62,874 research outputs found
Structuring the Unstructured: Unlocking pharmacokinetic data from journals with Natural Language Processing
The development of a new drug is an increasingly expensive and inefficient process. Many drug candidates are discarded due to pharmacokinetic (PK) complications detected at clinical phases. It is critical to accurately estimate the PK parameters of new drugs before being tested in humans since they will determine their efficacy and safety outcomes. Preclinical predictions of PK parameters are largely based on prior knowledge from other compounds, but much of this potentially valuable data is currently locked in the format of scientific papers. With an ever-increasing amount of scientific literature, automated systems are essential to exploit this resource efficiently. Developing text mining systems that can structure PK literature is critical to improving the drug development pipeline.
This thesis studied the development and application of text mining resources to accelerate the curation of PK databases. Specifically, the development of novel corpora and suitable natural language processing architectures in the PK domain were addressed. The work presented focused on machine learning approaches that can model the high diversity of PK studies, parameter mentions, numerical measurements, units, and contextual information reported across the literature. Additionally, architectures and training approaches that could efficiently deal with the scarcity of annotated examples were explored. The chapters of this thesis tackle the development of suitable models and corpora to (1) retrieve PK documents, (2) recognise PK parameter mentions, (3) link PK entities to a knowledge base and (4) extract relations between parameter mentions, estimated measurements, units and other contextual information. Finally, the last chapter of this thesis studied the feasibility of the whole extraction pipeline to accelerate tasks in drug development research.
The results from this thesis exhibited the potential of text mining approaches to automatically generate PK databases that can aid researchers in the field and ultimately accelerate the drug development pipeline. Additionally, the thesis presented contributions to biomedical natural language processing by developing suitable architectures and corpora for multiple tasks, tackling novel entities and relations within the PK domain
Optical tomography: Image improvement using mixed projection of parallel and fan beam modes
Mixed parallel and fan beam projection is a technique used to increase the quality images. This research focuses on enhancing the image quality in optical tomography. Image quality can be deïŹned by measuring the Peak Signal to Noise Ratio (PSNR) and Normalized Mean Square Error (NMSE) parameters. The ïŹndings of this research prove that by combining parallel and fan beam projection, the image quality can be increased by more than 10%in terms of its PSNR value and more than 100% in terms of its NMSE value compared to a single parallel beam
Deep fusion of multi-channel neurophysiological signal for emotion recognition and monitoring
How to fuse multi-channel neurophysiological signals for emotion recognition is emerging as a hot research topic in community of Computational Psychophysiology. Nevertheless, prior feature engineering based approaches require extracting various domain knowledge related features at a high time cost. Moreover, traditional fusion method cannot fully utilise correlation information between different channels and frequency components. In this paper, we design a hybrid deep learning model, in which the 'Convolutional Neural Network (CNN)' is utilised for extracting task-related features, as well as mining inter-channel and inter-frequency correlation, besides, the 'Recurrent Neural Network (RNN)' is concatenated for integrating contextual information from the frame cube sequence. Experiments are carried out in a trial-level emotion recognition task, on the DEAP benchmarking dataset. Experimental results demonstrate that the proposed framework outperforms the classical methods, with regard to both of the emotional dimensions of Valence and Arousal
mARC: Memory by Association and Reinforcement of Contexts
This paper introduces the memory by Association and Reinforcement of Contexts
(mARC). mARC is a novel data modeling technology rooted in the second
quantization formulation of quantum mechanics. It is an all-purpose incremental
and unsupervised data storage and retrieval system which can be applied to all
types of signal or data, structured or unstructured, textual or not. mARC can
be applied to a wide range of information clas-sification and retrieval
problems like e-Discovery or contextual navigation. It can also for-mulated in
the artificial life framework a.k.a Conway "Game Of Life" Theory. In contrast
to Conway approach, the objects evolve in a massively multidimensional space.
In order to start evaluating the potential of mARC we have built a mARC-based
Internet search en-gine demonstrator with contextual functionality. We compare
the behavior of the mARC demonstrator with Google search both in terms of
performance and relevance. In the study we find that the mARC search engine
demonstrator outperforms Google search by an order of magnitude in response
time while providing more relevant results for some classes of queries
- âŠ