"In this paper, we investigate a conjecture by von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This conjecture deals with the question whether Maximum Parsimony trees are hereditary. The conjecture suggests that a Maximum Parsimony tree for a particular (DNA) alignment necessarily has subtrees of all possible sizes which are most parsimonious for the corresponding subalignments. We answer the conjecture affirmatively for binary alignments on five taxa but also show how to construct examples for which Maximum Parsimony trees are not hereditary. …we also show that compatible most parsimonious quartets do not have to provide a most parsimonious supertree. Last, we show that our results can be generalized to Maximum Likelihood for certain nucleotide substitution models."

will I ever understand all the effort statisticians put into what I consider a solved problem? Pareto-GP is apparently utterly unknown, still

"Investigating the relation between the structure and behavior of complex biological networks often involves posing the following two questions: Is a hypothesized structure of a regulatory network consistent with the observed behavior? And can a proposed structure generate a desired behavior? Answering these questions presupposes that we are able to test the compatibility of network structure and behavior. We cast these questions into a parameter search problem for qualitative models of regulatory networks…. We develop a method based on symbolic model checking that avoids enumerating all possible parametrizations, and show that this method performs well on real biological problems, using the IRMA synthetic network and benchmark experimental data sets. We test the consistency between the IRMA network structure and the time-series data, and search for parameter modifications that would improve the robustness of the external control of the system behavior."

"…Generally speaking, modules are islands of highly connected nodes separated by a relatively small number of links. Every module can have contributions of links from any node in the network. The challenge is to disentangle these contributions to understand how the modular structure is built. The main problem is that the analysis of a certain partition into modules involves, in principle, as many data as number of modules times number of nodes. To confront this challenge, here we first define the contribution matrix, the mathematical object containing all the information about the partition of interest, and after, we use a Truncated Singular Value Decomposition to extract the best representation of this matrix in a plane. The analysis of this projection allow us to scrutinize the skeleton of the modular structure, revealing the structure of individual modules and their interrelations."

"Quantitative properties of stochastic systems are usually specified in logics that allow one to compare the measure of executions satisfying certain temporal properties with thresholds. The model checking problem for stochastic systems with respect to such logics is typically solved by a numerical approach that iteratively computes (or approximates) the exact measure of paths satisfying relevant subformulas; the algorithms themselves depend on the class of systems being analyzed as well as the logic used for specifying the properties. Another approach to solve the model checking problem is to \emph{simulate} the system for finitely many runs, and use \emph{hypothesis testing} to infer whether the samples provide a \emph{statistical} evidence for the satisfaction or violation of the specification. In this short paper, we survey the statistical approach, and outline its main advantages in terms of efficiency, uniformity, and simplicity."

"The study of high-dimensional differential equations is challenging and difficult due to the analytical and computational intractability. Here, we significantly improve the speed of waveform relaxation (WR), a method to simulate high-dimensional differential-algebraic equations. This new method termed adaptive waveform relaxation (AWR) is tested on a communication network example. Further we analyze different heuristics for computing graph partitions tailored to adaptive waveform relaxation."

"The place where I think Sloman is misguided is in his formulation of scientific models in an either/or way, as if, in truth, social variables are linked in simple causal paths, with a scientific goal of figuring out if A causes B or the reverse. I don't know much about intelligence, beer consumption, and socioeconomic status, but I certainly don't see any simple relationships between income, religious attendance, party identification, and voting--and I don't see how a search for such a pattern will advance our understanding, at least given current techniques. I'd rather start with description and then go toward causality following the approach of economists and statisticians by thinking about potential interventions one at a time. I'd love to see Sloman's and Pearl's ideas of the interplay between observational and experimental data developed in a framework that is less strongly tied to the notion of choice among simple causal structures."

"Ask Why
Finally, and this is the most important thing I've learned, always ask why. When you see a blip in a graph, you should wonder why it's there. If you find some correlation, you should think about whether or not it makes any sense. If it does make sense, then cool, but if not, dig deeper. Numbers are great, but you have to remember that when humans are involved, errors are always a possibility."