Vernier spectrometer using counter-propagating soliton microcombs

Acquisition of laser frequency with high resolution under continuous and abrupt tuning conditions is important for sensing, spectroscopy and communications. Here, a single microresonator provides rapid and broad-band measurement of frequencies across the optical C-band with a relative frequency precision comparable to conventional dual frequency comb systems. Dual-locked counter-propagating solitons having slightly different repetition rates are used to implement a Vernier spectrometer. Laser tuning rates as high as 10 THz/s, broadly step-tuned lasers, multi-line laser spectra and also molecular absorption lines are characterized using the device. Besides providing a considerable technical simplification through the dual-locked solitons and enhanced capability for measurement of arbitrarily tuned sources, this work reveals possibilities for chip-scale spectrometers that greatly exceed the performance of table-top grating and interferometer-based devices

ADAHESSIAN: An Adaptive Second Order Optimizer for Machine Learning

We introduce ADAHESSIAN, a second order stochastic optimization algorithm which dynamically incorporates the curvature of the loss function via ADAptive estimates of the HESSIAN. Second order algorithms are among the most powerful optimization algorithms with superior convergence properties as compared to first order methods such as SGD and Adam. The main disadvantage of traditional second order methods is their heavier per iteration computation and poor accuracy as compared to first order methods. To address these, we incorporate several novel approaches in ADAHESSIAN, including: (i) a fast Hutchinson based method to approximate the curvature matrix with low computational overhead; (ii) a root-mean-square exponential moving average to smooth out variations of the Hessian diagonal across different iterations; and (iii) a block diagonal averaging to reduce the variance of Hessian diagonal elements. We show that ADAHESSIAN achieves new state-of-the-art results by a large margin as compared to other adaptive optimization methods, including variants of Adam. In particular, we perform extensive tests on CV, NLP, and recommendation system tasks and find that ADAHESSIAN: (i) achieves 1.80%/1.45% higher accuracy on ResNets20/32 on Cifar10, and 5.55% higher accuracy on ImageNet as compared to Adam; (ii) outperforms AdamW for transformers by 0.13/0.33 BLEU score on IWSLT14/WMT14 and 2.7/1.0 PPL on PTB/Wikitext-103; (iii) outperforms AdamW for SqueezeBert by 0.41 points on GLUE; and (iv) achieves 0.032% better score than Adagrad for DLRM on the Criteo Ad Kaggle dataset. Importantly, we show that the cost per iteration of ADAHESSIAN is comparable to first order methods, and that it exhibits robustness towards its hyperparameters

Q-BERT: Hessian Based Ultra Low Precision Quantization of BERT

Transformer based architectures have become de-facto models used for a range of Natural Language Processing tasks. In particular, the BERT based models achieved significant accuracy gain for GLUE tasks, CoNLL-03 and SQuAD. However, BERT based models have a prohibitive memory footprint and latency. As a result, deploying BERT based models in resource constrained environments has become a challenging task. In this work, we perform an extensive analysis of fine-tuned BERT models using second order Hessian information, and we use our results to propose a novel method for quantizing BERT models to ultra low precision. In particular, we propose a new group-wise quantization scheme, and we use a Hessian based mix-precision method to compress the model further. We extensively test our proposed method on BERT downstream tasks of SST-2, MNLI, CoNLL-03, and SQuAD. We can achieve comparable performance to baseline with at most $2.3\%$ performance degradation, even with ultra-low precision quantization down to 2 bits, corresponding up to $13\times$ compression of the model parameters, and up to $4\times$ compression of the embedding table as well as activations. Among all tasks, we observed the highest performance loss for BERT fine-tuned on SQuAD. By probing into the Hessian based analysis as well as visualization, we show that this is related to the fact that current training/fine-tuning strategy of BERT does not converge for SQuAD

Insights into lignocellulose degradation: comparative genomics of anaerobic and cellulolytic Ruminiclostridium-type species

Mesophilic, anaerobic, and cellulolytic Ruminiclostridium-type bacterial species can secrete an extracellular, multi-enzyme machinery cellulosome, which efficiently degrades cellulose. In this study, we first reported the complete genome of Ruminiclostridium papyrosolvens DSM2782, a single circular 5,027,861-bp chromosome with 37.1% G + C content, and compared it with other Ruminiclostridium-type species. Pan-genome analysis showed that Ruminiclostridium-type species share a large number of core genes to conserve basic functions, although they have a high level of intraspecific genetic diversity. Especially, KEGG mapping revealed that Ruminiclostridium-type species mainly use ABC transporters regulated by two-component systems (TCSs) to absorb extracellular sugars but not phosphotransferase systems (PTSs) that are employed by solventogenic clostridia, such as Clostridium acetobutylicum. Furthermore, we performed comparative analyses of the species-specific repertoire of CAZymes for each of the Ruminiclostridium-type species. The high similarity of their cohesins suggests a common ancestor and potential cross-species recognition. Additionally, both differences between the C-terminal cohesins and other cohesins of scaffoldins and between the dockerins linking with cellulases and other catalytic domains indicate a preference for the location of cellulosomal catalytic subunits at scaffoldins. The information gained in this study may be utilized directly or developed further by genetic engineering and optimizing enzyme systems or cell factories for enhanced biotechnological biomass deconstruction and biofuel production

Vernier spectrometer using counterpropagating soliton microcombs

Determination of laser frequency with high resolution under continuous and abrupt tuning conditions is important for sensing, spectroscopy, and communications. We show that a single microresonator provides rapid and broadband measurement of optical frequencies with a relative frequency precision comparable to that of conventional dual-frequency comb systems. Dual-locked counterpropagating solitons having slightly different repetition rates were used to implement a vernier spectrometer, which enabled characterization of laser tuning rates as high as 10 terahertz per second, broadly step-tuned lasers, multiline laser spectra, and molecular absorption lines. Besides providing a considerable technical simplification through the dual-locked solitons and enhanced capability for measurement of arbitrarily tuned sources, our results reveal possibilities for chip-scale spectrometers that exceed the performance of tabletop grating and interferometer-based devices

Microresonator Spectrometer Using Counter-propagating Solitons

A spectrometer is demonstrated using self-locked counter-propagating soliton frequency combs in a high-Q silica microresonator. Fast tuning laser waveforms and molecular absorption features are measured with kiloHertz to MegaHertz resolution

A study of the Hippo pathway/Yap biology and its functions in proliferation control

Understanding how cells control cell sizes and proliferation provides crucial insights into the fundamentals of life and has major implications for regenerative and cancer therapeutics. My thesis project studies the mechanisms underlying the Hippo pathway mediated proliferation and cell cycle regulation. My research work elucidates how the Hippo pathway functions through its downstream effector, Yes-associate protein (Yap), using a combination of mouse genetics and cell-based in vitro systems. The results demonstrate that Yap requires Angiomotin isoform p130 (Amot p130) as a co-factor to function in target transcriptional activation. Consequently, Yap-dependent hepatoma becomes less aggressive upon the loss of Amot p130. Significantly, the findings help to clarify the controversy regarding the Yap and Angiomotin relationship in the Hippo pathway. This thesis also investigates the role of Yap in cell proliferation control using in vitro systems. Remarkably, Yap is required for endothelial cell proliferation, and likely through modulating the expression of G1-to-S transition genes. Genome array studies also implicate Yap in double stranded DNA break repair and homologous recombination occurred during DNA replication. Taken together, these results provide new insight into the biology of Yap and the mechanisms through which the Hippo pathway regulates proliferation