0000000000239934
AUTHOR
Juris Vīksna
Application of Graph Clustering and Visualisation Methods to Analysis of Biomolecular Data
In this paper we present an approach based on integrated use of graph clustering and visualisation methods for semi-supervised discovery of biologically significant features in biomolecular data sets. We describe several clustering algorithms that have been custom designed for analysis of biomolecular data and feature an iterated two step approach involving initial computation of thresholds and other parameters used in clustering algorithms, which is followed by identification of connected graph components, and, if needed, by adjustment of clustering parameters for processing of individual subgraphs.
Deciding reachability for planar multi-polynomial systems
In this paper we investigate the decidability of the reachability problem for planar non-linear hybrid systems. A planar hybrid system has the property that its state space corresponds to the standard Euclidean plane, which is partitioned into a finite number of (polyhedral) regions. To each of these regions is assigned some vector field which governs the dynamical behaviour of the system within this region. We prove the decidability of point to point and region to region reachability problems for planar hybrid systems for the case when trajectories within the regions can be described by polynomials of arbitrary degree.
INDUCTIVE INFERENCE OF LIMITING PROGRAMS WITH BOUNDED NUMBER OF MIND CHANGES
We consider inductive inference of total recursive functions in the case, when produced hypotheses are allowed some finite number of times to change “their mind” about each value of identifiable function. Such type of identification, which we call inductive inference of limiting programs with bounded number of mind changes, by its power lies somewhere between the traditional criteria of inductive inference and recently introduced inference of limiting programs. We consider such model of inductive inference for EX and BC types of identification, and we study • tradeoffs between the number of allowed mind changes and the number of anomalies, and • relations between classes of functions ident…
Assessment of the probabilities for evolutionary structural changes in protein folds.
Abstract Motivation: The evolution of protein sequences can be described by a stepwise process, where each step involves changes of a few amino acids. In a similar manner, the evolution of protein folds can be at least partially described by an analogous process, where each step involves comparatively simple changes affecting few secondary structure elements. A number of such evolution steps, justified by biologically confirmed examples, have previously been proposed by other researchers. However, unlike the situation with sequences, as far as we know there have been no attempts to estimate the comparative probabilities for different kinds of such structural changes. Results: We have tried …