Neural Distributed Autoassociative Memories: A Survey

Introduction. Neural network models of autoassociative, distributed memory allow storage and retrieval of many items (vectors) where the number of stored items can exceed the vector dimension (the number of neurons in the network). This opens the possibility of a sublinear time search (in the number of stored items) for approximate nearest neighbors among vectors of high dimension. The purpose of this paper is to review models of autoassociative, distributed memory that can be naturally implemented by neural networks (mainly with local learning rules and iterative dynamics based on information locally available to neurons). Scope. The survey is focused mainly on the networks of Hopfield, Willshaw and Potts, that have connections between pairs of neurons and operate on sparse binary vectors. We discuss not only autoassociative memory, but also the generalization properties of these networks. We also consider neural networks with higher-order connections and networks with a bipartite graph structure for non-binary data with linear constraints. Conclusions. In conclusion we discuss the relations to similarity search, advantages and drawbacks of these techniques, and topics for further research. An interesting and still not completely resolved question is whether neural autoassociative memories can search for approximate nearest neighbors faster than other index structures for similarity search, in particular for the case of very high dimensional vectors.Comment: 31 page

Global biogeophysical interactions between forest and climate

In two sensitivity experiments using the Earth System Model of the Max Planck Institute for Meteorology (MPI‐ESM), the vegetation cover of the ice‐free land surface has been set worldwide to either forest or grassland in order to quantify the quasi‐equilibrium response of the atmosphere and ocean components to extreme land surface boundary conditions. After 400 years of model integration, the global mean annual surface temperature increased by 0.7°K and declined by 0.6°K in the forest and grassland simulations, respectively, as compared to the control simulation. Thereafter, the geographic distribution of vegetation has been allowed to respond interactively to climate. After subsequent 500 years of interactive climate‐vegetation dynamics, both forest and grassland simulations converged to essentially the same climate state as in the control simulation. This convergence suggests an absence of multiple climate‐forest states in the current version of the MPI‐ESM

A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana

Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by the Arabidopsis genome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the MEME motif analysis algorithm. One motif (motif 4) was found in three diverse families. All proteins containing motif 4 demonstrated a degree of preference for substrates containing an ADP moiety. We conclude that HMM model-based genome scanning and MEME motif analysis, respectively, can significantly improve the identification and assignment of function of new members of this mechanistically-diverse protein superfamily

Towards a contrail climatology from NOAA—satellite images over Europe

Contrail cloudiness over Europe and the eastern part of the North Atlantic Ocean was analyzed for the two periods Sept. 1979-Dec. 1981 and Sept. 1989-Aug. 1992 by visual inspection of quicklook photographic prints of NOAA/AVHRR infrared images. The averaged contrail cover exhibits maximum values along the transat- lantic flight corridor around 50°N (of almost 2%) and over western Europe resillting in 0.5% contrail cloudiness on the average. A strong yearly cycle appears with a maximum (< 2%) in spring and summer over the Atlantic and a smaller maximum (< 1%) in winter over southwestern Europe. Comparing the two time periods of one decade separation there is a significant decrease in contrail cloudiness over west- ern Europe and a significant increase over the North Atlantic observable between March and July. Contrail cloud cover during daytime is about twice as high as dur- ing nighttime. Contrails are preferably found in larger fields of 1000 km diameter which last usually for more than one day. Causes, possible errors and consequences are discussed

Separation of atmosphere-ocean-vegetation feedbacks and synergies for mid-Holocene climate

We determine both the impact of atmosphere‐ocean and atmosphere‐vegetation feedback, and their synergy on northern latitude climate in response to the orbitally‐induced changes in mid‐Holocene insolation. For this purpose, we present results of eight simulations using the general circulation model ECHAM5‐MPIOM including the land surface scheme JSBACH with a dynamic vegetation module. The experimental set‐up allows us to apply a factor‐separation technique to isolate the contribution of dynamic Earth system components (atmosphere, atmosphere‐ocean, atmosphere‐vegetation, atmosphere‐ocean‐vegetation) to the total climate change signal. Moreover, in order to keep the definition of seasons consistent with insolation forcing, we define the seasons on an astronomical basis. Our results reveal that north of 40°N atmosphere‐vegetation feedback (maximum in spring of 0.08°C) and synergistic effects (maximum in winter of 0.25°C) are weaker than in previous studies. The most important modification of the orbital forcing is related to the atmosphere‐ocean component (maximum in autumn of 0.78°C)

Assessment of JSBACHv4.30 as a land component of ICON-ESM-V1 in comparison to its predecessor JSBACHv3.2 of MPI-ESM1.2

We assess the land surface model JSBACHv4 (Jena Scheme for Biosphere Atmosphere Coupling in Hamburg version 4), which was recently developed at the Max Planck Institute for Meteorology as part of the effort to build the new Icosahedral Nonhydrostatic (ICON) Earth system model (ESM), ICON-ESM. We assess JSBACHv4 in simulations coupled with ICON-A, the atmosphere model of ICON-ESM, hosting JSBACHv4 as land component to provide the surface boundary conditions. The assessment is based on a comparison of simulated albedo, land surface temperature (LST), leaf area index (LAI), terrestrial water storage (TWS), fraction of absorbed photosynthetic active radiation (FAPAR), net primary production (NPP), and water use efficiency (WUE) with corresponding observational data. JSBACHv4 is the successor of JSBACHv3; therefore, another purpose of this study is to document how this step in model development has changed model biases. This is achieved by also assessing, in parallel, the results of coupled land-atmosphere simulations with the preceding model ECHAM6 hosting JSBACHv3. Large albedo biases appear in both models over ice sheets and in central Asia. The temperate to boreal warm bias observed in simulations with JSBACHv3 largely remained in JSBACHv4, despite the very good agreement with observed LST in the global mean. For the assessment of changes in land water storage, a novel procedure is suggested to compare the gravitational data from the Gravity Recovery And Climate Experiment (GRACE) satellites to simulated TWS. It turns out that the agreement of the changes in the seasonal cycle of TWS is sensitive to the representation of precipitation in the atmosphere model. The LAI is generally too high, which is partly caused by too high soil moisture and also by the parameterization of the phenology itself. The pattern of WUE is, for both models, largely as observed. In India, WUE is too high, probably because JSBACH does not incorporate irrigation in our simulations. WUE differences between the two models can be traced back to differences in precipitation patterns in the two coupled land-atmosphere simulations. For both models, most NPP biases can be associated with biases in water stress, LAI, and FAPAR. In particular, the NPP bias of the Eurasian steppes has switched from positive in JSBACHv3 to negative in JSBACHv4. This difference is mainly caused by weaker precipitation and lower FAPAR of ICON-A-JSBACHv4 in July, which is most probably caused by a feedback loop between too little soil moisture, evaporation, and clouds. While the size and patterns of biases in albedo and LST are largely similar between the two model versions, they are less well correlated for precipitation- and vegetation-related variables like FAPAR. Overall, the biases found in the different assessment variables are either already known from the previous implementation in the Max Planck Institute Earth System Model (MPI-ESM) or have changed because of the coupling with the new atmospheric component ICON-A. Accordingly, this study demonstrates the technically successful completion of the re-implementation of JSBACH into ICON-ESM-V1. As discussed, there is a good perspective on mitigating the biases by an improved representation of the processes

Global and regional effects of land-use change on climate in 21st century simulations with interactive carbon cycle

Biogeophysical (BGP) and biogeochemical (BGC) effects of land-use and land cover change (LULCC) are separated at the global and regional scales in new interactive CO2 simulations for the 21st century. Results from four earth system models (ESMs) are analyzed for the future RCP8.5 scenario from simulations with and without land-use and land cover change (LULCC), contributing to the Land-Use and Climate, IDentification of robust impacts (LUCID) project. Over the period 2006–2100, LULCC causes the atmospheric CO2 concentration to increase by 12, 22, and 66 ppm in CanESM2, MIROC-ESM, and MPI-ESM-LR, respectively. Statistically significant changes in global near-surface temperature are found in three models with a BGC-induced global mean annual warming between 0.07 and 0.23 K. BGP-induced responses are simulated by three models in areas of intense LULCC of varying sign and magnitude (between −0.47 and 0.10 K). Modifications of the land carbon pool by LULCC are disentangled in accordance with processes that can lead to increases and decreases in this carbon pool. Global land carbon losses due to LULCC are simulated by all models: 218, 57, 35 and 34 Gt C by MPI-ESM-LR, MIROC-ESM, IPSL-CM5A-LR and CanESM2, respectively. On the contrary, the CO2-fertilization effect caused by elevated atmospheric CO2 concentrations due to LULCC leads to a land carbon gain of 39 Gt C in MPI-ESM-LR and is almost negligible in the other models. A substantial part of the spread in models' responses to LULCC is attributed to the differences in implementation of LULCC (e.g., whether pastures or crops are simulated explicitly) and the simulation of specific processes. Simple idealized experiments with clear protocols for implementing LULCC in ESMs are needed to increase the understanding of model responses and the statistical significance of results, especially when analyzing the regional-scale impacts of LULCC

Representation of natural and anthropogenic land cover change in MPI-ESM

The purpose of this paper is to give a rather comprehensive description of the models for natural and anthropogenically driven changes in biogeography as implemented in the land component JSBACH of the Max Planck Institute Earth system model (MPI-ESM). The model for natural land cover change (DYNVEG) features two types of competition: between the classes of grasses and woody types (trees, shrubs) controlled by disturbances (fire, windthrow) and within those vegetation classes between different plant functional types based on relative net primary productivity advantages. As part of this model, the distribution of land unhospitable to vegetation (hot and cold deserts) is determined dynamically from plant productivity under the prevailing climate conditions. The model for anthropogenic land cover change implements the land use transition approach by Hurtt et al. (2006). Our implementation is based on the assumption that historically pastures have been preferentially established on former grasslands (“pasture rule”). We demonstrate that due to the pasture rule, deforestation reduces global forest area between 1850 and 2005 by 15% less than without. Because of the pasture rule the land cover distribution depends on the full history of land use transitions. This has implications for the dynamics of natural land cover change because assumptions must be made on how agriculturalists react to a changing natural vegetation in their environment. A separate model representing this process has been developed so that natural and anthropogenic land cover change can be simulated consistently. Certain aspects of our model implementation are illustrated by selected results from the recent CMIP5 simulations