Learning few-shot imitation as cultural transmission.

Cultural transmission is the domain-general social skill that allows agents to acquire and use information from each other in real-time with high fidelity and recall. It can be thought of as the process that perpetuates fit variants in cultural evolution. In humans, cultural evolution has led to the accumulation and refinement of skills, tools and knowledge across generations.

Fast, approximate kinetics of RNA folding.

In this article, we introduce the software suite Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure S of a given RNA sequence has base pair distance x (resp. y) from reference structure A (resp.

Computing the probability of RNA hairpin and multiloop formation.

We describe four novel algorithms, RNAhairpin, RNAmloopNum, RNAmloopOrder, and RNAmloopHP, which compute the Boltzmann partition function for global structural constraints-respectively for the number of hairpins, the number of multiloops, maximum order (or depth) of multiloops, and the simultaneous number of hairpins and multiloops. Given an RNA sequence of length n and a user-specified integer 0 ≤ K ≤ n, RNAhairpin (resp. RNAmloopNum and RNAmloopOrder) computes the partition functions Z(k) for each 0 ≤ k ≤ K in time O(K(2)n(3)) and space O(Kn(2)), while RNAmloopHP computes the partition functions Z(m, h) for 0 ≤ mm ≤ M multiloops and 0 ≤ h ≤ H hairpins, with run time O(M(2)H(2)n(3)) and space O(MHn(2)).

RNA folding pathways and kinetics using 2D energy landscapes.

RNA folding pathways play an important role in various biological processes, such as (i) the hok/sok (host-killing/suppression of killing) system in E. coli to check for sufficient plasmid copy number, (ii) the conformational switch in spliced leader (SL) RNA from Leptomonas collosoma, which controls trans splicing of a portion of the '5 exon, and (iii) riboswitches--portions of the 5' untranslated region of messenger RNA that regulate genes by allostery. Since RNA folding pathways are determined by the energy landscape, we describe a novel algorithm, FFTbor2D, which computes the 2D projection of the energy landscape for a given RNA sequence.

Using the fast fourier transform to accelerate the computational search for RNA conformational switches.

Using complex roots of unity and the Fast Fourier Transform, we design a new thermodynamics-based algorithm, FFTbor, that computes the Boltzmann probability that secondary structures differ by [Formula: see text] base pairs from an arbitrary initial structure of a given RNA sequence. The algorithm, which runs in quartic time O(n(4)) and quadratic space O(n(2)), is used to determine the correlation between kinetic folding speed and the ruggedness of the energy landscape, and to predict the location of riboswitch expression platform candidates. A web server is available at http://bioinformatics.