Interactions between species introduce spurious associations in microbiome studies

Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance differences, however, reflect not only direct associations with the phenotype, but also indirect effects due to microbial interactions. We found that microbial interactions could easily generate a large number of spurious associations that provide no mechanistic insight. Using techniques from statistical physics, we developed a method to remove indirect associations and applied it to the largest dataset on pediatric inflammatory bowel disease. Our method corrected the inflation of p-values in standard association tests and showed that only a small subset of associations is directly linked to the disease. Direct associations had a much higher accuracy in separating cases from controls and pointed to immunomodulation, butyrate production, and the brain-gut axis as important factors in the inflammatory bowel disease.Comment: 4 main text figures, 15 supplementary figures (i.e appendix) and 6 supplementary tables. Overall 49 pages including reference

Towards Informed Exploration for Deep Reinforcement Learning

In this thesis, we discuss various techniques for improving exploration for deep reinforcement learning. We begin with a brief review of reinforcement learning (RL) and the fundamental v.s. exploitation trade-off. Then we review how deep RL has improved upon classical and summarize six categories of the latest exploration methods for deep RL, in the order increasing usage of prior information. We then explore representative works in three categories discuss their strengths and weaknesses. The first category, represented by Soft Q-learning, uses regularization to encourage exploration. The second category, represented by count-based via hashing, maps states to hash codes for counting and assigns higher exploration to less-encountered states. The third category utilizes hierarchy and is represented by modular architecture for RL agents to play StarCraft II. Finally, we conclude that exploration by prior knowledge is a promising research direction and suggest topics of potentially impact

Periodic behaviour of coronal mass ejections, eruptive events, and solar activity proxies during solar cycles 23 and 24

We report on the parallel analysis of the periodic behaviour of coronal mass ejections (CMEs) based on 21 years [1996 -- 2016] of observations with the SOHO/LASCO--C2 coronagraph, solar flares, prominences, and several proxies of solar activity. We consider values of the rates globally and whenever possible, distinguish solar hemispheres and solar cycles 23 and 24. Periodicities are investigated using both frequency (periodogram) and time-frequency (wavelet) analysis. We find that these different processes, in addition to following the $\approx$11-year Solar Cycle, exhibit diverse statistically significant oscillations with properties common to all solar, coronal, and heliospheric processes: variable periodicity, intermittence, asymmetric development in the northern and southern solar hemispheres, and largest amplitudes during the maximum phase of solar cycles, being more pronounced during solar cycle 23 than the weaker cycle 24. However, our analysis reveals an extremely complex and diverse situation. For instance, there exists very limited commonality for periods of less than one year. The few exceptions are the periods of 3.1--3.2 months found in the global occurrence rates of CMEs and in the sunspot area (SSA) and those of 5.9--6.1 months found in the northern hemisphere. Mid-range periods of $\approx$1 and $\approx$2 years are more wide spread among the studied processes, but exhibit a very distinct behaviour with the first one being present only in the northern hemisphere and the second one only in the southern hemisphere. These periodic behaviours likely results from the complexity of the underlying physical processes, prominently the emergence of magnetic flux.Comment: 33 pages, 15 figures, 2 table