Bayesian Nested Neural Networks for Uncertainty Calibration and Adaptive Compression

Nested networks or slimmable networks are neural networks whose architectures can be adjusted instantly during testing time, e.g., based on computational constraints. Recent studies have focused on a "nested dropout" layer, which is able to order the nodes of a layer by importance during training, thus generating a nested set of sub-networks that are optimal for different configurations of resources. However, the dropout rate is fixed as a hyper-parameter over different layers during the whole training process. Therefore, when nodes are removed, the performance decays in a human-specified trajectory rather than in a trajectory learned from data. Another drawback is the generated sub-networks are deterministic networks without well-calibrated uncertainty. To address these two problems, we develop a Bayesian approach to nested neural networks. We propose a variational ordering unit that draws samples for nested dropout at a low cost, from a proposed Downhill distribution, which provides useful gradients to the parameters of nested dropout. Based on this approach, we design a Bayesian nested neural network that learns the order knowledge of the node distributions. In experiments, we show that the proposed approach outperforms the nested network in terms of accuracy, calibration, and out-of-domain detection in classification tasks. It also outperforms the related approach on uncertainty-critical tasks in computer vision.Comment: 16 pages, 10 figure

Moby: Empowering 2D Models for Efficient Point Cloud Analytics on the Edge

3D object detection plays a pivotal role in many applications, most notably autonomous driving and robotics. These applications are commonly deployed on edge devices to promptly interact with the environment, and often require near real-time response. With limited computation power, it is challenging to execute 3D detection on the edge using highly complex neural networks. Common approaches such as offloading to the cloud induce significant latency overheads due to the large amount of point cloud data during transmission. To resolve the tension between wimpy edge devices and compute-intensive inference workloads, we explore the possibility of empowering fast 2D detection to extrapolate 3D bounding boxes. To this end, we present Moby, a novel system that demonstrates the feasibility and potential of our approach. We design a transformation pipeline for Moby that generates 3D bounding boxes efficiently and accurately based on 2D detection results without running 3D detectors. Further, we devise a frame offloading scheduler that decides when to launch the 3D detector judiciously in the cloud to avoid the errors from accumulating. Extensive evaluations on NVIDIA Jetson TX2 with real-world autonomous driving datasets demonstrate that Moby offers up to 91.9% latency improvement with modest accuracy loss over state of the art.Comment: Accepted to ACM International Conference on Multimedia (MM) 202

Laboratório de indicadores de Governança Pública: uma proposta para mensurar a efetividade dos gastos na Segurança Pública Municipal

Anais do 35º Seminário de Extensão Universitária da Região Sul - Área temática: EducaçãoPressões por maior transparência e accountability tem sido o mote de muitas mudanças no setor público. No entanto, parece existir uma dificuldade de colocar tais conceitos em prática na área de segurança pública. Este trabalho apresenta algumas iniciativas do Laboratório de Indicadores de Governança Pública, do CESFI-UDESC, na criação de indicadores de efetividade dos gastos dos municípios do Estado de Santa Catarina, em segurança pública. São apresentados no trabalho o que foi feito até o momento e quais os desafios na mensuração das ações de políticas públicas para esta ár

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe