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    California wildfire spread derived using VIIRS satellite observations and an object-based tracking system

    OverviewIn this study, we used VIIRS active fire detections to track the dynamic evolution of all fires in California from 2012 to 2020 (Fig. 1). We developed an approach that has the following steps. First, after reading the satellite fire pixel data at each 12-hour time step, the new fire pixels are aggregated into multiple clusters using the fire pixel locations and an automatic clustering algorithm. These clusters are then spatially compared to existing fire objects. If a cluster is not close to any existing active fire object, we use all fire pixels within the cluster to form a new fire object. If a cluster is located near an existing fire object which is still active, we view the cluster as an extension of the existing fire. In this case, we append all pixels within the cluster to the corresponding existing fire object, allowing the existing object to grow. When a fire expands and gets close enough (within a pre-defined distance threshold) to an existing active fire object, we merge the two objects. For each time step (12 hours in this case for the two overpasses), we derive or update a suite of attributes and status indicators associated with each fire event, including pixel-level attributes of fire and surface properties, vector geometries related to the fire shape, and meta-attributes characterizing the entire fire object.Data inputSatellite remote sensing instruments provide active fire detections with accurate geographical location and broad spatial coverage. The primary data for this fire tracking system are active fire locations and the fire radiative power (FRP) recorded by the VIIRS instrument aboard the Suomi National Polar-orbiting Partnership (Suomi-NPP) satellite24. VIIRS observes Earth’s surface twice each day in low and mid latitude regions, with local overpass times of approximately 1:30 am and 1:30 pm. Compared to its predecessor, the MODIS sensors on the Terra and Aqua satellites, VIIRS has a higher spatial resolution and can detect smaller and cooler fires24. Also, the VIIRS instrument provides a more consistent pixel area across the image swath25, resulting in more accurate estimates of active fire location. Therefore, compared with MODIS, the VIIRS active fire products can be used to map fire event progression with higher accuracy21. Two streams of VIIRS active fire data are operationally produced using a contextual fire detection algorithm24, drawing upon VIIRS moderate resolution band (M-band) and imaging band (I-band) reflectance and radiance data layers. In this fire tracking system, we used the Suomi-NPP VIIRS I-band fire location data product (VNP14IMGML, Collection 1 Version 4) that contains the centre location, FRP, scan angle, and other attribute fields associated with each pixel. The I-band fire detection product has a 375-m spatial resolution at nadir (the sub-satellite point) and an average resolution across the full swath of about 470 m. Theoretical estimates of fire detection efficiency for the VIIRS sensor indicate that during the day, VIIRS can detect 700 K fires with 50% probability that have a size of about 200 m2 (a 15 m × 15 m fire area)24. During night, the detection efficiency increases, and VIIRS can detect 700 K fires as small as 40 m2. From a fire spread tracking perspective, these detection efficiencies imply that in many instances, the area of a fire pixel that is covered with flaming fire combustion is several orders of magnitude smaller than the overall pixel size. The VNP14IMGML data, available from 2012 onwards, were downloaded from the University of Maryland VIIRS Active Fire website (https://viirsfire.geog.umd.edu/).Land cover data are an additional input in the system required to classify different fire types and determine the spatial connectivity threshold. Here we use the U.S. National Land Cover Database (NLCD 2016)26 that is available from the Multi-Resolution Land Characteristics (MRLC) Consortium website (https://www.mrlc.gov/national-land-cover-database-nlcd-2016). We aggregated the original 30-m data to match the spatial resolution of VIIRS active fire data, and merged the original 16 classes into several groups: ‘Water’, ‘Urban’, ‘Barren’, ‘Forest’, ‘Shrub’, ‘Grassland’, and ‘Agriculture’. We used the 1000-hour dead fuel moisture from the high-resolution (4 km) gridMET product27 for the purpose of separating wildfires and management fires. This gridMET dataset was computed from 7–day average conditions composed of day length, hours of rain, and daily temperature and humidity ranges. Regularly updated gridMET data are available from the Climatology Lab website (http://www.climatologylab.org/gridmet.html).Other ancillary and validation datasets used in this study included a shapefile of California borders and fire perimeters from the California Forestry and Fire Protection’s Fire and Resource Assessment Program (FRAP) dataset (https://frap.fire.ca.gov/mapping/maps/).Fire object hierarchyFire detections from VIIRS are dynamically tracked within the framework of a three-level object hierarchy (Fig. 1). The lowest level is the fire pixel object, which includes the geographical location (latitude and longitude), the FRP value, and the origin (first assigned fire object id). The second level is the fire object, which includes all attributes associated with each individual fire event at a particular time step (Table 2). Each fire object includes one or more fire pixel objects, a unique identification number (id), and a set of attributes associated with the whole fire. Two types of fire attributes are derived and recorded for each fire object. The first type encompasses temporal (e.g., ignition time, duration) and spatial (e.g., centroid, ignition location) characteristics of the object as well as general properties (e.g., size, type, active status). The second type is the geometric information related to the fire object, including the fire perimeter, the active fire front line, and the newly detected fire pixel locations (stored as vectors). All fire objects in the State of California are combined to form an allfires object, to characterize the whole-region fire situation at a specific time step. The allfires object comprises a list of fire objects, and also contains meta information representing the statistics of all fires and the records describing fire evolution. A full list of the attributes associated with the pixel object, the fire object, and the allfires object is presented in Table 2.Table 2 List of main attributes associated with pixel, fire and allfires objects.Full size tableFire event trackingThe fire records (locations and FRPs) from the monthly VIIRS active fire location products (VNP14IMGML) are read into the system at each half-daily time step (roughly 1:30 am and 1:30 pm local time). We apply spatial and temporal filters to the data to extract active fire pixels recorded in California during each 12-hour time interval. We also apply quality flag filters (thermal anomaly type of ‘0: presumed vegetation fire’ in VNP14IMGML)) to ensure the use of only pixels likely associated with vegetation fires. The fire location and FRP values are used to create fire pixel objects. To speed up the calculation, the newly detected active fire pixels after filtering are first aggregated to specific clusters using the distances between them and an automatic clustering algorithm. In this initial aggregation algorithm, a ball tree28 is created to partition all newly detected active fire pixels into a nested set of hyperspheres in a 2-D space (latitude and longitude). This space partitioning data structure can be used to expedite nearest neighbours search29 and allow for quick cluster grouping. Here we refer to a cluster as a collection of pixel objects that are recorded at the same time step and are also spatially nearby. In the following steps, all pixels within a cluster are considered as a whole for fire merging and creation.We define an extended area for every existing fire object as the fire vector perimeter (see the section of Calculating and recording fire attributes for detail) plus a radial buffer that depends on the fire type property of the object. The buffer is set to 5 km for forest fires and 1 km for other fire types (shrub, crop, urban), considering that the fire spread rate can differ across biomes13. We then evaluate the spatial distance between the perimeters of a newly classified cluster and all existing active fire objects (a fire object keeps an active status if one or more active fire pixels associated with it are detected during the past 5 days), and calculate the shortest distance. If the shortest distance is smaller than the buffer of the associated existing active fire (i.e., new cluster overlaps with the extended area of an existing fire object), we assume all fire pixels in the new cluster are associated with the growth of the existing fire object at the current time step (Fig. 2). The existing fire object is updated by appending all fire pixel objects within the new cluster. If a newly classified cluster does not overlap with the extended area of any existing active fire object, we assume this is a new fire. A new fire object (by assigning a new fire id) is created using all fire pixel objects in the cluster.With the addition of new fire pixels, an existing fire object may expand and touch the extended area of another existing active fire object. If this happens, we assume that these two existing fire objects merge into a single object at this time step. All fire pixels in the fire object with a higher id number (a later start date, termed as the ‘source fire’) are appended to the fire object with lower id number (earlier start date, termed as the ‘target fire’) in this case. We record the id of the target fire in a list of fire mergers, and update all attributes associated with this fire (Fig. 3). In order to avoid double counting, the source fire object (with all pixels being transferred to the target fire object) is flagged as invalid, and is excluded from statistical analysis of fire events.Fig. 3The time series of growth for the SCU Lightning Complex fire (2020). Panel (b) shows the fire size of the SCU fire (total area within the fire object perimeter) at half-daily time steps. A fraction of the fire growth (shown in orange) was due to the addition of newly detected fire pixels. Panel (a) shows the number of new fire pixels (associated with the SCU fire object) detected at each time step. The other part of the fire growth (shown in red) was due to the merging with existing fire objects. Panel (c) shows the number of fire pixels in the existing objects that were merged to the SCU fire object.Full size imageCalculating and recording fire attributesOther than individual fire pixels contained in a fire object, several core attributes (properties and geometries) are also dynamically updated at each time step and are used for fire tracking and characterization.Important time-related attributes include the fire ignition time (the time step at which the first fire pixel within the fire object was detected), the fire end time (the latest time step with an active fire observation), and the fire duration (the time difference between the ignition time and end time). If a fire object does not have new active fire pixels appended during 5 consecutive days (i.e., the fire end time is more than 5 days before the present time step), its status is set to inactive. Once inactive, a fire object is no longer evaluated for use in future clustering (i.e., new active fire detections later will form new fire objects, even if they are spatially close to the inactive fire object).Each fire object is assigned to a specific fire type. The fire type is identified using the major land cover type within the fire perimeter (Table 3). In an initial analysis, we found that prescribed fires, on average, have higher coarse fuel moisture levels than wildfires. Therefore, we also record the 1000-hour fuel moisture (fm1000) from the gridMET dataset27 for each fire object (corresponding to the ignition time step) and use this value to divide forest and shrub fires further to wildfire and prescribed types.Table 3 Classification of fire types based on dominant land cover type (from the US National Land Cover Database) within each fire perimeter and the 1000-hr fuel moisture (FM-1000, from gridMET dataset) at the time of ignition.Full size tableAn essential step in this object-based fire tracking system is to determine the vector shape of the fire perimeter. In this system, we use an alpha shape30 algorithm to derive bounding polygons containing fire pixels in a fire object. For an alpha shape, the radius of the disks forming the curves in the polygon is determined by the alpha parameter α. Compared with the commonly used convex hull, the alpha shape hull is able to capture the irregular shapes around the fire perimeter more accurately22.To identify the optimal values for the α parameter, we performed the following analysis. First, we derived the final fire perimeters for all large fires that occurred in California during the 2018 wildfire season using a set of α values ranging from 500 m to 10 km and compared the results with more refined fire perimeters from the Fire and Resource Assessment Program (FRAP) dataset (Fig. 4). Large magnitude α values tended to overestimate the total burned area, while small α values often fragmented a large fire event. We found that a value of α = 1 km was optimal in terms of balancing the ability of the hull to catch the boundary shape and to keep the integrity of a fire object. For each time step, we applied the alpha shape algorithm to all fire pixel locations associated with a fire object since the time of ignition. This processing step resulted in a concave hull with the shape of polygon or multipolygon. To account for the pixel size, we expanded the concave hull to the fire perimeter using a buffer size equal to half of the VIIRS nadir cross-track pixel width (187.5 m). The alpha shape algorithm does not work when the total number of fire pixels (npix) is less than 4. If npix equals 3, we used a convex hull algorithm and the same 187.5 m buffer to determine a polygon perimeter. If npix is 1 or 2, circles centered on the fire pixel location with radius of 187.5 m were used.Fig. 4Optimization of the alpha shape parameter (α). For all large fires (final size  > 4 km2) in California during 2018, fire perimeters were estimated using VIIRS active fires and different alpha parameters. By comparing (a) the burned area (BA) and (b) the number of fire objects with the FRAP data, an optimal alpha parameter of 1 km was identified for use in this study (shown in red). The vertical bars and lines show the mean and 1-std variability from all fires. The dashed blue lines indicate the ideal values when compared to FRAP. Panels (c)–(h) show the fire perimeters derived using different alpha shape parameters for two sample fires in 2018. The shapes with pink color are final FEDS fire perimeters derived from VIIRS active fires using the alpha shape algorithm. The blue shapes represent the corresponding fire perimeters from the FRAP dataset. Overlap between FRAP and FEDS is shown in purple.Full size imageWe also calculate the active front line for each fire object at each time step. The active fire front consists of the segments of the fire perimeter that are actively burning and releasing energy and emissions. The position of the active fire line is critical in evaluating the fire risk, estimating the fire emissions, and predicting fire spread. We derive the active portion of the fire perimeter as segments that are within a 500 m radius of newly detected fire pixel locations. We found that this threshold allowed for a continuous projection of the active fire front in rapidly expanding areas of large wildfires during the 2018 fire season; this threshold may be optimized in future work to maximize performance metrics for fire model forecasts. The resulting active line for each fire at each time step has the shape of a linestring (object representing a sequence of points and the line segments connecting them), a multi-linestring (a collection of multiple linestrings), or a linear ring (closed linestring). Figure 5 shows an example map of the fire perimeters and active fire front lines on September 8 during the 2020 wildfire season.Fig. 5An example map of fire perimeters and fire active fronts in California. The map was created using the fire event data suite (FEDS) as of the Suomi-NPP afternoon overpass (~1:30 pm local time) of Sep 8, 2020. The background is the Aqua MODIS Corrected Reflectance Imagery (true color) recorded at the same day (provided by the NASA Global Imagery Browse Services). The active front line of a fire is shown in yellow, active fire areas are shown in red, and the area of inactive (extinguished) fires are shown in dark red.Full size imageAdditional fire properties, such as the fire area and active fire line length, are also derived using these geometries of the fire object (see Table 2). Note this list can be easily expanded to include more user-defined properties with the help of the fire object core vector data.The allfires object contains a list of all existing fire objects at a time step. This object also records the ids of fire objects that have been modified (including fires newly formed, fires that expanded with new pixel additions, fires with pixels addition due to merging, and fires that just became invalid) at the current time step.Creating the fire event data suite (FEDS)By tracking the spatiotemporal evolution of all fire objects in California, we derived a complete dataset of fire events for each calendar year (Jan 1 am – Dec 31 pm) during the Suomi-NPP VIIRS era (2012–2020). The dataset contains four products that represent the fire information in California at multiple spatial scales and from different perspectives (Fig. 1 and Table 4), ranging from the most detailed and memory-intensive data format (Pickle) to the most high-level format (CSV).Table 4 Data structure of the FEDS.Full size tableThe first product is the direct serialization result of the allfires object at each time step (twice per day). The product is stored as a Pickle file31 which allows for analysis of the complex allfires object structure (including all attributes associated with all fire objects it contains). This file also serves as the restart file for continued fire tracking at any time step, which is essential for the operational mode using the near-real-time fire data. By restoring an exact copy of the previously pickled allfires object, any attribute in the allfires object can be deserialized from the saved files. The Pickle file is the most basic data product in the dataset, and is created at each half-day time step.The second product (Snapshot) represents a more accessible and self-explanatory variant of the Pickle serialization product. In this product, we tabulated important diagnostic attributes for each fire and saved them in GeoPackage32 data files. Each GeoPackage file includes three data layers: one contains the properties and the fire perimeter geometry, another contains the active fire line geometry, and a third contains the new fire pixel location geometry. This product, created at a half-daily time step, allows for a more straightforward interpretation of regional fire status at a particular time step. We also created a GeoPackage file that summarizes the final fire perimeters and attributes for all fires during the whole study period (2012–2020).The third product (Largefire) focuses on the temporal evolution of individual large fires with an area greater than 4 km2. At each time step, the time series of properties and geometries (fire perimeter, active fire line, and new fire pixel locations) for each of the large fires are extracted and saved to GeoPackage files. This product facilitates the visualization and analysis for an individual targeted fire (Fig. 6) and is particularly useful in the near-real-time evaluation, forecasting, and policy making.Fig. 6The spatiotemporal evolution of the Creek fire (2020). Contours and dots reflect the fire perimeters and newly detected fire pixels at each 12-hour time step. Data for the period of Sep 5 am–Nov 6 am, 2020 are shown.Full size imageThe fourth product (Summary), which is stored as NetCDF and CSV files and created at the end of a fire season, records the all-year time series of fire statistics (including major fire attributes such as number, size, duration, fire line length, etc.) over the whole State of California. This product provides a feasible regional summary of the temporal evolution of fires.Potential for near-real-time (NRT) fire event trackingWhile the main objective of this paper is to apply the object-based fire tracking system to historical VIIRS fire detections and create a retrospective multi-year FEDS, we note that this system has the potential to be used for tracking fire events in near-real-time, providing rich and valuable information for fire management and short-term risk assessment. We have experimented with the use of this system for NRT fire event tracking in California using the daily NRT Suomi-NPP VIIRS active fire detection product (VNP14IMGTDL, collection 6) as the main data source. The VNP14IMGTDL product is routinely produced and is publicly available at the NASA Fire Information for Resource Management System (FIRMS). Since the NRT product undergoes less rigorous quality assurance, we use only fires with ‘nominal’ or ‘high’ confidence levels from the NRT product for fire tracking. Some active fire detections from the NRT data are potentially associated with static non-vegetation fires (e.g., fires from gas flaring in oil and gas or landfill industries or false detections due to reflection from solar panels) and are not the main interest for vegetation fire studies. To avoid the unnecessary computation associated with these static fires, we record and evaluate the fire pixel density for each fire object at each time step. When a small fire ( 20 per km2), it is considered to be a static fire and subsequently labelled as invalid.Similar to the retrospective FEDS, we use the active fire detections to create an object serialization product, a regional snapshot GIS product, and a time series product of large fire evolution twice daily. This experimental NRT data will be available upon publication through a university hosted server. More

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    Visible-NIR hyperspectral classification of grass based on multivariate smooth mapping and extreme active learning approach

    Study areaGrassland herbage samples are from Shaerqin base, institute of grassland research of CAAS (Chinese Academy of Agricultural Sciences). We obtained the permission of the institution to take HSI of the grassland sample. Our work did not cause damage to grassland. Researcher Weihong Yan of the institute provided us with relevant information about grassland. The land use type in the study area is mainly grassland, which is composed of forage species, most of which are representative species of typical grassland. We take this area as an example to conduct research on grass classification. By enriching the relevant recognition technology, it can also be used as a reference for the pastures of other grasslands. The grass species Grass1 for the experiment is shown in Table 1. The official introduction of plant materials is detailed in the flora of China15.Table 1 Samples information for Grass1 dataset.Full size tableThe field hyperspectral platformWe assemble a system for collecting HSI in the field: HyperSpec©PTU-D48E HSI instrument, high-precision scanning PTZ, tripod, data analysis software Hyperspec, etc. The light source is natural light. The imaging instrument is in line scanning mode. Table 2 shows the technical parameters.Table 2 Technical parameters of hyperspectral instrument.Full size tableData collectionIn July 2021, the data was collected during the lush grass growth period. Collect data from 11:00 a.m. to 2:00 p.m. every day. At this time, it is sunny, cloudless and the wind force does not exceed level 2. So as to ensure the consistency of the acquisition time line and avoid the influence of different degrees of light on the reflectivity as far as possible. The measuring points are arranged facing the sun and the opposite direction of the shadow. We collect data from different angles of the grassland, which is based on the growth of various types of forages, and selects relatively concentrated places within the study area. Each shot is a single category of grass. The image resolution is 1166 × 1004 pixels (Fig. 1). The imaging spectrometer is fixed with scanning head when shooting. Data acquisition and transmission are executed on Hyperspec software. Then save it as a BIL file. The ENVI5.3 software was used to extract the forage spectrum to establish the dataset Grass1. Well balanced regions with a clear image, uniform spectral distribution are selected for further segmentation. The average value of spectral reflectance of grass pixels was taken as the reflectance spectrum of a single type of grass.Figure 1True color map of grass samples.Full size imageMethodologyIn Fig. 2, we present the framework of visible-NIR hyperspectral classification of grass based on multivariate smooth mapping and extreme active learning (MSM–EAL). Specifically, we first introduce the proposed MSM algorithm for global enhanced spectral reconstruction, which utilizes smooth manifold projection technology to alleviate the problems of difficult feature selection and redundant data. Then, the EAL framework is proposed to address the matter of hyperspectral labeled samples and spectral classification. In the following, each step of this method will be presented in detail.Figure 2Proposed MSM–EAL framework for grass HSI classification.Full size imageThe proposed MSM algorithmIn the process of field HSI acquisition, on the one hand, the surface distribution of grass is uneven and the plant height is different, causing certain scattering effect and coverage spectrum change. On the other hand, HSI is easy to be disturbed by external natural factors such as light, wind and shadow, resulting in a certain degree of distortion. Multiplicative scatter correction (MSC) is a scattering correction effect, which helps to eliminate the scattering effect caused by the above reasons and enhance the spectral variability. The moving window smooth spectral matrix (Nirmaf) belongs to the smooth effect, which improve the signal-to-noise ratio of the spectrum and reduce the influence of random noise16,17. Preprocessing methods are different and related to each other. We design an enhanced preprocessing multivariate smooth (MS) method that fusing MSC and smooth Nirmaf to target grass spectral signal features. In the follow-up, a model will be established to verify the validity of MS.Most of the high-dimensional spatial data have the characteristics of being embedded in a manifold body, so the manifold learning isometric feature mapping (Isomap) based on spectral theory is adopted. Isomap preserves the global geometric features of the initial data and extracts features by reconstructing the underlying smooth manifold of HSI. It is nonlinear dimensionality reduction based on linear and multidimensional scaling transformation18. Isomap has been applied in image and HSI classification19,20, but there is no report on visible-NIR hyperspectral classification of grass.In view of the above, we proposed the multivariate smooth mapping (MSM) spectral reconstruction algorithm, which can be represented as follows:$$ MSM_{z} { } = { }frac{{left( {P_{j} – b_{j} } right)left( {2n + 1} right) + n_{j} cdot mathop sum nolimits_{j = – n}^{n} C_{j} P_{k + j} }}{{n_{j} left( {2n + 1} right)}} + V_{Z} F_{Z}^{frac{1}{2}} { } $$
    (1)
    where Pj, bj, and Cj represent the raw reflectance value of spectrum j, baseline shift amount, and weight factor, respectively, k and nj represent the polynomial degree and offset, respectively. MSMz is the feature cube reconstructed to Z dimension from the spectrum calculated by 2n + 1 moving window width, V eigenvector matrix and F eigenvalue matrix.In Isomap equidistant mapping, the shortest path of edge Pi Pj needs to be solved, and the representation matrix is:$$ D_{G} = [d_{G}^{2} (P_{i} ,P_{j} )]_{i,j = 1}^{n} $$
    (2)
    where d (Pi, Pj) is the weight of the edge Pi Pj calculated from the neighborhood graph G and its side Pi Pj.The proposed EAL frameworkLabeling hyperspectral samples is expensive in terms of time and cost, at the same time, the lower spatial resolution and more bands increase the difficulty of labeling. Active learning (AL) provides an efficient labeling strategy, which only needs to label a relatively small number of samples to learn a more accurate model21. The pool-based AL selects the most informative samples according to the query strategy for limited labeling through iteration, so as to facilitate model improvement. Commonly used query strategies are uncertainty criteria, such as least confidence22, the bayesian active learning disagreement (BALD), the entropy sampling23, etc.Due to there is still an over-fitting problem, different strategies such as hybrid prediction and regularization need to be used for non-recursive datasets24. The research25 proposed that extreme gradient boosting algorithm (XGBoost) based on gradient boosting. As a classification method, XGBoost has been successfully applied in Kaggle competition and other fields. Its most important feature for visible-NIR hyperspectral classification is that can easily and directly classify according to features, and the physical interpretation of features can help understand the electronic nature behind spectral classification. XGBoost is a machine learning algorithm based tree structure that integrates multiple weak classifiers to achieve flexible and high-precision classification. It is an upgraded version of gradient boosting decision tree. The optimization process of XGBoost entailed: (1) Expanding the objective function to the second order, and finds a new objective function for the new base model to improve the calculation accuracy. (2) L2 regularization term is added to the loss function to prevent over-fitting. (3) Using blocks storage structure realize automatic parallel computing26,27. The algorithm steps are as follows:The objective function:$$ Lleft( Phi right) = mathop sum limits_{i} lleft( {y^{i} ,widehat{{y^{i} }}} right) + mathop sum limits_{k} Omega left( {f_{k} } right) $$
    (3)
    In formula (3), the first and second terms are the loss function term and the regularization term, respectively. Where,$$ Omega left( {f_{k} } right) =upgamma {text{T}} + frac{1}{2}lambda left| w right|^{2} $$
    (4)
    γ and λ are regularization parameters which are used to adjust complexity of the tree.Next, second derivative Taylor expansion of the objective function. Where (g_{i}) and (h_{i}) are the first derivative and second derivative, respectively.$$ L^{left( t right)} = mathop sum limits_{i = 1}^{n} lleft( {y_{i} ,widehat{{y_{i}^{t – 1} }} + f_{t} left( {x_{i} } right)} right) + Omega left( {f_{t} } right) $$
    (5)
    $$ g_{i} = partial_{{hat{y}_{i} (t – 1)}} lleft( {y_{i} ,widehat{{y_{i}^{t – 1} }}} right) $$
    (6)
    $$ h_{i} = partial_{{widehat{{y_{i} }}(t – 1)}}^{2} lleft( {y_{i} ,widehat{{y_{i}^{t – 1} }}} right) $$
    (7)
    $$ {text{L}}^{left( t right)} approx mathop sum limits_{i = 1}^{n} left[ {lleft( {y_{i} ,widehat{{y_{i}^{t – 1} }}} right) + g_{i} f_{i} left( {x_{i} } right) + frac{1}{2}h_{i} f_{t}^{2} left( {x_{i} } right)} right] + Omega left( {f_{t} } right) $$
    (8)
    Final objective function:$$ {hat{text{L}}}^{ i} left( q right) = – frac{1}{2}mathop sum limits_{j = 1}^{T} frac{{(mathop sum nolimits_{{i in I_{j} }} g_{i} )^{2} }}{{mathop sum nolimits_{{i in I_{j} }} h_{i} + lambda }} + gamma T $$
    (9)
    Equation (9) can be used as the fraction of tree cotyledons, and the tree structure is directly proportional to the fraction. If the result after splitting is less than the maximum value of the given parameter, the cotyledon depth stops growing24,28.AL solves the problems of limited number and high cost of grass hyperspectral labeling samples. The default model of traditional AL is logistic regression, which is mostly studied on the ideal public dataset. However, the actual data has more uncertain noise, which still poses a certain challenge to AL. Consequently, we propose the extreme active learning (EAL) framework to minimize the classification cost of visible-NIR hyperspectral. The framework replaces the logistic regression model with XGBoost. Taking advantage of AL, XGBoost can improve performance with less training marker samples. By jointing of XGBoost and AL, EAL provides significantly better results than AL in field Grassl dataset recognition. Additionally, based on the characteristics of XGBoost, EAL more intuitively enhances the physical essence behind spectral classification than AL. Algorithm 1 summarizes the workflow of EAL framework.Random forest (RF) and decision tree (DT) were used to compare with EAL. RF and DT are frequently used in the field of grassland remote sensing9,29. Furthermore, RF, DT and XGBoost have the same point is that are learning algorithms based on tree structure. DT determines the direction by judging the conditions of the decision node12. RF is an integrated learning of multiple decision trees30. More

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    Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships

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    Whales from space dataset, an annotated satellite image dataset of whales for training machine learning models

    Very high-resolution (VHR) satellite imagery allows us to survey regularly remote and large areas of the ocean, difficult to access by boats or planes. The interest in using VHR satellite imagery for the study of great whales (including sperm whales and baleen whales) has grown in the past years1,2,3,4,5 since Abileah6 and Fretwell et al.7 showed its potential. This growing interest may be linked to the improvement in the spatial resolution of satellite imagery, which increased in 2014 from 46 cm to 31 cm. This upgrade enhanced the confidence in the detection of whales in satellite imagery, as more details could be seen, such as whale-defining features (e.g. flukes).Detecting whales in the imagery is either conducted manually1,4,5,7, or automatically2,3. A downside of the manual approach is that it is time-demanding, with manual counter often having to view hundred and sometimes thousands of square kilometres of open ocean. The development of automated approaches to detect whales by satellite would not only speed up this application, but also reduce the possibility of missing whales due to observer fatigue and standardize the procedure. Various automated approaches exist from pixel-based to artificial intelligence. Machine learning, an application of artificial intelligence, seems to be the most appropriate automated method to detect whales efficiently in satellite imagery2,3,8,9.In machine learning an algorithm learns how to identify features by repeatedly testing different search parameters against a training dataset10,11. Concerning whales, the algorithm needs to be trained to detect the wide variety of shapes and colour characterising whales. Shapes and colour will be influenced by the type of species, the environment (e.g. various degree of turbidity), the light conditions, and the behaviours (e.g. foraging, travelling, breaching), as different behaviours will result in different postures. The larger a training dataset is, the more accurate and transferable to other satellite images the algorithm will be. At the time of writing, such a dataset does not exist or is not publicly available.Creating a large enough dataset necessary to train algorithms to detect whales in VHR satellite imagery will require the various research groups analysing VHR satellite imagery to openly share examples of whales and non-whale objects in VHR satellite imagery, which could be facilitated by uploading such data on a central open source repository, similar to the GenBank12 for DNA code or OBIS-Seamap13 for marine wildlife observations. Ideally clipped out image chips of the whale objects would be shared as tiff files, which retains most of the characteristics of the original image. However, all VHR satellites are commercially owned, except for the Cartosat-3 owned by the government of India14, which means it is not possible to publicly share image chips as tiff file. Instead, image chips could be shared in a png or jepg format, which involve loosing some spectral information. If tiff files are required, georeferenced and labelled boxes encompassing the whale objects could also be shared, including information on the satellite imagery to allow anyone to ask the commercial providers for the exact imagery.Here we present a database of whale objects found in VHR satellite imagery. It represents four different species of whales (i.e. southern right whale, Eubalaena australis; grey whale, Eschrichtius robustus; humpback whale, Megaptera novaeangliae; fin whale, Balaenoptera physalus; Fig. 1), which were manually detected in images captured by different satellites (i.e., GeoEye-1, Quickbird-2, WorldView-2, WorldView-3). We created the database by (i) first detecting whale objects manually in satellite imagery, (ii) then we classified whale objects as either “definite”, “probable” or “possible” as in Cubaynes et al.1; and (iii) finally we created georeferenced and labelled points and boxes centered around each whale object, as well as providing image chips in a png format. With this database made publicly available, we aim to initiate the creation of a central database that can be built upon.Fig. 1Database of annotated whales detected in satellite imagery covering different species and areas. Humpback whales were detected in Maui Nui, US (a); grey whales in Laguna San Ignacio, Mexico (b); fin whales in the Pelagos Sanctuary, France, Monaco and Italy (c); southern right whales were observed in three areas, off the Peninsula Valdes, Argentina (d); off Witsand, South Africa (e); and off the Auckland Islands, New Zealand (f). The dot size represents the number of annotated whales per location. Whale silhouettes were sourced from philopic.com (the grey and humpback whales silhouettes are from Chris Luh).Full size image More

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    A trait database and updated checklist for European subterranean spiders

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