality is a
>
-inequality while
standard algorithms only accept closed convex polytopes. To cope with this problem, we approximated
a > b
by
a ≥ b+
constraints.
√
(very small number).
We also used a rational approximation to
2
in the quant
In both cases, we have repeated the computations with decreasing values of very small
number until it was obvious where the results converged.