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Book ; Online: Semi-supervised voice conversion with amortized variational inference

Stephenson, Cory / Keskin, Gokce / Thomas, Anil / Elibol, Oguz H.

2019

Abstract: In this work we introduce a semi-supervised approach to the voice conversion problem, in which speech from a source speaker is converted into speech of a target speaker. The proposed method makes use of both parallel and non-parallel utterances from the ... ...

Abstract	In this work we introduce a semi-supervised approach to the voice conversion problem, in which speech from a source speaker is converted into speech of a target speaker. The proposed method makes use of both parallel and non-parallel utterances from the source and target simultaneously during training. This approach can be used to extend existing parallel data voice conversion systems such that they can be trained with semi-supervision. We show that incorporating semi-supervision improves the voice conversion performance compared to fully supervised training when the number of parallel utterances is limited as in many practical applications. Additionally, we find that increasing the number non-parallel utterances used in training continues to improve performance when the amount of parallel training data is held constant. Comment: Accepted for publication at Interspeech 2019
Keywords	Statistics - Machine Learning ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Audio and Speech Processing
Subject code	006
Publishing date	2019-09-30
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Measuring the Effectiveness of Voice Conversion on Speaker Identification and Automatic Speech Recognition Systems

Keskin, Gokce / Lee, Tyler / Stephenson, Cory / Elibol, Oguz H.

2019

Abstract: This paper evaluates the effectiveness of a Cycle-GAN based voice converter (VC) on four speaker identification (SID) systems and an automated speech recognition (ASR) system for various purposes. Audio samples converted by the VC model are classified by ...

Abstract	This paper evaluates the effectiveness of a Cycle-GAN based voice converter (VC) on four speaker identification (SID) systems and an automated speech recognition (ASR) system for various purposes. Audio samples converted by the VC model are classified by the SID systems as the intended target at up to 46% top-1 accuracy among more than 250 speakers. This encouraging result in imitating the target styles led us to investigate if converted (synthetic) samples can be used to improve ASR training. Unfortunately, adding synthetic data to the ASR training set only marginally improves word and character error rates. Our results indicate that even though VC models can successfully mimic the style of target speakers as measured by SID systems, improving ASR training with synthetic data from VC systems needs further research to establish its efficacy. Comment: Accepted for publication at ICML 2019 Synthetic Realities: Workshop on Detecting Audio-Visual Fakes
Keywords	Electrical Engineering and Systems Science - Audio and Speech Processing
Subject code	400
Publishing date	2019-05-29
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Shifted and Squeezed 8-bit Floating Point format for Low-Precision Training of Deep Neural Networks

Cambier, Léopold / Bhiwandiwalla, Anahita / Gong, Ting / Nekuii, Mehran / Elibol, Oguz H / Tang, Hanlin

2020

Abstract: Training with larger number of parameters while keeping fast iterations is an increasingly adopted strategy and trend for developing better performing Deep Neural Network (DNN) models. This necessitates increased memory footprint and computational ... ...

Abstract	Training with larger number of parameters while keeping fast iterations is an increasingly adopted strategy and trend for developing better performing Deep Neural Network (DNN) models. This necessitates increased memory footprint and computational requirements for training. Here we introduce a novel methodology for training deep neural networks using 8-bit floating point (FP8) numbers. Reduced bit precision allows for a larger effective memory and increased computational speed. We name this method Shifted and Squeezed FP8 (S2FP8). We show that, unlike previous 8-bit precision training methods, the proposed method works out-of-the-box for representative models: ResNet-50, Transformer and NCF. The method can maintain model accuracy without requiring fine-tuning loss scaling parameters or keeping certain layers in single precision. We introduce two learnable statistics of the DNN tensors - shifted and squeezed factors that are used to optimally adjust the range of the tensors in 8-bits, thus minimizing the loss in information due to quantization.
Keywords	Computer Science - Machine Learning
Subject code	006
Publishing date	2020-01-16
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Scalable Nanogap Sensors for Non-Redox Enzyme Assays.

Su, Xing / Tayebi, Noureddine / Credo, Grace M / Wu, Kai / Elibol, Oguz H / Liu, David J / Daniels, Jonathan S / Li, Handong / Hall, Drew A / Varma, Madoo

ACS sensors

2018 Volume 3, Issue 9, Page(s) 1773–1781

Abstract: Clinical diagnostic assays that monitor redox enzyme activity are widely used in small, low-cost readout devices for point-of-care monitoring (e.g., a glucometer); however, monitoring non-redox enzymes in real-time using compact electronic devices ... ...

Abstract	Clinical diagnostic assays that monitor redox enzyme activity are widely used in small, low-cost readout devices for point-of-care monitoring (e.g., a glucometer); however, monitoring non-redox enzymes in real-time using compact electronic devices remains a challenge. We address this problem by using a highly scalable nanogap sensor array to observe electrochemical signals generated by a model non-redox enzyme system, the DNA polymerase-catalyzed incorporation of four modified, redox-tagged nucleotides. Using deoxynucleoside triphosphates (dNTPs) tagged with para-aminophenyl monophosphate (pAPP) to form pAP-deoxyribonucleoside tetra-phosphates (AP-dN4Ps), incorporation of the nucleotide analogs by DNA polymerase results in the release of redox inactive pAP-triphosphates (pAPP
MeSH term(s)	Alkaline Phosphatase/chemistry ; Aminophenols/chemistry ; Aniline Compounds/chemistry ; Animals ; Cattle ; DNA/chemistry ; DNA Polymerase I/analysis ; DNA Polymerase I/chemistry ; Electrochemical Techniques/methods ; Enzyme Assays/methods ; Escherichia coli/enzymology ; Escherichia coli Proteins/analysis ; Escherichia coli Proteins/chemistry ; Exodeoxyribonucleases/chemistry ; Nucleotides/chemistry ; Organophosphorus Compounds/chemistry ; Oxidation-Reduction
Chemical Substances	Aminophenols ; Aniline Compounds ; Escherichia coli Proteins ; Nucleotides ; Organophosphorus Compounds ; 4-aminophenylphosphate (72962-65-3) ; DNA (9007-49-2) ; DNA Polymerase I (EC 2.7.7.-) ; Exodeoxyribonucleases (EC 3.1.-) ; exodeoxyribonuclease III (EC 3.1.11.2) ; Alkaline Phosphatase (EC 3.1.3.1) ; 4-aminophenol (R7P8FRP05V)
Language	English
Publishing date	2018-09-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2379-3694
ISSN (online)	2379-3694
DOI	10.1021/acssensors.8b00500
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Surface immobilizable chelator for label-free electrical detection of pyrophosphate.

Liu, David J / Credo, Grace M / Su, Xing / Wu, Kai / Lim, Hsiao C / Elibol, Oguz H / Bashir, Rashid / Varma, Madoo

Chemical communications (Cambridge, England)

2011 Volume 47, Issue 29, Page(s) 8310–8312

Abstract: A new pyrophosphate (PPi) chelator was designed for surface-sensitive electrical detection of biomolecular reactions. This article describes the synthesis of the PPi-selective receptor, its surface immobilization and application to label-free electrical ... ...

Abstract	A new pyrophosphate (PPi) chelator was designed for surface-sensitive electrical detection of biomolecular reactions. This article describes the synthesis of the PPi-selective receptor, its surface immobilization and application to label-free electrical detection on a silicon-based field-effect transistor (FET) sensor.
MeSH term(s)	Catechols/chemistry ; Chelating Agents/chemistry ; Diphosphates/analysis ; Electrochemical Techniques/methods ; Fluorescent Dyes/chemistry ; Silicon/chemistry ; Surface Properties ; Transistors, Electronic
Chemical Substances	Catechols ; Chelating Agents ; Diphosphates ; Fluorescent Dyes ; catechol (LF3AJ089DQ) ; Silicon (Z4152N8IUI)
Language	English
Publishing date	2011-06-20
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/c1cc12073e
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Article: Surface immobilizable chelator for label-free electrical detection of pyrophosphate

Liu, David J / Credo, Grace M / Su, Xing / Wu, Kai / Lim, Hsiao C / Elibol, Oguz H / Bashir, Rashid / Varma, Madoo

Chemical communications. 2011 July 11, v. 47, no. 29

2011

Abstract	A new pyrophosphate (PPi) chelator was designed for surface-sensitive electrical detection of biomolecular reactions. This article describes the synthesis of the PPi-selective receptor, its surface immobilization and application to label-free electrical detection on a silicon-based field-effect transistor (FET) sensor.
Keywords	chelating agents ; chemical compounds ; chemical reactions ; transistors
Language	English
Dates of publication	2011-0711
Size	p. 8310-8312.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/c1cc12073e
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Article ; Online: Label-free electrical detection of pyrophosphate generated from DNA polymerase reactions on field-effect devices.

Credo, Grace M / Su, Xing / Wu, Kai / Elibol, Oguz H / Liu, David J / Reddy, Bobby / Tsai, Ta-Wei / Dorvel, Brian R / Daniels, Jonathan S / Bashir, Rashid / Varma, Madoo

The Analyst

2012 Volume 137, Issue 6, Page(s) 1351–1362

Abstract: We introduce a label-free approach for sensing polymerase reactions on deoxyribonucleic acid (DNA) using a chelator-modified silicon-on-insulator field-effect transistor (SOI-FET) that exhibits selective and reversible electrical response to ... ...

Abstract	We introduce a label-free approach for sensing polymerase reactions on deoxyribonucleic acid (DNA) using a chelator-modified silicon-on-insulator field-effect transistor (SOI-FET) that exhibits selective and reversible electrical response to pyrophosphate anions. The chemical modification of the sensor surface was designed to include rolling-circle amplification (RCA) DNA colonies for locally enhanced pyrophosphate (PPi) signal generation and sensors with immobilized chelators for capture and surface-sensitive detection of diffusible reaction by-products. While detecting arrays of enzymatic base incorporation reactions is typically accomplished using optical fluorescence or chemiluminescence techniques, our results suggest that it is possible to develop scalable and portable PPi-specific sensors and platforms for broad biomedical applications such as DNA sequencing and microbe detection using surface-sensitive electrical readout techniques.
MeSH term(s)	Base Sequence ; Biosensing Techniques ; Chelating Agents/chemistry ; DNA/chemistry ; DNA/metabolism ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/metabolism ; Diphosphates/analysis ; Electrochemical Techniques ; Molecular Sequence Data ; Molecular Structure ; Silanes/chemistry ; Silicon/chemistry ; Surface Properties ; Transistors, Electronic
Chemical Substances	Chelating Agents ; Diphosphates ; Silanes ; DNA (9007-49-2) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; Silicon (Z4152N8IUI)
Language	English
Publishing date	2012-01-19
Publishing country	England
Document type	Evaluation Study ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/c2an15930a
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Zs.A 2423: Show issues

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Article: High-k dielectric Al₂O₃ nanowire and nanoplate field effect sensors for improved pH sensing

Reddy, Bobby Jr / Dorvel, Brian R / Go, Jonghyun / Nair, Pradeep R / Elibol, Oguz H / Credo, Grace M / Daniels, Jonathan S / Chow, Edmond K. C / Su, Xing / Varma, Madoo / Alam, Muhammad A / Bashir, Rashid

Biomedical microdevices. 2011 Apr., v. 13, no. 2

2011

Abstract: Over the last decade, field-effect transistors (FETs) with nanoscale dimensions have emerged as possible label-free biological and chemical sensors capable of highly sensitive detection of various entities and processes. While significant progress has ... ...

Abstract	Over the last decade, field-effect transistors (FETs) with nanoscale dimensions have emerged as possible label-free biological and chemical sensors capable of highly sensitive detection of various entities and processes. While significant progress has been made towards improving their sensitivity, much is yet to be explored in the study of various critical parameters, such as the choice of a sensing dielectric, the choice of applied front and back gate biases, the design of the device dimensions, and many others. In this work, we present a process to fabricate nanowire and nanoplate FETs with Al₂O₃ gate dielectrics and we compare these devices with FETs with SiO₂ gate dielectrics. The use of a high-k dielectric such as Al₂O₃ allows for the physical thickness of the gate dielectric to be thicker without losing sensitivity to charge, which then reduces leakage currents and results in devices that are highly robust in fluid. This optimized process results in devices stable for up to 8 h in fluidic environments. Using pH sensing as a benchmark, we show the importance of optimizing the device bias, particularly the back gate bias which modulates the effective channel thickness. We also demonstrate that devices with Al₂O₃ gate dielectrics exhibit superior sensitivity to pH when compared to devices with SiO₂ gate dielectrics. Finally, we show that when the effective electrical silicon channel thickness is on the order of the Debye length, device response to pH is virtually independent of device width. These silicon FET sensors could become integral components of future silicon based Lab on Chip systems.
Keywords	nanowires ; width
Language	English
Dates of publication	2011-04
Size	p. 335-344.
Publisher	Springer US
Publishing place	Boston
Document type	Article
ZDB-ID	2004019-2
ISSN	1572-8781 ; 1387-2176
ISSN (online)	1572-8781
ISSN	1387-2176
DOI	10.1007/s10544-010-9497-z
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Article ; Online: Silicon field effect transistors as dual-use sensor-heater hybrids.

Reddy, Bobby / Elibol, Oguz H / Nair, Pradeep R / Dorvel, Brian R / Butler, Felice / Ahsan, Zahab / Bergstrom, Donald E / Alam, Muhammad A / Bashir, Rashid

Analytical chemistry

2011 Volume 83, Issue 3, Page(s) 888–895

Abstract: We demonstrate the temperature mediated applications of a previously proposed novel localized dielectric heating method on the surface of dual purpose silicon field effect transistor (FET) sensor-heaters and perform modeling and characterization of the ... ...

Abstract	We demonstrate the temperature mediated applications of a previously proposed novel localized dielectric heating method on the surface of dual purpose silicon field effect transistor (FET) sensor-heaters and perform modeling and characterization of the underlying mechanisms. The FETs are first shown to operate as electrical sensors via sensitivity to changes in pH in ionic fluids. The same devices are then demonstrated as highly localized heaters via investigation of experimental heating profiles and comparison to simulation results. These results offer further insight into the heating mechanism and help determine the spatial resolution of the technique. Two important biosensor platform applications spanning different temperature ranges are then demonstrated: a localized heat-mediated DNA exchange reaction and a method for dense selective functionalization of probe molecules via the heat catalyzed complete desorption and reattachment of chemical functionalization to the transistor surfaces. Our results show that the use of silicon transistors can be extended beyond electrical switching and field-effect sensing to performing localized temperature controlled chemical reactions on the transistor itself.
MeSH term(s)	Catalysis ; Hot Temperature ; Microscopy, Electron, Scanning ; Silicon/chemistry ; Surface Properties ; Transistors, Electronic
Chemical Substances	Silicon (Z4152N8IUI)
Language	English
Publishing date	2011-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac102566f
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Zs.A 4033: Show issues

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Article ; Online: High-k dielectric Al₂O₃ nanowire and nanoplate field effect sensors for improved pH sensing.

Reddy, Bobby / Dorvel, Brian R / Go, Jonghyun / Nair, Pradeep R / Elibol, Oguz H / Credo, Grace M / Daniels, Jonathan S / Chow, Edmond K C / Su, Xing / Varma, Madoo / Alam, Muhammad A / Bashir, Rashid

Biomedical microdevices

2011 Volume 13, Issue 2, Page(s) 335–344

Abstract	Over the last decade, field-effect transistors (FETs) with nanoscale dimensions have emerged as possible label-free biological and chemical sensors capable of highly sensitive detection of various entities and processes. While significant progress has been made towards improving their sensitivity, much is yet to be explored in the study of various critical parameters, such as the choice of a sensing dielectric, the choice of applied front and back gate biases, the design of the device dimensions, and many others. In this work, we present a process to fabricate nanowire and nanoplate FETs with Al(2)O(3) gate dielectrics and we compare these devices with FETs with SiO(2) gate dielectrics. The use of a high-k dielectric such as Al(2)O(3) allows for the physical thickness of the gate dielectric to be thicker without losing sensitivity to charge, which then reduces leakage currents and results in devices that are highly robust in fluid. This optimized process results in devices stable for up to 8 h in fluidic environments. Using pH sensing as a benchmark, we show the importance of optimizing the device bias, particularly the back gate bias which modulates the effective channel thickness. We also demonstrate that devices with Al(2)O(3) gate dielectrics exhibit superior sensitivity to pH when compared to devices with SiO(2) gate dielectrics. Finally, we show that when the effective electrical silicon channel thickness is on the order of the Debye length, device response to pH is virtually independent of device width. These silicon FET sensors could become integral components of future silicon based Lab on Chip systems.
MeSH term(s)	Aluminum Oxide/chemistry ; Electric Impedance ; Hydrogen-Ion Concentration ; Nanowires/chemistry ; Reproducibility of Results ; Silicon/chemistry ; Transistors, Electronic
Chemical Substances	Aluminum Oxide (LMI26O6933) ; Silicon (Z4152N8IUI)
Language	English
Publishing date	2011-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2004019-2
ISSN	1572-8781 ; 1387-2176
ISSN (online)	1572-8781
ISSN	1387-2176
DOI	10.1007/s10544-010-9497-z
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