Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation

BACKGROUND: The ability to distinguish between genes and proteins is essential for understanding biological text. Support Vector Machines (SVMs) have been proven to be very efficient in general data mining tasks. We explore their capability for the gene versus protein name disambiguation task. RESULTS: We incorporated into the conventional SVM a weighting scheme based on distances of context words from the word to be disambiguated. This weighting scheme increased the performance of SVMs by five percentage points giving performance better than 85% as measured by the area under ROC curve and outperformed the Weighted Additive Classifier, which also incorporates the weighting, and the Naive Bayes classifier. CONCLUSION: We show that the performance of SVMs can be improved by the proposed weighting scheme. Furthermore, our results suggest that in this study the increase of the classification performance due to the weighting is greater than that obtained by selecting the underlying classifier or the kernel part of the SVM

Improving the performance of dictionary-based approaches in protein name recognition

AbstractDictionary-based protein name recognition is often a first step in extracting information from biomedical documents because it can provide ID information on recognized terms. However, dictionary-based approaches present two fundamental difficulties: (1) false recognition mainly caused by short names; (2) low recall due to spelling variations. In this paper, we tackle the former problem using machine learning to filter out false positives and present two alternative methods for alleviating the latter problem of spelling variations. The first is achieved by using approximate string searching, and the second by expanding the dictionary with a probabilistic variant generator, which we propose in this paper. Experimental results using the GENIA corpus revealed that filtering using a naive Bayes classifier greatly improved precision with only a slight loss of recall, resulting in 10.8% improvement in F-measure, and dictionary expansion with the variant generator gave further 1.6% improvement and achieved an F-measure of 66.6%

Information Extraction from Biomedical Texts

V poslední době bylo vynaloženo velké úsilí k tomu, aby byly biomedicínské znalosti, typicky uložené v podobě vědeckých článků, snadněji přístupné a bylo možné je efektivně sdílet. Ve skutečnosti ale nestrukturovaná podstata těchto textů způsobuje velké obtíže při použití technik pro získávání a vyvozování znalostí. Anotování entit nesoucích jistou sémantickou informaci v textu je prvním krokem k vytvoření znalosti analyzovatelné počítačem. V této práci nejdříve studujeme metody pro automatickou extrakci informací z textů přirozeného jazyka. Dále zhodnotíme hlavní výhody a nevýhody současných systémů pro extrakci informací a na základě těchto znalostí se rozhodneme přijmout přístup strojového učení pro automatické získávání exktrakčních vzorů při našich experimentech. Bohužel, techniky strojového učení často vyžadují obrovské množství trénovacích dat, která může být velmi pracné získat. Abychom dokázali čelit tomuto nepříjemnému problému, prozkoumáme koncept tzv. bootstrapping techniky. Nakonec ukážeme, že během našich experimentů metody strojového učení pracovaly dostatečně dobře a dokonce podstatně lépe než základní metody. Navíc v úloze využívající techniky bootstrapping se podařilo významně snížit množství dat potřebných pro trénování extrakčního systému.Recently, there has been much effort in making biomedical knowledge, typically stored in scientific articles, more accessible and interoperable. As a matter of fact, the unstructured nature of such texts makes it difficult to apply  knowledge discovery and inference techniques. Annotating information units with semantic information in these texts is the first step to make the knowledge machine-analyzable.  In this work, we first study methods for automatic information extraction from natural language text. Then we discuss the main benefits and disadvantages of the state-of-art information extraction systems and, as a result of this, we adopt a machine learning approach to automatically learn extraction patterns in our experiments. Unfortunately, machine learning techniques often require a huge amount of training data, which can be sometimes laborious to gather. In order to face up to this tedious problem, we investigate the concept of weakly supervised or bootstrapping techniques. Finally, we show in our experiments that our machine learning methods performed reasonably well and significantly better than the baseline. Moreover, in the weakly supervised learning task we were able to substantially bring down the amount of labeled data needed for training of the extraction system.

New kernel functions and learning methods for text and data mining

Recent advances in machine learning methods enable increasingly the automatic construction of various types of computer assisted methods that have been difficult or laborious to program by human experts. The tasks for which this kind of tools are needed arise in many areas, here especially in the fields of bioinformatics and natural language processing. The machine learning methods may not work satisfactorily if they are not appropriately tailored to the task in question. However, their learning performance can often be improved by taking advantage of deeper insight of the application domain or the learning problem at hand. This thesis considers developing kernel-based learning algorithms incorporating this kind of prior knowledge of the task in question in an advantageous way. Moreover, computationally efficient algorithms for training the learning machines for specific tasks are presented. In the context of kernel-based learning methods, the incorporation of prior knowledge is often done by designing appropriate kernel functions. Another well-known way is to develop cost functions that fit to the task under consideration. For disambiguation tasks in natural language, we develop kernel functions that take account of the positional information and the mutual similarities of words. It is shown that the use of this information significantly improves the disambiguation performance of the learning machine. Further, we design a new cost function that is better suitable for the task of information retrieval and for more general ranking problems than the cost functions designed for regression and classification. We also consider other applications of the kernel-based learning algorithms such as text categorization, and pattern recognition in differential display. We develop computationally efficient algorithms for training the considered learning machines with the proposed kernel functions. We also design a fast cross-validation algorithm for regularized least-squares type of learning algorithm. Further, an efficient version of the regularized least-squares algorithm that can be used together with the new cost function for preference learning and ranking tasks is proposed. In summary, we demonstrate that the incorporation of prior knowledge is possible and beneficial, and novel advanced kernels and cost functions can be used in algorithms efficiently.Siirretty Doriast

A Novel Method for Epileptic Seizure Detection Using Coupled Hidden Markov Models

We propose a novel Coupled Hidden Markov Model to detect epileptic seizures in multichannel electroencephalography (EEG) data. Our model defines a network of seizure propagation paths to capture both the temporal and spatial evolution of epileptic activity. To address the intractability introduced by the coupled interactions, we derive a variational inference procedure to efficiently infer the seizure evolution from spectral patterns in the EEG data. We validate our model on EEG aquired under clinical conditions in the Epilepsy Monitoring Unit of the Johns Hopkins Hospital. Using 5-fold cross validation, we demonstrate that our model outperforms three baseline approaches which rely on a classical detection framework. Our model also demonstrates the potential to localize seizure onset zones in focal epilepsy.Comment: To appear in MICCAI 2018 Proceeding

Complex extreme learning machine applications in terahertz pulsed signals feature sets

This paper presents a novel approach to the automatic classification of very large data sets composed of terahertz pulse transient signals, highlighting their potential use in biochemical, biomedical, pharmaceutical and security applications. Two different types of THz spectra are considered in the classification process. Firstly a binary classification study of poly-A and poly-C ribonucleic acid samples is performed. This is then contrasted with a difficult multi-class classification problem of spectra from six different powder samples that although have fairly indistinguishable features in the optical spectrum, they also possess a few discernable spectral features in the terahertz part of the spectrum. Classification is performed using a complex-valued extreme learning machine algorithm that takes into account features in both the amplitude as well as the phase of the recorded spectra. Classification speed and accuracy are contrasted with that achieved using a support vector machine classifier. The study systematically compares the classifier performance achieved after adopting different Gaussian kernels when separating amplitude and phase signatures. The two signatures are presented as feature vectors for both training and testing purposes. The study confirms the utility of complex-valued extreme learning machine algorithms for classification of the very large data sets generated with current terahertz imaging spectrometers. The classifier can take into consideration heterogeneous layers within an object as would be required within a tomographic setting and is sufficiently robust to detect patterns hidden inside noisy terahertz data sets. The proposed study opens up the opportunity for the establishment of complex-valued extreme learning machine algorithms as new chemometric tools that will assist the wider proliferation of terahertz sensing technology for chemical sensing, quality control, security screening and clinic diagnosis. Furthermore, the proposed algorithm should also be very useful in other applications requiring the classification of very large datasets

Arabic named entity recognition

En esta tesis doctoral se describen las investigaciones realizadas con el objetivo de determinar las mejores tecnicas para construir un Reconocedor de Entidades Nombradas en Arabe. Tal sistema tendria la habilidad de identificar y clasificar las entidades nombradas que se encuentran en un texto arabe de dominio abierto. La tarea de Reconocimiento de Entidades Nombradas (REN) ayuda a otras tareas de Procesamiento del Lenguaje Natural (por ejemplo, la Recuperacion de Informacion, la Busqueda de Respuestas, la Traduccion Automatica, etc.) a lograr mejores resultados gracias al enriquecimiento que a~nade al texto. En la literatura existen diversos trabajos que investigan la tarea de REN para un idioma especifico o desde una perspectiva independiente del lenguaje. Sin embargo, hasta el momento, se han publicado muy pocos trabajos que estudien dicha tarea para el arabe. El arabe tiene una ortografia especial y una morfologia compleja, estos aspectos aportan nuevos desafios para la investigacion en la tarea de REN. Una investigacion completa del REN para elarabe no solo aportaria las tecnicas necesarias para conseguir un alto rendimiento, sino que tambien proporcionara un analisis de los errores y una discusion sobre los resultados que benefician a la comunidad de investigadores del REN. El objetivo principal de esta tesis es satisfacer esa necesidad. Para ello hemos: 1. Elaborado un estudio de los diferentes aspectos del arabe relacionados con dicha tarea; 2. Analizado el estado del arte del REN; 3. Llevado a cabo una comparativa de los resultados obtenidos por diferentes tecnicas de aprendizaje automatico; 4. Desarrollado un metodo basado en la combinacion de diferentes clasificadores, donde cada clasificador trata con una sola clase de entidades nombradas y emplea el conjunto de caracteristicas y la tecnica de aprendizaje automatico mas adecuados para la clase de entidades nombradas en cuestion. Nuestros experimentos han sido evaluados sobre nueve conjuntos de test.Benajiba, Y. (2009). Arabic named entity recognition [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/8318Palanci