Deep Learning on Abnormal Chromosome Segments: An Intelligent Copy Number Variants Detection System Design

Gene testing emerged as a business in the last two decades, and the testing cost has been reduced from 100 million to 1000 dollars for the development of technologies. Preimplantation genetic screening (PGS) is a popular genetic profiling of embryos prior to implantation in gene testing. Copy number variants (CNVs) detection is a key task in PGS which still needs the manual operation and evaluation. At the same time, deep learning technology earns a booming development and wide application in recent years for its strong computing and learning capability. This research redesigns the PGS workflow with the intelligent CNVs detection system, and proposes the corresponding system framework. Deep learning is selected as the proper technology in the system design for CNVs detection, which also fit the task of denoising. The evaluation is conducted on simulation dataset with high accuracy and low time cost, which may achieve the requirements of clinical application and reduce the workload of bioinformatics experts. Moreover, the redesigned process and proposed framework may enlighten the intelligent system design for gene testing in following work, and provide a guidance of deep learning application in AI healthcar

Optimal control for one-qubit quantum sensing

Quantum systems can be exquisite sensors thanks to their sensitivity to external perturbations. This same characteristic also makes them fragile to external noise. Quantum control can tackle the challenge of protecting quantum sensors from environmental noise, while leaving their strong coupling to the target field to be measured. As the compromise between these two conflicting requirements does not always have an intuitive solution, optimal control based on numerical search could prove very effective. Here we adapt optimal control theory to the quantum sensing scenario, by introducing a cost function that, unlike the usual fidelity of operation, correctly takes into account both the unknown field to be measured and the environmental noise. We experimentally implement this novel control paradigm using a Nitrogen Vacancy center in diamond, finding improved sensitivity to a broad set of time varying fields. The demonstrated robustness and efficiency of the numerical optimization, as well as the sensitivity advantaged it bestows, will prove beneficial to many quantum sensing applications

Enhanced PON Infrastructure Enabled by Silicon Photonics

Les systèmes de courte portée et de détection directe sont le dernier/premier kilomètre de la fourniture des services Internet d'aujourd'hui. Deux cas d'application sont abordés dans cette thèse, l'un concerne l'amélioration des performances des services Internet par la Fibre-To-TheHome ou les réseaux optiques passifs (PONs). L'autre est le radio access network (RAN) pour le fronthaul. Notre objectif pour RAN est de superposer les signaux 5G sur une infrastructure PON. Nous démontrons expérimentalement la génération d'un signal de répartition multiplexée de fréquences orthogonales (OFDM) à bande latérale unique en utilisant un modulateur IQ sur puce basé sur les photoniques au silicium à micro-anneau. Il s'agit d'une solution à coût bas permettant aux PONs d'augmenter les débits de données grâce à l'utilisation d'OFDM. Nous avons généré un signal OFDM à large bande avec un ratio de suppression de bande latérale de plus de 18 dB. Afin de confirmer la robustesse de la dispersion chromatique (CD), nous transmettons le signal généré OFDM SSB dans plus de 20 km de fibre de monomode standard. Aucun fading induit par la CD n'a été observé et le taux d'erreur sur les bits était bon. Nous proposons une solution de photoniques au silicium pour un réseau optique passif afin de mitiger l'interférence de battement signal-signal (SSBI) dans la transmission OFDM, et de récupérer une partie des porteuses de la liaison descendante pour une utilisation dans la liaison montante. Le sous-système recrée les interférences à une entrée du détecteur équilibré ; le signal de données corrompu par SSBI est à la deuxième entrée. L'annulation se produit via la soustraction dans la détection équilibrée. Comme notre solution de photoniques au silicium (SiP) ne peut pas filtrer les signaux idéalement, nous examinons un facteur d'échelle introduit dans la détection équilibrée qui peut balancer les effets de filtrage non idéaux. Nous montrons expérimentalement l'annulation de l'interférence donne de bonnes performances même avec une porteuse faible, soit pour un ratio porteuse/signal ultra bas de 0 dB. Bien que notre solution soit sensible aux effets de la température, notre démonstration expérimentale montre que le réglage de la fréquence résonante peut dériver jusqu'à 12 GHz de la valeur ciblée et présenter toujours de bonnes performances. Nous effectuons des simulations extensives du schéma d'annulation SSBI proposé, et suggérons une diverse conception polarisée pour le sous-système SiP. Nous examinons via la simulation la vulnérabilité à la variation de température et introduisons une nouvelle métrique de performance : Q-facteur minimum garanti. Nous nous servons de cette métrique pour évaluer la robustesse d'annulation SSBI contre la dérive de fréquence induite par les changements de température. Nous maximisons l'efficacité spectrale sous différentes conditions du système en balayant les paramètres de conception contrôlables. Finalement, les résultats de la simulation du système fournissent des indications sur la conception du résonateur micro-anneau, ainsi que sur le choix de la bande de garde et du format de modulation pour obtenir la plus grande efficacité spectrale. Finalement, nous nous concentrons sur la superposition des signaux 5G sur une infrastructure PON pour RAN. Nous expérimentalement validons un sous-système photonique au silicium conçu pour les réseaux optiques passifs avec réutilisation de porteuses et compatibilité radiosur-fibre (RoF) analogique 5G. Le sous-système permet la détection simultanée des signaux RoF et du signal PON transmis dans une seule tranche assignée de longueur d'onde. Tout en maintenant une qualité suffisante de détection des signaux RoF et PON, il n'y a que la puissance minimale de la porteuse qui est extraite pour chaque détection, ce qui conserve ainsi la puissance de la porteuse pour la modulation de liaison montante. Nous réalisons une suppression efficace du signal de liaison descendante en laissant une porteuse propre et forte pour la remodulation. Nous démontrons expérimentalement le signal RoF de liaison montante via un modulateur à micro-anneau. Nous avons détecté avec succès un signal à large bande de 8 GHz et cinq signaux RoF de 125 MHz simultanément. Et deux signaux RoF de 125 MHz sont remodulés sur la même porteuse. Le signal RoF de liaison montante généré est de 13 dB de plus que les signaux de liaison descendante, ce qui indique leur robustesse contre la diaphonie des signaux résiduels de la liaison descendante.Short reach, direct detection systems are the last/first mile of today's internet service provision. Two use cases are addressed in this thesis, one is for enhancing performance of Internet services on fiber-to-the-home or passive optical networks (PON). The other is radio access networks (RAN) for fronthaul. Our focus for RAN is to overlay 5G signals on a PON infrastructure. We experimentally demonstrate the generation of a single-sideband orthogonal frequency division multiplexed (OFDM) signal using an on-chip silicon photonics microring-based IQ modulator. This is a low cost solution enabling PONs to increase data rates through the use of OFDM. We generated a wideband OFDM signal with over 18 dB sideband suppression ratio. To confirm chromatic dispersion (CD) robustness, we transmit the generated SSB OFDM signal over 20 km of standard single mode fiber. No CD-induced fading was observed and bit error rate was good. We propose a silicon photonics solution for a passive optical network to mitigate signal-signal beat interference (SSBI) in OFDM transmission, and to recuperate a part of the downlink carrier for use in the uplink. The subsystem recreates the interference at one balanced detector input; the data signal corrupted with SSBI is at the second input. Cancellation occurs via subtraction in the balanced detection. As our silicon photonics (SiP) solution cannot filter the signals ideally, we examine a scaling factor to be introduced to the balanced detection that can trade-off the non-ideal filtering effects. We show experimentally that the interference is cancelled, allowing good performance even with a weak carrier, that is, for ultra low carrier to signal ratio of 0 dB. Although our solution is sensitive to temperature effects, our experimental demonstration shows the tuning of the resonant frequency can drift by as much as 12 GHz from the targeted value and still provide good performance. We perform extensive simulations of the proposed SSBI cancellation scheme, and suggest a polarization diverse design for the SiP subsystem. We examine via simulation the vulnerability to temperature variation and introduce a new performance metric: minimum guaranteed Qfactor. We use this metric to evaluate the SSBI cancellation robustness against the frequency drift induced by temperature changes. We maximize the spectral efficiency under different system conditions by sweeping the controllable design parameters. Finally the system simulation results provide guidance on the microring resonator design, as well as choice of guard band and modulation format to achieve the highest spectral efficiency. Finally, we turn to focus on overlay 5G signals on a PON infrastructure for RAN. We experimentally validate a silicon photonic subsystem designed for passive optical networks with carrier reuse and 5G analog radio-over-fiber (RoF) compatibility. The subsystem enables the simultaneous detection of RoF signals and a PON signal transmitted in a single assigned wavelength slot. While maintaining sufficient quality of RoF and PON signal detection, only the minimum carrier power is leached off for each detection, thus conserving carrier power for uplink modulation. We realize effective downlink signal suppression to leave a clean and strong carrier for remodulation. We demonstrate experimentally the RoF uplink signal via a micro ring modulator. We successfully detected an 8 GHz broadband signal and five 125 MHz RoF signals simultaneously. And two 125 MHz radio over fiber signals are remodulated onto the same carrier. The generated uplink RoF signal is 13 dB over the downlink signals, indicating their robustness against the crosstalk from residual downlink signals

The BIOMASS level 2 prototype processor : design and experimental results of above-ground biomass estimation

BIOMASS is ESA’s seventh Earth Explorer mission, scheduled for launch in 2022. The satellite will be the first P-band SAR sensor in space and will be operated in fully polarimetric interferometric and tomographic modes. The mission aim is to map forest above-ground biomass (AGB), forest height (FH) and severe forest disturbance (FD) globally with a particular focus on tropical forests. This paper presents the algorithms developed to estimate these biophysical parameters from the BIOMASS level 1 SAR measurements and their implementation in the BIOMASS level 2 prototype processor with a focus on the AGB product. The AGB product retrieval uses a physically-based inversion model, using ground-canceled level 1 data as input. The FH product retrieval applies a classical PolInSAR inversion, based on the Random Volume over Ground Model (RVOG). The FD product will provide an indication of where significant changes occurred within the forest, based on the statistical properties of SAR data. We test the AGB retrieval using modified airborne P-Band data from the AfriSAR and TropiSAR campaigns together with reference data from LiDAR-based AGB maps and plot-based ground measurements. For AGB estimation based on data from a single heading, comparison with reference data yields relative Root Mean Square Difference (RMSD) values mostly between 20% and 30%. Combining different headings in the estimation process significantly improves the AGB retrieval to slightly less than 20%. The experimental results indicate that the implemented retrieval scheme provides robust results that are within mission requirements

A comparative study of the effectiveness of vibration and acoustic emission in diagnosing a defective bearing in a planetry gearbox

Whilst vibration analysis of planetary gearbox faults is relatively well established, the application of Acoustic Emission (AE) to this field is still in its infancy. For planetary-type gearboxes it is more challenging to diagnose bearing faults due to the dynamically changing transmission paths which contribute to masking the vibration signature of interest. The present study is aimed to reduce the effect of background noise whilst extracting the fault feature from AE and vibration signatures. This has been achieved through developing of internal AE sensor for helicopter transmission system. In addition, series of signal processing procedure has been developed to improved detection of incipient damage. Three signal processing techniques including an adaptive filter, spectral kurtosis and envelope analysis, were applied to AE and vibration data acquired from a simplified planetary gearbox test rig with a seeded bearing defect. The results show that AE identified the defect earlier than vibration analysis irrespective of the tortuous transmission pat

Ultra-low power mixed-signal frontend for wearable EEGs

Electronics circuits are ubiquitous in daily life, aided by advancements in the chip design industry, leading to miniaturised solutions for typical day to day problems. One of the critical healthcare areas helped by this advancement in technology is electroencephalography (EEG). EEG is a non-invasive method of tracking a person's brain waves, and a crucial tool in several healthcare contexts, including epilepsy and sleep disorders. Current ambulatory EEG systems still suffer from limitations that affect their usability. Furthermore, many patients admitted to emergency departments (ED) for a neurological disorder like altered mental status or seizures, would remain undiagnosed hours to days after admission, which leads to an elevated rate of death compared to other conditions. Conducting a thorough EEG monitoring in early-stage could prevent further damage to the brain and avoid high mortality. But lack of portability and ease of access results in a long wait time for the prescribed patients. All real signals are analogue in nature, including brainwaves sensed by EEG systems. For converting the EEG signal into digital for further processing, a truly wearable EEG has to have an analogue mixed-signal front-end (AFE). This research aims to define the specifications for building a custom AFE for the EEG recording and use that to review the suitability of the architectures available in the literature. Another critical task is to provide new architectures that can meet the developed specifications for EEG monitoring and can be used in epilepsy diagnosis, sleep monitoring, drowsiness detection and depression study. The thesis starts with a preview on EEG technology and available methods of brainwaves recording. It further expands to design requirements for the AFE, with a discussion about critical issues that need resolving. Three new continuous-time capacitive feedback chopped amplifier designs are proposed. A novel calibration loop for setting the accurate value for a pseudo-resistor, which is a crucial block in the proposed topology, is also discussed. This pseudoresistor calibration loop achieved the resistor variation of under 8.25%. The thesis also presents a new design of a curvature corrected bandgap, as well as a novel DDA based fourth-order Sallen-Key filter. A modified sensor frontend architecture is then proposed, along with a detailed analysis of its implementation. Measurement results of the AFE are finally presented. The AFE consumed a total power of 3.2A (including ADC, amplifier, filter, and current generation circuitry) with the overall integrated input-referred noise of 0.87V-rms in the frequency band of 0.5-50Hz. Measurement results confirmed that only the proposed AFE achieved all defined specifications for the wearable EEG system with the smallest power consumption than state-of-art architectures that meet few but not all specifications. The AFE also achieved a CMRR of 131.62dB, which is higher than any studied architectures.Open Acces

Quantum Cryptography

Quantum cryptography could well be the first application of quantum mechanics at the individual quanta level. The very fast progress in both theory and experiments over the recent years are reviewed, with emphasis on open questions and technological issues.Comment: 55 pages, 32 figures; to appear in Reviews of Modern Physic

Control of feedback for assistive listening devices

Acoustic feedback refers to the undesired acoustic coupling between the loudspeaker and microphone in hearing aids. This feedback channel poses limitations to the normal operation of hearing aids under varying acoustic scenarios. This work makes contributions to improve the performance of adaptive feedback cancellation techniques and speech quality in hearing aids. For this purpose a two microphone approach is proposed and analysed; and probe signal injection methods are also investigated and improved upon

Self-induced parametric amplification arising from nonlinear elastic coupling in a micromechanical resonating disk gyroscope

Parametric amplification, resulting from intentionally varying a parameter in a resonator at twice its resonant frequency, has been successfully employed to increase the sensitivity of many micro- and nano-scale sensors. Here, we introduce the concept of self-induced parametric amplification, which arises naturally from nonlinear elastic coupling between the degenerate vibration modes in a micromechanical disk-resonator, and is not externally applied. The device functions as a gyroscope wherein angular rotation is detected from Coriolis coupling of elastic vibration energy from a driven vibration mode into a second degenerate sensing mode. While nonlinear elasticity in silicon resonators is extremely weak, in this high quality-factor device, ppm-level nonlinear elastic effects result in an order-of-magnitude increase in the observed sensitivity to Coriolis force relative to linear theory. Perfect degeneracy of the primary and secondary vibration modes is achieved through electrostatic frequency tuning, which also enables the phase and frequency of the parametric coupling to be varied, and we show that the resulting phase and frequency dependence of the amplification follow the theory of parametric resonance. We expect that this phenomenon will be useful for both fundamental studies of dynamic systems with low dissipation and for increasing signal-to-noise ratio in practical applications such as gyroscopes