On the Anatomy of MCMC-Based Maximum Likelihood Learning of Energy-Based Models

This study investigates the effects of Markov chain Monte Carlo (MCMC) sampling in unsupervised Maximum Likelihood (ML) learning. Our attention is restricted to the family of unnormalized probability densities for which the negative log density (or energy function) is a ConvNet. We find that many of the techniques used to stabilize training in previous studies are not necessary. ML learning with a ConvNet potential requires only a few hyper-parameters and no regularization. Using this minimal framework, we identify a variety of ML learning outcomes that depend solely on the implementation of MCMC sampling. On one hand, we show that it is easy to train an energy-based model which can sample realistic images with short-run Langevin. ML can be effective and stable even when MCMC samples have much higher energy than true steady-state samples throughout training. Based on this insight, we introduce an ML method with purely noise-initialized MCMC, high-quality short-run synthesis, and the same budget as ML with informative MCMC initialization such as CD or PCD. Unlike previous models, our energy model can obtain realistic high-diversity samples from a noise signal after training. On the other hand, ConvNet potentials learned with non-convergent MCMC do not have a valid steady-state and cannot be considered approximate unnormalized densities of the training data because long-run MCMC samples differ greatly from observed images. We show that it is much harder to train a ConvNet potential to learn a steady-state over realistic images. To our knowledge, long-run MCMC samples of all previous models lose the realism of short-run samples. With correct tuning of Langevin noise, we train the first ConvNet potentials for which long-run and steady-state MCMC samples are realistic images.Comment: Code available at: https://github.com/point0bar1/ebm-anatom

Recreational Exposure to Low Concentrations of Microcystins During an Algal Bloom in a Small Lake

We measured microcystins in blood from people at risk for swallowing water or inhaling spray while swimming, water skiing, jet skiing, or boating during an algal bloom. We monitored water samples from a small lake as a Microcystis aeruginosa bloom developed. We recruited 97 people planning recreational activities in that lake and seven others who volunteered to recreate in a nearby bloom-free lake. We conducted our field study within a week of finding a 10-μg/L microcystin concentration. We analyzed water, air, and human blood samples for water quality, potential human pathogens, algal taxonomy, and microcystin concentrations. We interviewed study participants for demographic and current health symptom information. Water samples were assayed for potential respiratory viruses (adenoviruses and enteroviruses), but none were detected. We did find low concentrations of Escherichia coli, indicating fecal contamination. We found low levels of microcystins (2 μg/L to 5 μg/L) in the water and (<0.1 ng/m3) in the aerosol samples. Blood levels of microcystins for all participants were below the limit of detection (0.147μg/L). Given this low exposure level, study participants reported no symptom increases following recreational exposure to microcystins. This is the first study to report that water-based recreational activities can expose people to very low concentrations of aerosol-borne microcystins; we recently conducted another field study to assess exposures to higher concentrations of these algal toxins

Distribution of microRNA profiles in pre-clinical and clinical forms of murine and human prion disease

Prion diseases are distinguished by long pre-clinical incubation periods during which prions actively propagate in the brain and cause neurodegeneration. In the pre-clinical stage, we hypothesize that upon prion infection, transcriptional changes occur that can lead to early neurodegeneration. A longitudinal analysis of miRNAs in pre-clinical and clinical forms of murine prion disease demonstrated dynamic expression changes during disease progression in the affected thalamus region and serum. Serum samples at each timepoint were collected whereby extracellular vesicles (EVs) were isolated and used to identify blood-based biomarkers reflective of pathology in the brain. Differentially expressed EV miRNAs were validated in human clinical samples from patients with human sporadic Creutzfeldt-Jakob disease (sCJD), with the molecular subtype at codon 129 either methionine-methionine (MM, n = 14) or valine-valine (VV, n = 12) compared to controls (n = 20). EV miRNA biomarkers associated with prion infection predicted sCJD with an AUC of 0.800 (85% sensitivity and 66.7% specificity) in a second independent validation cohort (n = 26) of sCJD and control patients with MM or VV subtype. This study discovered clinically relevant miRNAs that benefit diagnostic development to detect prion-related diseases and therapeutic development to inhibit prion infectivity

Abundant small RNAs in the reproductive tissues and eggs of the honey bee, Apis mellifera

Background: Polyandrous social insects such as the honey bee are prime candidates for parental manipulation of gene expression in offspring. Although there is good evidence for parent-of-origin effects in honey bees the epigenetic mechanisms that underlie these effects remain a mystery. Small RNA molecules such as miRNAs, piRNAs and siRNAs play important roles in transgenerational epigenetic inheritance and in the regulation of gene expression during development. Results: Here we present the first characterisation of small RNAs present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes. We show that semen contains fewer piRNAs relative to eggs and ovaries, and that piRNAs and miRNAs which map antisense to genes involved in DNA regulation and developmental processes are differentially expressed between tissues. tRNA fragments are highly abundant in semen and have a similar profile to those seen in the semen of other animals. Intriguingly we also find abundant piRNAs that target the sex determination locus, suggesting that piRNAs may play a role in honey bee sex determination. Conclusions: We conclude that small RNAs may play a fundamental role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of-origin effects on gene expression and reproductive physiology