An Ontology-Based Recommender System with an Application to the Star Trek Television Franchise

Collaborative filtering based recommender systems have proven to be extremely successful in settings where user preference data on items is abundant. However, collaborative filtering algorithms are hindered by their weakness against the item cold-start problem and general lack of interpretability. Ontology-based recommender systems exploit hierarchical organizations of users and items to enhance browsing, recommendation, and profile construction. While ontology-based approaches address the shortcomings of their collaborative filtering counterparts, ontological organizations of items can be difficult to obtain for items that mostly belong to the same category (e.g., television series episodes). In this paper, we present an ontology-based recommender system that integrates the knowledge represented in a large ontology of literary themes to produce fiction content recommendations. The main novelty of this work is an ontology-based method for computing similarities between items and its integration with the classical Item-KNN (K-nearest neighbors) algorithm. As a study case, we evaluated the proposed method against other approaches by performing the classical rating prediction task on a collection of Star Trek television series episodes in an item cold-start scenario. This transverse evaluation provides insights into the utility of different information resources and methods for the initial stages of recommender system development. We found our proposed method to be a convenient alternative to collaborative filtering approaches for collections of mostly similar items, particularly when other content-based approaches are not applicable or otherwise unavailable. Aside from the new methods, this paper contributes a testbed for future research and an online framework to collaboratively extend the ontology of literary themes to cover other narrative content.Comment: 25 pages, 6 figures, 5 tables, minor revision

Investigating the Relationships Between Disorder, Structure, and Dynamics in Amorphous Systems

In this thesis, we investigate the relationships between the disorder, structure, and deformation in amorphous materials. First, to understand the surprising low-frequency vibrational modes in structural glasses, and how it arises from the microscopic disorder in the system, we study the spectra of a large ensemble of sparse random matrices where disorder is controlled by the distribution of bond weights and network coordination. When there is a finite probability density of infinitesimal bond weights, we find a region in the vibrational density of states that is consistent with the low-frequency behavior in structural glasses. Next, in order to investigate structural properties of active systems, we develop a novel method to generate static, finite packings in an artificial potential that reproduce the packing structures observed in a class of point-of-interest active self-propelled particle simulations. This allows us to compute structural measures, such as the vibrational modes, in an unstable active system. Finally, we evaluate the evolution of structure during strain-induced avalanches in athermal, amorphous systems using numerical simulation of soft spheres. We find that these avalanches can be decomposed into a series of bursts of localized deformations, and we develop an extension of persistent homology to isolate these bursts of localized deformations. Further, we extend existing tools for the structural evaluation of mechanically stable systems to generically unstable systems to identify how soft regions evolve and change throughout an avalanche

Discovery of potent, novel, non-toxic anti-malarial compounds via quantum modelling, virtual screening and in vitro experimental validation

<p>Abstract</p> <p>Background</p> <p>Developing resistance towards existing anti-malarial therapies emphasize the urgent need for new therapeutic options. Additionally, many malaria drugs in use today have high toxicity and low therapeutic indices. Gradient Biomodeling, LLC has developed a quantum-model search technology that uses quantum similarity and does not depend explicitly on chemical structure, as molecules are rigorously described in fundamental quantum attributes related to individual pharmacological properties. Therapeutic activity, as well as toxicity and other essential properties can be analysed and optimized simultaneously, independently of one another. Such methodology is suitable for a search of novel, non-toxic, active anti-malarial compounds.</p> <p>Methods</p> <p>A set of innovative algorithms is used for the fast calculation and interpretation of electron-density attributes of molecular structures at the quantum level for rapid discovery of prospective pharmaceuticals. Potency and efficacy, as well as additional physicochemical, metabolic, pharmacokinetic, safety, permeability and other properties were characterized by the procedure. Once quantum models are developed and experimentally validated, the methodology provides a straightforward implementation for lead discovery, compound optimizzation and <it>de novo </it>molecular design.</p> <p>Results</p> <p>Starting with a diverse training set of 26 well-known anti-malarial agents combined with 1730 moderately active and inactive molecules, novel compounds that have strong anti-malarial activity, low cytotoxicity and structural dissimilarity from the training set were discovered and experimentally validated. Twelve compounds were identified <it>in silico </it>and tested <it>in vitro</it>; eight of them showed anti-malarial activity (IC50 ≤ 10 μM), with six being very effective (IC50 ≤ 1 μM), and four exhibiting low nanomolar potency. The most active compounds were also tested for mammalian cytotoxicity and found to be non-toxic, with a therapeutic index of more than 6,900 for the most active compound.</p> <p>Conclusions</p> <p>Gradient's metric modelling approach and electron-density molecular representations can be powerful tools in the discovery and design of novel anti-malarial compounds. Since the quantum models are agnostic of the particular biological target, the technology can account for different mechanisms of action and be used for <it>de novo </it>design of small molecules with activity against not only the asexual phase of the malaria parasite, but also against the liver stage of the parasite development, which may lead to true causal prophylaxis.</p

One-Class Classification: Taxonomy of Study and Review of Techniques

One-class classification (OCC) algorithms aim to build classification models when the negative class is either absent, poorly sampled or not well defined. This unique situation constrains the learning of efficient classifiers by defining class boundary just with the knowledge of positive class. The OCC problem has been considered and applied under many research themes, such as outlier/novelty detection and concept learning. In this paper we present a unified view of the general problem of OCC by presenting a taxonomy of study for OCC problems, which is based on the availability of training data, algorithms used and the application domains applied. We further delve into each of the categories of the proposed taxonomy and present a comprehensive literature review of the OCC algorithms, techniques and methodologies with a focus on their significance, limitations and applications. We conclude our paper by discussing some open research problems in the field of OCC and present our vision for future research.Comment: 24 pages + 11 pages of references, 8 figure

Gender and innovation processes in rice-based systems

This GRiSP report is based on the perspectives of women and men from three rice-growing villages in the Nueva Ecija province of the Philippines

Harnessing the Power of Collective Intelligence: the Case Study of Voxel-based Soft Robots

The field of Evolutionary Robotics (ER) is concerned with the evolution of artificial agents---robots. Albeit groundbreaking, progress in the field has recently stagnated. In the research community, there is a strong feeling that a paradigm change has become necessary to disentangle ER. In particular, a solution has emerged from ideas from Collective Intelligence (CI). In CI---which has many relevant examples in nature---behavior emerges from the interaction between several components. In the absence of central intelligence, collective systems are usually more adaptable. In this thesis, we set out to harness the power of CI, focusing on the case study of simulated Voxel-based Soft Robots (VSRs): they are aggregations of homogeneous and soft cubic blocks that actuate by altering their volume. We investigate two axes. First, the morphologies of VSRs are intrinsically modular and an ideal substrate for CI; nevertheless, controllers employed until now do not take advantage of such modularity. Our results prove that VSRs can truly be controlled by the CI of their modules. Second, we investigate the spatial and time scales of CI. In particular, we evolve a robot to detect its global body properties given only local information processing, and, in a different study, generalize better to unseen environmental conditions through Hebbian learning. We also consider how evolution and learning interact in VSRs. Looking beyond VSRs, we propose a novel soft robot formalism that more closely resembles natural tissues and blends local with global actuation.The field of Evolutionary Robotics (ER) is concerned with the evolution of artificial agents---robots. Albeit groundbreaking, progress in the field has recently stagnated. In the research community, there is a strong feeling that a paradigm change has become necessary to disentangle ER. In particular, a solution has emerged from ideas from Collective Intelligence (CI). In CI---which has many relevant examples in nature---behavior emerges from the interaction between several components. In the absence of central intelligence, collective systems are usually more adaptable. In this thesis, we set out to harness the power of CI, focusing on the case study of simulated Voxel-based Soft Robots (VSRs): they are aggregations of homogeneous and soft cubic blocks that actuate by altering their volume. We investigate two axes. First, the morphologies of VSRs are intrinsically modular and an ideal substrate for CI; nevertheless, controllers employed until now do not take advantage of such modularity. Our results prove that VSRs can truly be controlled by the CI of their modules. Second, we investigate the spatial and time scales of CI. In particular, we evolve a robot to detect its global body properties given only local information processing, and, in a different study, generalize better to unseen environmental conditions through Hebbian learning. We also consider how evolution and learning interact in VSRs. Looking beyond VSRs, we propose a novel soft robot formalism that more closely resembles natural tissues and blends local with global actuation

Variety demand within the framework of an agricultural household model with attributes: the case of bananas in Uganda

Ugandan smallholder farmers produce the nation's major food crop using numerous banana varieties with distinctive attributes, while coping with important biotic constraints and imperfect markets. This empirical context motivates a trait-based model of the agricultural household that establishes the economic association between household preferences for specific variety attributes (yield, disease and pest resistance, and taste), among other exogenous factors, and variety demand, or the extent of cultivation. Six variety demands are estimated in reduced form, each in terms of both plant counts (“absolute” or levels demand) and plant shares (“relative” demand). Two salient findings emerge from the analysis: 1) the determinants of both absolute and relative demands are variety-specific and cannot be generalized across groups of cultivars; and 2) the determinants of absolute and relative demand are not the same in sign or significance. These findings raise questions about commonly used econometric specifications in the adoption literature. Grouping varieties together masks individual differences, and differences may be important for predicting the adoption of new technologies such as genetically transformed, endemic or local varieties. The development of methods to estimate a complete variety demand system might permit resolution of cross-variety relationships. The purpose of this research is to contribute information of use in identifying suitable local host varieties for the insertion of resistance traits through genetic transformation, and the factors affecting their potential adoption.Households Models, Variety demand, Variety attributes,