Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento

A large number of clustering approaches have been proposed for the analysis of gene expression data obtained from microarray experiments. However, the results from the application of standard clustering methods to genes are limited. This limitation is imposed by the existence of a number of experimental conditions where the activity of genes is uncorrelated. A similar limitation exists when clustering of conditions is performed. For this reason, a number of algorithms that perform simultaneous clustering on the row and column dimensions of the data matrix has been proposed. The goal is to find submatrices, that is, subgroups of genes and subgroups of conditions, where the genes exhibit highly correlated activities for every condition. In this paper, we refer to this class of algorithms as biclustering. Biclustering is also referred in the literature as coclustering and direct clustering, among others names, and has also been used in fields such as information retrieval and data mining. In this comprehensive survey, we analyze a large number of existing approaches to biclustering, and classify them in accordance with the type of biclusters they can find, the patterns of biclusters that are discovered, the methods used to perform the search, the approaches used to evaluate the solution, and the target applications.

The functional Fourier transform (FRFT), which is a generalization of the classical Fourier transform, was introduced a number of years ago in the mathematics literature but appears to have remained largely unknown to the signal processing community, to which it may, however, be potentially useful. The FRFT depends on a parameter /spl alpha/ and can be interpreted as a rotation by an angle /spl alpha/ in the time-frequency plane. An FRFT with /spl alpha/=/spl pi//2 corresponds to the classical Fourier transform, and an FRFT with /spl alpha/=0 corresponds to the identity operator. On the other hand, the angles of successively performed FRFTs simply add up, as do the angles of successive rotations. The FRFT of a signal can also be interpreted as a decomposition of the signal in terms of chirps. The authors briefly introduce the FRFT and a number of its properties and then present some new results: the interpretation as a rotation in the time-frequency plane, and the FRFT's relationships with time-frequency representations such as the Wigner distribution, the ambiguity function, the short-time Fourier transform and the spectrogram. These relationships have a very simple and natural form and support the FRFT's interpretation as a rotation operator. Examples of FRFTs of some simple signals are given. An example of the application of the FRFT is also given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

This paper introduces GRASP (Generic seaRch Algorithm for the Satisfiability Problem), a new search algorithm for Propositional Satisfiability (SAT). GRASP incorporates several search-pruning techniques that proved to be quite powerful on a wide variety of SAT problems. Some of these techniques are specific to SAT, whereas others are similar in spirit to approaches in other fields of Artificial Intelligence. GRASP is premised on the inevitability of conflicts during the search and its most distinguishing feature is the augmentation of basic backtracking search with a powerful conflict analysis procedure. Analyzing conflicts to determine their causes enables GRASP to backtrack nonchronologically to earlier levels in the search tree, potentially pruning large portions of the search space. In addition, by "recording" the causes of conflicts, GRASP can recognize and preempt the occurrence of similar conflicts later on in the search. Finally, straightforward bookkeeping of the causality chains leading up to conflicts allows GRASP to identify assignments that are necessary for a solution to be found. Experimental results obtained from a large number of benchmarks indicate that application of the proposed conflict analysis techniques to SAT algorithms can be extremely effective for a large number of representative classes of SAT instances.

The latest generation of smartphones are increasingly viewed as handheld computers rather than as phones, due to their powerful on-board computing capability, capacious memories, large screens and open operating systems that encourage application development. This paper provides a brief state-of-the-art overview of health and healthcare smartphone apps (applications) on the market today, including emerging trends and market uptake. Platforms available today include Android, Apple iOS, RIM BlackBerry, Symbian, and Windows (Windows Mobile 6.x and the emerging Windows Phone 7 platform). The paper covers apps targeting both laypersons/patients and healthcare professionals in various scenarios, e.g., health, fitness and lifestyle education and management apps; ambient assisted living apps; continuing professional education tools; and apps for public health surveillance. Among the surveyed apps are those assisting in chronic disease management, whether as standalone apps or part of a BAN (Body Area Network) and remote server configuration. We describe in detail the development of a smartphone app within eCAALYX (Enhanced Complete Ambient Assisted Living Experiment, 2009-2012), an EU-funded project for older people with multiple chronic conditions. The eCAALYX Android smartphone app receives input from a BAN (a patient-wearable smart garment with wireless health sensors) and the GPS (Global Positioning System) location sensor in the smartphone, and communicates over the Internet with a remote server accessible by healthcare professionals who are in charge of the remote monitoring and management of the older patient with multiple chronic conditions. Finally, we briefly discuss barriers to adoption of health and healthcare smartphone apps (e.g., cost, network bandwidth and battery power efficiency, usability, privacy issues, etc.), as well as some workarounds to mitigate those barriers.

Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.

&lt;p&gt;Ammonia, a molecule that is gaining more interest as a fueling vector, has been considered as a candidate to power transport, produce energy, and support heating applications for decades. However, the particular characteristics of the molecule always made it a chemical with low, if any, benefit once compared to conventional fossil fuels. Still, the current need to decarbonize our economy makes the search of new methods crucial to use chemicals, such as ammonia, that can be produced and employed without incurring in the emission of carbon oxides. Therefore, current efforts in this field are leading scientists, industries, and governments to seriously invest efforts in the development of holistic solutions capable of making ammonia a viable fuel for the transition toward a clean future. On that basis, this review has approached the subject gathering inputs from scientists actively working on the topic. The review starts from the importance of ammonia as an energy vector, moving through all of the steps in the production, distribution, utilization, safety, legal considerations, and economic aspects of the use of such a molecule to support the future energy mix. Fundamentals of combustion and practical cases for the recovery of energy of ammonia are also addressed, thus providing a complete view of what potentially could become a vector of crucial importance to the mitigation of carbon emissions. Different from other works, this review seeks to provide a holistic perspective of ammonia as a chemical that presents benefits and constraints for storing energy from sustainable sources. State-of-the-art knowledge provided by academics actively engaged with the topic at various fronts also enables a clear vision of the progress in each of the branches of ammonia as an energy carrier. Further, the fundamental boundaries of the use of the molecule are expanded to real technical issues for all potential technologies capable of using it for energy purposes, legal barriers that will be faced to achieve its deployment, safety and environmental considerations that impose a critical aspect for acceptance and wellbeing, and economic implications for the use of ammonia across all aspects approached for the production and implementation of this chemical as a fueling source. Herein, this work sets the principles, research, practicalities, and future views of a transition toward a future where ammonia will be a major energy player. &lt;/p&gt;

Accurate text classification and placement remain challenges in U.S. higher education, with traditional automated systems like Accuplacer functioning as "black-box" models with limited assessment transparency. This study evaluates Large Language Models (LLMs) as complementary placement tools by comparing their classification performance against a human-rated gold standard and Accuplacer. A 450-essay corpus was classified using Claude, Gemini, GPT-3.5-turbo, and GPT-4o across four prompting strategies: Zero-shot, Few-shot, Enhanced, and Enhanced+ (definitions with examples). Two classification approaches were tested: (i) a 1-step, 3 class classification task, distinguishing DevEd Level 1, DevEd Level 2, and College-level texts in one single run; and (ii) a 2-step classification task, first separating College vs. Non-College texts before further classifying Non-College texts into DevEd sublevels. The results show that structured prompt refinement improves the precision of LLMs' classification, with Claude Enhanced + achieving 62.22% precision (1 step) and Gemini Enhanced + reaching 69.33% (2 step), both surpassing Accuplacer (58.22%). Gemini and Claude also demonstrated strong correlation with human ratings, with Claude achieving the highest Pearson scores (ρ = 0.75; 1-step, ρ = 0.73; 2-step) vs. Accuplacer (ρ = 0.67). While LLMs show promise for DevEd placement, their precision remains a work in progress, highlighting the need for further refinement and safeguards to ensure ethical and equitable placement.

BACKGROUND: Multilocus Sequence Typing (MLST) is a frequently used typing method for the analysis of the clonal relationships among strains of several clinically relevant microbial species. MLST is based on the sequence of housekeeping genes that result in each strain having a distinct numerical allelic profile, which is abbreviated to a unique identifier: the sequence type (ST). The relatedness between two strains can then be inferred by the differences between allelic profiles. For a more comprehensive analysis of the possible patterns of evolutionary descent, a set of rules were proposed and implemented in the eBURST algorithm. These rules allow the division of a data set into several clusters of related strains, dubbed clonal complexes, by implementing a simple model of clonal expansion and diversification. Within each clonal complex, the rules identify which links between STs correspond to the most probable pattern of descent. However, the eBURST algorithm is not globally optimized, which can result in links, within the clonal complexes, that violate the rules proposed. RESULTS: Here, we present a globally optimized implementation of the eBURST algorithm - goeBURST. The search for a global optimal solution led to the formalization of the problem as a graphic matroid, for which greedy algorithms that provide an optimal solution exist. Several public data sets of MLST data were tested and differences between the two implementations were found and are discussed for five bacterial species: Enterococcus faecium, Streptococcus pneumoniae, Burkholderia pseudomallei, Campylobacter jejuni and Neisseria spp.. A novel feature implemented in goeBURST is the representation of the level of tiebreak rule reached before deciding if a link should be drawn, which can used to visually evaluate the reliability of the represented hypothetical pattern of descent. CONCLUSION: goeBURST is a globally optimized implementation of the eBURST algorithm, that identifies alternative patterns of descent for several bacterial species. Furthermore, the algorithm can be applied to any multilocus typing data based on the number of differences between numeric profiles. A software implementation is available at http://goeBURST.phyloviz.net.

BACKGROUND: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. RESULTS: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. CONCLUSIONS: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research. We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.

With the expansion of smart meters, like the Advanced Metering Infrastructure (AMI), and the Internet of Things (IoT), each smart city is equipped with various kinds of electronic devices. Therefore, equipment and technologies enable us to be smarter and make various aspects of smart cities more accessible and applicable. The goal of the current paper is to provide an inclusive review on the concept of the smart city besides their different applications, benefits, and advantages. In addition, most of the possible IoT technologies are introduced, and their capabilities to merge into and apply to the different parts of smart cities are discussed. The potential application of smart cities with respect to technology development in the future provides another valuable discussion in this paper. Meanwhile, some practical experiences all across the world and the key barriers to its implementation are thoroughly expressed.

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> This paper proposes a control scheme that allows doubly fed induction wind generators (DFIWG) to participate effectively in system frequency regulation. In this control approach, wind generators operate according to a deloaded optimum power extraction curve such that the active power provided by each wind turbine increases or decreases during system frequency changes. The control strategy defined at the wind generator to supply primary frequency regulation capability exploits a combination of control of the static converters and pitch control, adjusting the rotor speed and the active power according to the deloaded optimum power extraction curve. Results obtained in a small isolated system are presented to demonstrate the effectiveness of the approach. </para>

Wang Ling, Chris Dyer, Alan W Black, Isabel Trancoso, Ramón Fermandez, Silvio Amir, Luís Marujo, Tiago Luís. Proceedings of the 2015 Conference on Empirical Methods in Natural Language Processing. 2015.

International audience

Abstract The 2022 Roadmap is the next update in the series of Plasma Roadmaps published by Journal of Physics D with the intent to identify important outstanding challenges in the field of low-temperature plasma (LTP) physics and technology. The format of the Roadmap is the same as the previous Roadmaps representing the visions of 41 leading experts representing 21 countries and five continents in the various sub-fields of LTP science and technology. In recognition of the evolution in the field, several new topics have been introduced or given more prominence. These new topics and emphasis highlight increased interests in plasma-enabled additive manufacturing, soft materials, electrification of chemical conversions, plasma propulsion, extreme plasma regimes, plasmas in hypersonics, data-driven plasma science and technology and the contribution of LTP to combat COVID-19. In the last few decades, LTP science and technology has made a tremendously positive impact on our society. It is our hope that this roadmap will help continue this excellent track record over the next 5–10 years.

As the smart grid solutions enable active consumer participation, demand response (DR) strategies have drawn much interest in the literature recently, especially for residential areas. As a new type of consumer load in the electric power system, electric vehicles (EVs) also provide different opportunities, including the capability of utilizing EVs as a storage unit via vehicle-to-home (V2H) and vehicle-to-grid (V2G) options instead of peak power procurement from the grid. In this paper, as the main contribution to the literature, a collaborative evaluation of dynamic-pricing and peak power limiting-based DR strategies with a bi-directional utilization possibility for EV and energy storage system (ESS) is realized. A mixed-integer linear programming (MILP) framework-based modeling of a home energy management (HEM) structure is provided for this purpose. A distributed small-scale renewable energy generation system, the V2H and V2G capabilities of an EV together with two-way energy trading of ESS, and different DR strategies are all combined in a single HEM system for the first time in the literature. The impacts of different EV owner consumer preferences together with the availability of ESS and two-way energy trading capabilities on the reduction of total electricity prices are examined with case studies.

We present Posterior Regularization, a probabilistic framework for structured, weakly supervised learning. Our framework efficiently incorporates indirect supervision via constraints on posterior distributions of probabilistic models with latent variables. Posterior Regularization separates model complexity from the complexity of structural constraints it is desired to satisfy. By directly imposing decomposable regularization on the posterior moments of latent variables during learning, we retain the computational efficiency of the unconstrained model while ensuring desired constraints hold in expectation. We present an efficient algorithm for learning with posterior regularization and illustrate its versatility on a diverse set of structural constraints such as bijectivity, symmetry and group sparsity in several large scale experiments, including multi-view learning, cross-lingual dependency grammar induction, unsupervised part-of-speech induction, and bitext word alignment. 1 1.

The world is undergoing an unprecedented technological transformation, evolving into a state where ubiquitous Internet-enabled “things” will be able to generate and share large amounts of security- and privacy-sensitive data. To cope with the security threats that are thus foreseeable, system designers can find in Arm TrustZone hardware technology a most valuable resource. TrustZone is a System-on-Chip and CPU system-wide security solution, available on today’s Arm application processors and present in the new generation Arm microcontrollers, which are expected to dominate the market of smart “things.” Although this technology has remained relatively underground since its inception in 2004, over the past years, numerous initiatives have significantly advanced the state of the art involving Arm TrustZone. Motivated by this revival of interest, this paper presents an in-depth study of TrustZone technology. We provide a comprehensive survey of relevant work from academia and industry, presenting existing systems into two main areas, namely, Trusted Execution Environments and hardware-assisted virtualization. Furthermore, we analyze the most relevant weaknesses of existing systems and propose new research directions within the realm of tiniest devices and the Internet of Things, which we believe to have potential to yield high-impact contributions in the future.

High Throughput Sequencing provides a cost effective means of generating high resolution data for hundreds or even thousands of strains, and is rapidly superseding methodologies based on a few genomic loci. The wealth of genomic data deposited on public databases such as Sequence Read Archive/European Nucleotide Archive provides a powerful resource for evolutionary analysis and epidemiological surveillance. However, many of the analysis tools currently available do not scale well to these large datasets, nor provide the means to fully integrate ancillary data. Here we present PHYLOViZ 2.0, an extension of PHYLOViZ tool, a platform independent Java tool that allows phylogenetic inference and data visualization for large datasets of sequence based typing methods, including Single Nucleotide Polymorphism (SNP) and whole genome/core genome Multilocus Sequence Typing (wg/cgMLST) analysis. PHYLOViZ 2.0 incorporates new data analysis algorithms and new visualization modules, as well as the capability of saving projects for subsequent work or for dissemination of results. AVAILABILITY AND IMPLEMENTATION: http://www.phyloviz.net/ (licensed under GPLv3). CONTACT: cvaz@inesc-id.ptSupplementary information: Supplementary data are available at Bioinformatics online.

In this paper, a detailed home energy management system structure is developed to determine the optimal day-ahead appliance scheduling of a smart household under hourly pricing and peak power-limiting (hard and soft power limitation)-based demand response strategies. All types of controllable assets have been explicitly modeled, including thermostatically controllable (air conditioners and water heaters) and nonthermostatically controllable (washing machines and dishwashers) appliances, together with electric vehicles (EVs). Furthermore, an energy storage system (ESS) and distributed generation at the end-user premises are taken into account. Bidirectional energy flow is also considered through advanced options for EV and ESS operation. Finally, a realistic test-case is presented with a sufficiently reduced time granularity being thoroughly discussed to investigate the effectiveness of the model. Stringent simulation results are provided using data gathered from real appliances and real measurements.