A Seeded Genetic Algorithm for RNA Secondary Structural Prediction with Pseudoknots

This work explores a new approach in using genetic algorithm to predict RNA secondary structures with pseudoknots. Since only a small portion of most RNA structures is comprised of pseudoknots, the majority of structural elements from an optimal pseudoknot-free structure are likely to be part of the true structure. Thus seeding the genetic algorithm with optimal pseudoknot-free structures will more likely lead it to the true structure than a randomly generated population. The genetic algorithm uses the known energy models with an additional augmentation to allow complex pseudoknots. The nearest-neighbor energy model is used in conjunction with Turner’s thermodynamic parameters for pseudoknot-free structures, and the H-type pseudoknot energy estimation for simple pseudoknots. Testing with known pseudoknot sequences from PseudoBase shows that it out performs some of the current popular algorithms

Agent-based modelling of air transport demand

Constraints such as opening hours or passenger capacities influence travel options that can be offered by an airport and by the connecting airlines. If infrastructure, policy or technological measures modify transport options, then the benefits do not only depend on the technology, but also on possibly heterogeneous user preferences such as desired arrival times or on the availability of alternative travel modes. This paper proposes an agent-based, iterative assignment procedure to model European air traffic and German passenger demand on a microscopic level, capturing individual passenger preferences. Air transport technology is simulated microscopically, i.e. each aircraft is represented as single unit with attached attributes such as departure time, flight duration or seat availability. Trip-chaining and delay propagation can be added. Microsimulation is used to verify and assess passengers’ choices of travel alternatives, where those choices improve over iterations until an agent-based stochastic user equilibrium is reached. This requires fast simulation models, thus, similar to other approaches in air traffic modelling a queue model is used. In contrast to those approaches, the queue model in this work is solved algorithmically. Overall, the approach is suited to analyze, forecast and evaluate the consequences of mid-distance transport measures

An attentive neural architecture for joint segmentation and parsing and its application to real estate ads

In processing human produced text using natural language processing (NLP) techniques, two fundamental subtasks that arise are (i) segmentation of the plain text into meaningful subunits (e.g., entities), and (ii) dependency parsing, to establish relations between subunits. In this paper, we develop a relatively simple and effective neural joint model that performs both segmentation and dependency parsing together, instead of one after the other as in most state-of-the-art works. We will focus in particular on the real estate ad setting, aiming to convert an ad to a structured description, which we name property tree, comprising the tasks of (1) identifying important entities of a property (e.g., rooms) from classifieds and (2) structuring them into a tree format. In this work, we propose a new joint model that is able to tackle the two tasks simultaneously and construct the property tree by (i) avoiding the error propagation that would arise from the subtasks one after the other in a pipelined fashion, and (ii) exploiting the interactions between the subtasks. For this purpose, we perform an extensive comparative study of the pipeline methods and the new proposed joint model, reporting an improvement of over three percentage points in the overall edge F1 score of the property tree. Also, we propose attention methods, to encourage our model to focus on salient tokens during the construction of the property tree. Thus we experimentally demonstrate the usefulness of attentive neural architectures for the proposed joint model, showcasing a further improvement of two percentage points in edge F1 score for our application.Comment: Preprint - Accepted for publication in Expert Systems with Application

Identifying Unknown Response Styles: A Latent-Class Bilinear Multinomial Logit Model

Respondents can vary significantly in the way they use rating scales. Specifically, respondents can exhibit varying degrees of response style, which threatens the validity of the responses. The purpose of this article is to investigate to what extent rating scale responses show response style and substantive content of the item. The authors develop a novel model that accounts for possibly unknown kinds of response styles, content of the items, and background characteristics of respondents. By imposing a bilinear structure on the parameters of a multinomial logit model, the authors can visually distinguish the effects on the response behavior of both the characteristics of a respondent and the content of the item. This approach is combined with finite mixture modeling, so that two separate segmentations of the respondents are obtained: one for response style and one for item content. This latent-class bilinear multinomial logit (LC-BML) model is applied to a cross-national data set. The results show that item content is highly influential in explaining response behavior and reveal the presence of several response styles, including the prominent response styles acquiescence and extreme response style.multinomial logit model;visualization;segmentation;cross-cultural research;response style

RosettaBackrub--a web server for flexible backbone protein structure modeling and design.

The RosettaBackrub server (http://kortemmelab.ucsf.edu/backrub) implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling. Backrub modeling is applied to three related applications using the Rosetta program for structure prediction and design: (I) modeling of structures of point mutations, (II) generating protein conformational ensembles and designing sequences consistent with these conformations and (III) predicting tolerated sequences at protein-protein interfaces. The three protocols have been validated on experimental data. Starting from a user-provided single input protein structure in PDB format, the server generates near-native conformational ensembles. The predicted conformations and sequences can be used for different applications, such as to guide mutagenesis experiments, for ensemble-docking approaches or to generate sequence libraries for protein design

A Finite State and Data-Oriented Method for Grapheme to Phoneme Conversion

A finite-state method, based on leftmost longest-match replacement, is presented for segmenting words into graphemes, and for converting graphemes into phonemes. A small set of hand-crafted conversion rules for Dutch achieves a phoneme accuracy of over 93%. The accuracy of the system is further improved by using transformation-based learning. The phoneme accuracy of the best system (using a large set of rule templates and a `lazy' variant of Brill's algoritm), trained on only 40K words, reaches 99% accuracy.Comment: 8 page

ICARUS: Intelligent coupon allocation for retailers using search

Many retailers run loyalty card schemes for their customers offering incentives in the form of money off coupons. The total value of the coupons depends on how much the customer has spent. This paper deals with the problem of finding the smallest set of coupons such that each possible total can be represented as the sum of a pre-defined number of coupons. A mathematical analysis of the problem leads to the development of a genetic algorithm solution. The algorithm is applied to real world data using several crossover operators and compared to well known straw-person methods. Results are promising showing that considerable time can be saved by using this method, reducing a few days worth of consultancy time to a few minutes of computation