Kuan-Tsae Huang, Wilbur B. Davenport, Jr. / "December 1981" / Bibliography: leaf [1] / "Contract ONR/N00014-77-C-0532"

Indiana University-Purdue University Indianapolis (IUPUI) / Neural signal processing to decode neural activity has been an active research area in the last few decades. The next generation of advanced multi-electrode neuroprosthetic devices aim to detect a multiplicity of channels from multiple electrodes, making the relatively time-critical processing problem massively parallel and pushing the computational demands beyond the limits of current embedded digital signal processing (DSP) techniques. To overcome these limitations, a new hybrid computational technique was explored, the Extended Analog Computer (EAC). The EAC is a digitally confgurable analog computer that takes advantage of the intrinsic ability of manifolds to solve partial diferential equations (PDEs). They are extremely fast, require little power, and have great potential for mobile computing applications. In this thesis, the EAC architecture and the mechanism of the formation of potential/current manifolds was derived and analyzed to capture its theoretical mode of operation. A new mode of operation, resistance mode, was developed and a method was devised to sample temporal data and allow their use on the EAC. The method was validated by demonstration of the device solving linear diferential equations and linear functions, and implementing arbitrary finite impulse response (FIR) and infinite impulse response (IIR) linear flters. These results were compared to conventional DSP results. A practical application to the neural computing task was further demonstrated by implementing a matched filter with the EAC simulator and the physical prototype to detect single fiber action potential from multiunit data streams derived from recorded raw electroneurograms. Exclusion error (type 1 error) and inclusion error (type 2 error) were calculated to evaluate the detection rate of the matched filter implemented on the EAC. The detection rates were found to be statistically equivalent to that from DSP simulations with exclusion and inclusion errors at 0% and 1%, respectively.

Indiana University-Purdue University Indianapolis (IUPUI) / Proteins are the building blocks in a biological system. They interact with other proteins to make unique biological phenomenon. Protein-protein interactions play a valuable role in understanding the molecular mechanisms occurring in any biological system. Protein interaction databases are a rich source on protein interaction related information. They gather large amounts of information from published literature to enrich their data. Expert curators put in most of these efforts manually. The amount of accessible and publicly available literature is growing very rapidly. Manual annotation is a time consuming process. And with the rate at which available information is growing, it cannot be dealt with only manual curation. There need to be tools to process this huge amounts of data to bring out valuable gist than can help curators proceed faster. In case of extracting protein-protein interaction evidences from literature, just a mere mention of a certain protein by look-up approaches cannot help validate the interaction. Supporting protein interaction information with experimental evidence can help this cause. In this study, we are applying machine learning based classification techniques to classify and given protein interaction related document into an interaction detection method. We use biological attributes and experimental factors, different combination of which define any particular interaction detection method. Then using predicted detection methods, proteins identified using named entity recognition techniques and decomposing the parts-of-speech composition we search for sentences with experimental evidence for a protein-protein interaction. We report an accuracy of 75.1% with a F-score of 47.6% on a dataset containing 2035 training documents and 300 test documents.