An MILP-based heuristic for staff scheduling problems with acceptance levels

We present a real-world staff-assignment problem that was reported to us by a provider of an online workforce scheduling software. The problem consists of assigning employees to work shifts subject to a large variety of requirements related to work laws, work shift compatibility, workload balancing, and personal preferences of employees. A target value is given for each requirement, and all possible deviations from these values are associated with acceptance levels. The objective is to minimize the total number of deviations in ascending order of the acceptance levels. We present an exact lexicographic goal programming MILP formulation and an MILP-based heuristic. The heuristic consists of two phases: in the first phase a feasible schedule is built and in the second phase parts of the schedule are iteratively re-optimized by applying an exact MILP model. A major advantage of such MILP-based approaches is the flexibility to account for additional constraints or modified planning objectives, which is important as the requirements may vary depending on the company or planning period. The applicability of the heuristic is demonstrated for a test set derived from real-world data. Our computational results indicate that the heuristic is able to devise optimal solutions to non-trivial problem instances, and outperforms the exact lexicographic goal programming formulation on medium- and large-sized problem instances.

A note on the selection of priority rules in software packages for project management

Various software packages for project management include a procedure for resource-constrained scheduling. In several packages, the user can influence this procedure by selecting a priority rule. However, the resource-allocation methods that are implemented in the procedures are proprietary information; therefore, the question of how the priority-rule selection impacts the performance of the procedures arises. We experimentally evaluate the resource-allocation methods of eight recent software packages using the 600 instances of the PSPLIB J120 test set. The results of our analysis indicate that applying the default rule tends to outperform a randomly selected rule, whereas applying two randomly selected rules tends to outperform the default rule. Applying a small set of more than two rules further improves the project durations considerably. However, a large number of rules must be applied to obtain the best possible project durations.

Classification of cellular malignancy associated changes in cervical cancer

Cervical cancer is the leading cause of death and disease from malignant neoplasms among women in developing countries. Even though the Pap smear has significantly decreased the number of deaths from cervical cancer in the past years, it has its limitations. Researchers have developed an automated screening machine which can potentially detect abnormal cases that are overlooked by conventional screening. The goal of quantitative cytology is to classify the patient's tissue sample based on quantitative measurements of the individual cells. It is also much cheaper and potentially can take less time. One of the major challenges of collecting cells with a cytobrush is the possibility of not sampling any existing dysplastic cells on the cervix. Being able to correctly classify patients who have disease without the presence of dysplastic cells could improve the accuracy of quantitative cytology algorithms. Subtle morphologic changes in normal-appearing tissues adjacent to or distant from malignant tumors have been shown to exist, but a comparison of various statistical methods, including many recent advances in the statistical learning field, has not previously been done. The objective of this thesis is to use different classification methods applied to quantitative cytology data for the detection of malignancy associated changes (MACs). In this thesis, Elastic Net is the best algorithm. When we applied the Elastic Net algorithm to the test set, we combined the training set and validation set as "training" set and used 5-fold cross validation to choose the parameter for Elastic Net. It has a sensitivity of 47% at 80% specificity, an AUC 0.52, and a partial AUC 0.10 (95% CI 0.09-0.11).^

The impact of ocean acidification and warming on the skeletal mechanical properties of the sea urchin Paracentrotus lividus from laboratory and field observations

Increased atmospheric CO2 concentration is leading to changes in the carbonate chemistry and the temperature of the ocean. The impact of these processes on marine organisms will depend on their ability to cope with those changes, particularly the maintenance of calcium carbonate structures. Both a laboratory experiment (long-term exposure to decreased pH and increased temperature) and collections of individuals from natural environments characterized by low pH levels (individuals from intertidal pools and around a CO2 seep) were here coupled to comprehensively study the impact of near-future conditions of pH and temperature on the mechanical properties of the skeleton of the euechinoid sea urchin Paracentrotus lividus. To assess skeletal mechanical properties, we characterized the fracture force, Young's modulus, second moment of area, material nanohardness, and specific Young's modulus of sea urchin test plates. None of these parameters were significantly affected by low pH and/or increased temperature in the laboratory experiment and by low pH only in the individuals chronically exposed to lowered pH from the CO2 seeps. In tidal pools, the fracture force was higher and the Young's modulus lower in ambital plates of individuals from the rock pool characterized by the largest pH variations but also a dominance of calcifying algae, which might explain some of the variation. Thus, decreases of pH to levels expected for 2100 did not directly alter the mechanical properties of the test of P. lividus. Since the maintenance of test integrity is a question of survival for sea urchins and since weakened tests would increase the sea urchins' risk of predation, our findings indicate that the decreasing seawater pH and increasing seawater temperature expected for the end of the century should not represent an immediate threat to sea urchins vulnerability

Ocean acidification alters the material properties of Mytilus edulis shells

Ocean acidification (OA) and the resultant changing carbonate saturation states is threatening the formation of calcium carbonate shells and exoskeletons of marine organisms. The production of biominerals in such organisms relies on the availability of carbonate and the ability of the organism to biomineralize in changing environments. To understand how biomineralizers will respond to OA the common blue mussel, Mytilus edulis, was cultured at projected levels of pCO2 (380, 550, 750, 1000 µatm) and increased temperatures (ambient, ambient plus 2°C). Nanoindentation (a single mussel shell) and microhardness testing were used to assess the material properties of the shells. Young's modulus (E), hardness (H) and toughness (KIC) were measured in mussel shells grown in multiple stressor conditions. OA caused mussels to produce shell calcite that is stiffer (higher modulus of elasticity) and harder than shells grown in control conditions. The outer shell (calcite) is more brittle in OA conditions while the inner shell (aragonite) is softer and less stiff in shells grown under OA conditions. Combining increasing ocean pCO2 and temperatures as projected for future global ocean appears to reduce the impact of increasing pCO2 on the material properties of the mussel shell. OA may cause changes in shell material properties that could prove problematic under predation scenarios for the mussels; however, this may be partially mitigated by increasing temperature.

Qualitative Monitoring of Video Quality of Experience

Real-time monitoring of multimedia Quality of Experience is a critical task for the providers of multimedia delivery services: from television broadcasters to IP content delivery networks or IPTV. For such scenarios, meaningful metrics are required which can generate useful information to the service providers that overcome the limitations of pure Quality of Service monitoring probes. However, most of objective multimedia quality estimators, aimed at modeling the Mean Opinion Score, are difficult to apply to massive quality monitoring. Thus we propose a lightweight and scalable monitoring architecture called Qualitative Experience Monitoring (QuEM), based on detecting identifiable impairment events such as the ones reported by the customers of those services. We also carried out a subjective assessment test to validate the approach and calibrate the metrics. Preliminary results of this test set support our approach.

UPM system for the translation task

This paper describes the UPM system for translation task at the EMNLP 2011 workshop on statistical machine translation (http://www.statmt.org/wmt11/), and it has been used for both directions: Spanish-English and English-Spanish. This system is based on Moses with two new modules for pre and post processing the sentences. The main contribution is the method proposed (based on the similarity with the source language test set) for selecting the sentences for training the models and adjusting the weights. With system, we have obtained a 23.2 BLEU for Spanish-English and 21.7 BLEU for EnglishSpanish

Estudio de la fiabilidad software, según defectos, en controladores de velocidad para robots autónomos móviles

Tanto los robots autónomos móviles como los robots móviles remotamente operados se utilizan con éxito actualmente en un gran número de ámbitos, algunos de los cuales son tan dispares como la limpieza en el hogar, movimiento de productos en almacenes o la exploración espacial. Sin embargo, es difícil garantizar la ausencia de defectos en los programas que controlan dichos dispositivos, al igual que ocurre en otros sectores informáticos. Existen diferentes alternativas para medir la calidad de un sistema en el desempeño de las funciones para las que fue diseñado, siendo una de ellas la fiabilidad. En el caso de la mayoría de los sistemas físicos se detecta una degradación en la fiabilidad a medida que el sistema envejece. Esto es debido generalmente a efectos de desgaste. En el caso de los sistemas software esto no suele ocurrir, ya que los defectos que existen en ellos generalmente no han sido adquiridos con el paso del tiempo, sino que han sido insertados en el proceso de desarrollo de los mismos. Si dentro del proceso de generación de un sistema software se focaliza la atención en la etapa de codificación, podría plantearse un estudio que tratara de determinar la fiabilidad de distintos algoritmos, válidos para desempeñar el mismo cometido, según los posibles defectos que pudieran introducir los programadores. Este estudio básico podría tener diferentes aplicaciones, como por ejemplo elegir el algoritmo menos sensible a los defectos, para el desarrollo de un sistema crítico o establecer procedimientos de verificación y validación, más exigentes, si existe la necesidad de utilizar un algoritmo que tenga una alta sensibilidad a los defectos. En el presente trabajo de investigación se ha estudiado la influencia que tienen determinados tipos de defectos software en la fiabilidad de tres controladores de velocidad multivariable (PID, Fuzzy y LQR) al actuar en un robot móvil específico. La hipótesis planteada es que los controladores estudiados ofrecen distinta fiabilidad al verse afectados por similares patrones de defectos, lo cual ha sido confirmado por los resultados obtenidos. Desde el punto de vista de la planificación experimental, en primer lugar se realizaron los ensayos necesarios para determinar si los controladores de una misma familia (PID, Fuzzy o LQR) ofrecían una fiabilidad similar, bajo las mismas condiciones experimentales. Una vez confirmado este extremo, se eligió de forma aleatoria un representante de clase de cada familia de controladores, para efectuar una batería de pruebas más exhaustiva, con el objeto de obtener datos que permitieran comparar de una forma más completa la fiabilidad de los controladores bajo estudio. Ante la imposibilidad de realizar un elevado número de pruebas con un robot real, así como para evitar daños en un dispositivo que generalmente tiene un coste significativo, ha sido necesario construir un simulador multicomputador del robot. Dicho simulador ha sido utilizado tanto en las actividades de obtención de controladores bien ajustados, como en la realización de los diferentes ensayos necesarios para el experimento de fiabilidad. ABSTRACT Autonomous mobile robots and remotely operated robots are used successfully in very diverse scenarios, such as home cleaning, movement of goods in warehouses or space exploration. However, it is difficult to ensure the absence of defects in programs controlling these devices, as it happens in most computer sectors. There exist different quality measures of a system when performing the functions for which it was designed, among them, reliability. For most physical systems, a degradation occurs as the system ages. This is generally due to the wear effect. In software systems, this does not usually happen, and defects often come from system development and not from use. Let us assume that we focus on the coding stage in the software development pro¬cess. We could consider a study to find out the reliability of different and equally valid algorithms, taking into account any flaws that programmers may introduce. This basic study may have several applications, such as choosing the algorithm less sensitive to pro¬gramming defects for the development of a critical system. We could also establish more demanding procedures for verification and validation if we need an algorithm with high sensitivity to programming defects. In this thesis, we studied the influence of certain types of software defects in the reliability of three multivariable speed controllers (PID, Fuzzy and LQR) designed to work in a specific mobile robot. The hypothesis is that similar defect patterns affect differently the reliability of controllers, and it has been confirmed by the results. From the viewpoint of experimental planning, we followed these steps. First, we conducted the necessary test to determine if controllers of the same family (PID, Fuzzy or LQR) offered a similar reliability under the same experimental conditions. Then, a class representative was chosen at ramdom within each controller family to perform a more comprehensive test set, with the purpose of getting data to compare more extensively the reliability of the controllers under study. The impossibility of performing a large number of tests with a real robot and the need to prevent the damage of a device with a significant cost, lead us to construct a multicomputer robot simulator. This simulator has been used to obtain well adjusted controllers and to carry out the required reliability experiments.

UPM system for WMT 2012

This paper describes the UPM system for the Spanish-English translation task at the NAACL 2012 workshop on statistical machine translation. This system is based on Moses. We have used all available free corpora, cleaning and deleting some repetitions. In this paper, we also propose a technique for selecting the sentences for tuning the system. This technique is based on the similarity with the sentences to translate. With our approach, we improve the BLEU score from 28.37% to 28.57%. And as a result of the WMT12 challenge we have obtained a 31.80% BLEU with the 2012 test set. Finally, we explain different experiments that we have carried out after the competition.

Selection of TDOA Parameters for MDM Speaker Diarization

Several methods to improve multiple distant microphone (MDM) speaker diarization based on Time Delay of Arrival (TDOA) features are evaluated in this paper. All of them avoid the use of a single reference channel to calculate the TDOA values and, based on different criteria, select among all possible pairs of microphones a set of pairs that will be used to estimate the TDOA's. The evaluated methods have been named the "Dynamic Margin" (DM), the "Extreme Regions" (ER), the "Most Common" (MC), the "Cross Correlation" (XCorr) and the "Principle Component Analysis" (PCA). It is shown that all methods improve the baseline results for the development set and four of them improve also the results for the evaluation set. Improvements of 3.49% and 10.77% DER relative are obtained for DM and ER respectively for the test set. The XCorr and PCA methods achieve an improvement of 36.72% and 30.82% DER relative for the test set. Moreover, the computational cost for the XCorr method is 20% less than the baseline.

QSAR e dinâmica molecular no estudo de sistemas biomoleculares: predição da atividade biológica de antagonistas do receptor sigma-1 e simulações de bicamadas lipídicas

Diferentes abordagens teóricas têm sido utilizadas em estudos de sistemas biomoleculares com o objetivo de contribuir com o tratamento de diversas doenças. Para a dor neuropática, por exemplo, o estudo de compostos que interagem com o receptor sigma-1 (Sig-1R) pode elucidar os principais fatores associados à atividade biológica dos mesmos. Nesse propósito, estudos de Relações Quantitativas Estrutura-Atividade (QSAR) utilizando os métodos de regressão por Mínimos Quadrados Parciais (PLS) e Rede Neural Artificial (ANN) foram aplicados a 64 antagonistas do Sig-1R pertencentes à classe de 1-arilpirazóis. Modelos PLS e ANN foram utilizados com o objetivo de descrever comportamentos lineares e não lineares, respectivamente, entre um conjunto de descritores e a atividade biológica dos compostos selecionados. O modelo PLS foi obtido com 51 compostos no conjunto treinamento e 13 compostos no conjunto teste (r² = 0,768, q² = 0,684 e r²teste = 0,785). Testes de leave-N-out, randomização da atividade biológica e detecção de outliers confirmaram a robustez e estabilidade dos modelos e mostraram que os mesmos não foram obtidos por correlações ao acaso. Modelos também foram gerados a partir da Rede Neural Artificial Perceptron de Multicamadas (MLP-ANN), sendo que a arquitetura 6-12-1, treinada com as funções de transferência tansig-tansig, apresentou a melhor resposta para a predição da atividade biológica dos compostos (r²treinamento = 0,891, r²validação = 0,852 e r²teste = 0,793). Outra abordagem foi utilizada para simular o ambiente de membranas sinápticas utilizando bicamadas lipídicas compostas por POPC, DOPE, POPS e colesterol. Os estudos de dinâmica molecular desenvolvidos mostraram que altas concentrações de colesterol induzem redução da área por lipídeo e difusão lateral e aumento na espessura da membrana e nos valores de parâmetro de ordem causados pelo ordenamento das cadeias acil dos fosfolipídeos. As bicamadas lipídicas obtidas podem ser usadas para simular interações entre lipídeos e pequenas moléculas ou proteínas contribuindo para as pesquisas associadas a doenças como Alzheimer e Parkinson. As abordagens usadas nessa tese são essenciais para o desenvolvimento de novas pesquisas em Química Medicinal Computacional.

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Includes index.

Classification of oximetry signals using Bayesian neural networks to assist in the detection of obstructive sleep apnoea syndrome

In the present study, multilayer perceptron (MLP) neural networks were applied to help in the diagnosis of obstructive sleep apnoea syndrome (OSAS). Oxygen saturation (SaO2) recordings from nocturnal pulse oximetry were used for this purpose. We performed time and spectral analysis of these signals to extract 14 features related to OSAS. The performance of two different MLP classifiers was compared: maximum likelihood (ML) and Bayesian (BY) MLP networks. A total of 187 subjects suspected of suffering from OSAS took part in the study. Their SaO2 signals were divided into a training set with 74 recordings and a test set with 113 recordings. BY-MLP networks achieved the best performance on the test set with 85.58% accuracy (87.76% sensitivity and 82.39% specificity). These results were substantially better than those provided by ML-MLP networks, which were affected by overfitting and achieved an accuracy of 76.81% (86.42% sensitivity and 62.83% specificity). Our results suggest that the Bayesian framework is preferred to implement our MLP classifiers. The proposed BY-MLP networks could be used for early OSAS detection. They could contribute to overcome the difficulties of nocturnal polysomnography (PSG) and thus reduce the demand for these studies.

Urinary proteomic biomarkers in coronary artery disease

Urinary proteomics is emerging as a powerful non-invasive tool for diagnosis and monitoring of variety of human diseases. We tested whether signatures of urinary polypeptides can contribute to the existing biomarkers for coronary artery disease (CAD). We examined a total of 359 urine samples from 88 patients with severe CAD and 282 controls. Spot urine was analyzed using capillary electrophoresis on-line coupled to ESI-TOF-MS enabling characterization of more than 1000 polypeptides per sample. In a first step a "training set" for biomarker definition was created. Multiple biomarker patterns clearly distinguished healthy controls from CAD patients, and we extracted 15 peptides that define a characteristic CAD signature panel. In a second step, the ability of the CAD-specific panel to predict the presence of CAD was evaluated in a blinded study using a "test set." The signature panel showed sensitivity of 98% (95% confidence interval, 88.7-99.6) and 83% specificity (95% confidence interval, 51.6-97.4). Furthermore the peptide pattern significantly changed toward the healthy signature correlating with the level of physical activity after therapeutic intervention. Our results show that urinary proteomics can identify CAD patients with high confidence and might also play a role in monitoring the effects of therapeutic interventions. The workflow is amenable to clinical routine testing suggesting that non-invasive proteomics analysis can become a valuable addition to other biomarkers used in cardiovascular risk assessment.

HLA-DP2 binding prediction by molecular dynamics simulations

Major histocompatibility complex (MHC) II proteins bind peptide fragments derived from pathogen antigens and present them at the cell surface for recognition by T cells. MHC proteins are divided into Class I and Class II. Human MHC Class II alleles are grouped into three loci: HLA-DP, HLA-DQ, and HLA-DR. They are involved in many autoimmune diseases. In contrast to HLA-DR and HLA-DQ proteins, the X-ray structure of the HLA-DP2 protein has been solved quite recently. In this study, we have used structure-based molecular dynamics simulation to derive a tool for rapid and accurate virtual screening for the prediction of HLA-DP2-peptide binding. A combinatorial library of 247 peptides was built using the "single amino acid substitution" approach and docked into the HLA-DP2 binding site. The complexes were simulated for 1 ns and the short range interaction energies (Lennard-Jones and Coulumb) were used as binding scores after normalization. The normalized values were collected into quantitative matrices (QMs) and their predictive abilities were validated on a large external test set. The validation shows that the best performing QM consisted of Lennard-Jones energies normalized over all positions for anchor residues only plus cross terms between anchor-residues.