Genomic data sampling and its effect on classification performance assessment

BACKGROUND: Supervised classification is fundamental in bioinformatics. Machine learning models, such as neural networks, have been applied to discover genes and expression patterns. This process is achieved by implementing training and test phases. In the training phase, a set of cases and their respective labels are used to build a classifier. During testing, the classifier is used to predict new cases. One approach to assessing its predictive quality is to estimate its accuracy during the test phase. Key limitations appear when dealing with small-data samples. This paper investigates the effect of data sampling techniques on the assessment of neural network classifiers. RESULTS: Three data sampling techniques were studied: Cross-validation, leave-one-out, and bootstrap. These methods are designed to reduce the bias and variance of small-sample estimations. Two prediction problems based on small-sample sets were considered: Classification of microarray data originating from a leukemia study and from small, round blue-cell tumours. A third problem, the prediction of splice-junctions, was analysed to perform comparisons. Different accuracy estimations were produced for each problem. The variations are accentuated in the small-data samples. The quality of the estimates depends on the number of train-test experiments and the amount of data used for training the networks. CONCLUSION: The predictive quality assessment of biomolecular data classifiers depends on the data size, sampling techniques and the number of train-test experiments. Conservative and optimistic accuracy estimations can be obtained by applying different methods. Guidelines are suggested to select a sampling technique according to the complexity of the prediction problem under consideration

Lie integrability for time-independent and time-dependent Hamiltonian systems

In this paper we present the theorem on Lie integrability by quadratures for time-independent Hamiltonian systems on symplectic and contact manifolds, and for time-dependent Hamiltonian systems on cosymplectic and cocontact manifolds. We show that having a solvable Lie algebra of constants of motion for a Hamiltonian system is equivalent to having a solvable Lie algebra of symmetries of the vector field defining the dynamics of the system, which allows us to find the solutions of the equations of motion by quadratures.Comment: Comments are welcome. arXiv admin note: text overlap with arXiv:2211.0297

Análisis clínico-radiológico de los pacientes coinfectados con tuberculosis y el virus de la inmunodeficiencia humana (VIH) Hospital General Universitari Vall d'Hebron, 1986-2000

Consultable des del TDXTítol obtingut de la portada digitalitzadaLa tuberculosis (TB) es una enfermedad conocida en Europa desde épocas remotas. En España, la tuberculosis no es un problema nuevo; ocupa el segundo lugar en incidencia notificada entre los países de la Unión Europea, sólo superado por Portugal. En Cataluña constituye un problema de salud pública de primer orden, con una incidencia global más elevada que la declarada por otros países del mismo entorno social y económico. La ciudad de Barcelona presenta uno de los mejores registros de notificación, con datos totalmente fiables. Posiblemente por esta razón, las cifras sean tan elevadas en Cataluña. La aparición de la infección por el virus de la inmunodeficiencia humana (VIH) y su expansión a nivel epidémico por el mundo, añadió un factor coadyuvante en el resurgimiento de la TB en los países desarrollados. En España, al igual que en otros países, la población joven es la más afectada. En el inicio de la epidemia, el SIDA fue la causa principal del aumento de la mortalidad en este grupo de población. La introducción de la terapia antirretroviral (1996), altamente efectiva, ha incrementado la supervivencia de los pacientes infectados por el VIH. Esto explica en gran parte el descenso que han experimentado las tasas de mortalidad y de casos nuevos. Este trabajo da a conocer los patrones epidemiológicos, clínicos, radiológicos, de farmacorresistencia y los efectos adversos del tratamiento antituberculoso, así como los parámetros analíticos, inmunológicos y virológicos, a través de un estudio descriptivo, evaluativo y retrospectivo de casos consecutivos en pacientes coinfectados con TB/VIH entre 1986 y 2000 en el Hospital General Universitario de Vall d'Hebron. A lo largo del período estudiado se observó en este grupo de pacientes un progresivo descenso en la incidencia de la coinfección entre TB y VIH. El grupo de edad más afectado fue el comprendido entre 25 y 40 años, en su mayoría hombres. El factor de riesgo más importante para la infección por el VIH fue la adicción a drogas de uso parenteral. La principal forma de presentación clínica fue la tuberculosis pulmonar, seguida por la diseminada y finalmente por la extrapulmonar. El PPD fue anérgico en la mitad de los casos. Dos tercios de los pacientes presentaron un patrón radiológico post-primario. Por otro lado, un 10,35% de los pacientes con afectación pulmonar tenían un patrón radiológico normal. El patrón primario estuvo asociado a una cifra de CD4+ inferior a 200 cel/ml. La mayoría de los pacientes presentaron un estado avanzado de inmunodepresión. El diagnóstico se realizó a través de la tinción de Z-N y cultivo de muestras respiratorias o bien por medio de punción-aspiración con aguja fina y biopsia en los casos con compromiso extrapulmonar. La resistencia total a los antituberculosos estuvo presente en el 9,30%, mientras que la multirresistencia en el 1,60% de los casos. El análisis de los anteriores datos viene a corroborar la importancia epidemiológica y clínica de la coinfección entre la tuberculosis y el VIH.Tuberculosis (TB) as a well-known desease in Europe since early times, is not by far a new problem, therefore, TB's incidence reported in Spain puts the illness in a second place among European Union's countries, only surpassed by Portugal. TB in Catalonia has become a problem of public health first order and above all its remarkable level global incidence, even much higher than those reports «officially» admited by countries of similar social and economic standards. The fact that Barcelona displays one of the best TB's notification registries with trustworthy integrated and validated datas, might be one of the reason why TB's numbers are so high in Catalonia. Besides, infection caused by Human Immunodeficiency Virus (HIV) widely spread throughout in a short term to reach world epidemic levels added a side factor of TB's resurgence in developed countries. Unfortunately in Spain, like other countries, young people were the most affected. In the first stages of the epidemic, AIDS was by far the main cause of mortality in this group of population. The introduction of antirretroviral therapy (1996), highly effective, has raised the survival of HIV's patients and can explain so far the decrease shown in mortality rates or new infected cases reported. The actual study presents the epidemiologist, clinical, radiological and pharmacological resistence patterns and the adverse effects of antituberculosis treatment, as well as analytical, immunological and virology parameters, throughout a descriptive study, post-evaluation and above all, a consecutive cases restrospective in patients which were infected with TB/HIV and had treatment at Barcelona's Vall d'Hebron University General Hospital, between 1986 and 2000. Along the researched period a progressive reduction in the incidence of coinfection closely related between TB and HIV, was observed in this group of patients, mostly men, 25 to 40' s age range and being the addiction to drugs of parenteral use, the more important risk factor of HIV's infection. Pulmonary tuberculosis was the main form of clinical presentation, followed by scattered/diffusion TB and finally, by extrapulmonary TB. The PPD was anergic in half of the cases while one third of all patients presented a radiological post primary pattern. Besides, a 10.35% of patients with pulmonary affectation showed a normal radiological pattern while the primary pattern was associated to an inferior number of 200 CD4+ cel/ml. Meanwhile, most patients presented an advanced state of inmunodepression and subsequent diagnosis was made through the smear of Z-N either by respiratory samples's culture or puncture-aspiration with a fine needle in order to perform further biopsy in those cases with extrapulmonary engagement. Total resistance to antituberculosis treatment was presented in 9.30% of patients whereas multiresistance in 1.60% of the cases. The analysis of all these previous data helps to corroborate the epidemiologist and clinic importance of coinfection between tuberculosis and HIV

An assessment of recently published gene expression data analyses: reporting experimental design and statistical factors

BACKGROUND: The analysis of large-scale gene expression data is a fundamental approach to functional genomics and the identification of potential drug targets. Results derived from such studies cannot be trusted unless they are adequately designed and reported. The purpose of this study is to assess current practices on the reporting of experimental design and statistical analyses in gene expression-based studies. METHODS: We reviewed hundreds of MEDLINE-indexed papers involving gene expression data analysis, which were published between 2003 and 2005. These papers were examined on the basis of their reporting of several factors, such as sample size, statistical power and software availability. RESULTS: Among the examined papers, we concentrated on 293 papers consisting of applications and new methodologies. These papers did not report approaches to sample size and statistical power estimation. Explicit statements on data transformation and descriptions of the normalisation techniques applied prior to data analyses (e.g. classification) were not reported in 57 (37.5%) and 104 (68.4%) of the methodology papers respectively. With regard to papers presenting biomedical-relevant applications, 41(29.1 %) of these papers did not report on data normalisation and 83 (58.9%) did not describe the normalisation technique applied. Clustering-based analysis, the t-test and ANOVA represent the most widely applied techniques in microarray data analysis. But remarkably, only 5 (3.5%) of the application papers included statements or references to assumption about variance homogeneity for the application of the t-test and ANOVA. There is still a need to promote the reporting of software packages applied or their availability. CONCLUSION: Recently-published gene expression data analysis studies may lack key information required for properly assessing their design quality and potential impact. There is a need for more rigorous reporting of important experimental factors such as statistical power and sample size, as well as the correct description and justification of statistical methods applied. This paper highlights the importance of defining a minimum set of information required for reporting on statistical design and analysis of expression data. By improving practices of statistical analysis reporting, the scientific community can facilitate quality assurance and peer-review processes, as well as the reproducibility of results

Scaling symmetries and canonoid transformations in Hamiltonian systems

We investigate various types of symmetries and their mutual relationships in Hamiltonian systems defined on manifolds with different geometric structures: symplectic, cosymplectic, contact and cocontact. In each case we pay special attention to non-standard (non-canonical) symmetries, in particular scaling symmetries and canonoid transformations, as they provide new interesting tools for the qualitative study of these systems. Our main results are the characterizations of these non-standard symmetries and the analysis of their relation with conserved (or dissipated) quantities.Comment: 22 pages. Comments are welcom