A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al

Guiding CTC Posterior Spike Timings for Improved Posterior Fusion and Knowledge Distillation

Conventional automatic speech recognition (ASR) systems trained from frame-level alignments can easily leverage posterior fusion to improve ASR accuracy and build a better single model with knowledge distillation. End-to-end ASR systems trained using the Connectionist Temporal Classification (CTC) loss do not require frame-level alignment and hence simplify model training. However, sparse and arbitrary posterior spike timings from CTC models pose a new set of challenges in posterior fusion from multiple models and knowledge distillation between CTC models. We propose a method to train a CTC model so that its spike timings are guided to align with those of a pre-trained guiding CTC model. As a result, all models that share the same guiding model have aligned spike timings. We show the advantage of our method in various scenarios including posterior fusion of CTC models and knowledge distillation between CTC models with different architectures. With the 300-hour Switchboard training data, the single word CTC model distilled from multiple models improved the word error rates to 13.7%/23.1% from 14.9%/24.1% on the Hub5 2000 Switchboard/CallHome test sets without using any data augmentation, language model, or complex decoder.Comment: Accepted to Interspeech 201

2.5D multi-view gait recognition based on point cloud registration

This paper presents a method for modeling a 2.5-dimensional (2.5D) human body and extracting the gait features for identifying the human subject. To achieve view-invariant gait recognition, a multi-view synthesizing method based on point cloud registration (MVSM) to generate multi-view training galleries is proposed. The concept of a density and curvature-based Color Gait Curvature Image is introduced to map 2.5D data onto a 2D space to enable data dimension reduction by discrete cosine transform and 2D principle component analysis. Gait recognition is achieved via a 2.5D view-invariant gait recognition method based on point cloud registration. Experimental results on the in-house database captured by a Microsoft Kinect camera show a significant performance gain when using MVSM

Reinforced Mnemonic Reader for Machine Reading Comprehension

In this paper, we introduce the Reinforced Mnemonic Reader for machine reading comprehension tasks, which enhances previous attentive readers in two aspects. First, a reattention mechanism is proposed to refine current attentions by directly accessing to past attentions that are temporally memorized in a multi-round alignment architecture, so as to avoid the problems of attention redundancy and attention deficiency. Second, a new optimization approach, called dynamic-critical reinforcement learning, is introduced to extend the standard supervised method. It always encourages to predict a more acceptable answer so as to address the convergence suppression problem occurred in traditional reinforcement learning algorithms. Extensive experiments on the Stanford Question Answering Dataset (SQuAD) show that our model achieves state-of-the-art results. Meanwhile, our model outperforms previous systems by over 6% in terms of both Exact Match and F1 metrics on two adversarial SQuAD datasets.Comment: Published in 27th International Joint Conference on Artificial Intelligence (IJCAI), 201

In-Situ Defect Detection in Laser Powder Bed Fusion by Using Thermography and Optical Tomography—Comparison to Computed Tomography

Among additive manufacturing (AM) technologies, the laser powder bed fusion (L-PBF) is one of the most important technologies to produce metallic components. The layer-wise build-up of components and the complex process conditions increase the probability of the occurrence of defects. However, due to the iterative nature of its manufacturing process and in contrast to conventional manufacturing technologies such as casting, L-PBF offers unique opportunities for in-situ monitoring. In this study, two cameras were successfully tested simultaneously as a machine manufacturer independent process monitoring setup: a high-frequency infrared camera and a camera for long time exposure, working in the visible and infrared spectrum and equipped with a near infrared filter. An AISI 316L stainless steel specimen with integrated artificial defects has been monitored during the build. The acquired camera data was compared to data obtained by computed tomography. A promising and easy to use examination method for data analysis was developed and correlations between measured signals and defects were identified. Moreover, sources of possible data misinterpretation were specified. Lastly, attempts for automatic data analysis by data integration are presented