Site description. This data package consists of data obtained from sampling surface soil (the 0-7.6 cm depth profile) in black mangrove (Avicennia germinans) dominated forest and black needlerush (Juncus roemerianus) saltmarsh along the Gulf of Mexico coastline in peninsular west-central Florida, USA. This location has a subtropical climate with mean daily temperatures ranging from 15.4 °C in January to 27.8 °C in August, and annual precipitation of 1336 mm. Precipitation falls as rain primarily between June and September. Tides are semi-diurnal, with 0.57 m median amplitudes during the year preceding sampling (U.S. NOAA National Ocean Service, Clearwater Beach, Florida, station 8726724). Sea-level rise is 4.0 ± 0.6 mm per year (1973-2020 trend, mean ± 95 % confidence interval, NOAA NOS Clearwater Beach station). The A. germinans mangrove zone is either adjacent to water or fringed on the seaward side by a narrow band of red mangrove (Rhizophora mangle). A near-monoculture of J. roemerianus is often adjacent to and immediately landward of the A. germinans zone. The transition from the mangrove to the J. roemerianus zone is variable in our study area. An abrupt edge between closed-canopy mangrove and J. roemerianus monoculture may extend for up to several hundred meters in some locations, while other stretches of ecotone present a gradual transition where smaller, widely spaced trees are interspersed into the herbaceous marsh. Juncus roemerianus then extends landward to a high marsh patchwork of succulent halophytes (including Salicornia bigellovi, Sesuvium sp., and Batis maritima), scattered dwarf mangrove, and salt pans, followed in turn by upland vegetation that includes Pinus sp. and Serenoa repens. Field design and sample collection. We established three study sites spaced at approximately 5 km intervals along the western coastline of the central Florida peninsula. The sites consisted of the Salt Springs (28.3298°, -82.7274°), Energy Marine Center (28.2903°, -82.7278°), and Green Key (28.2530°, -82.7496°) sites on the Gulf of Mexico coastline in Pasco County, Florida, USA. At each site, we established three plot pairs, each consisting of one saltmarsh plot and one mangrove plot. Plots were 50 m^2 in size. Plots pairs within a site were separated by 230-1070 m, and the mangrove and saltmarsh plots composing a pair were 70-170 m apart. All plot pairs consisted of directly adjacent patches of mangrove forest and J. roemerianus saltmarsh, with the mangrove forests exhibiting a closed canopy and a tree architecture (height 4-6 m, crown width 1.5-3 m). Mangrove plots were located at approximately the midpoint between the seaward edge (water-mangrove interface) and landward edge (mangrove-marsh interface) of the mangrove zone. Saltmarsh plots were located 20-25 m away from any mangrove trees and into the J. roemerianus zone (i.e., landward from the mangrove-marsh interface). Plot pairs were coarsely similar in geomorphic setting, as all were located on the Gulf of Mexico coastline, rather than within major sheltering formations like Tampa Bay, and all plot pairs fit the tide-dominated domain of the Woodroffe classification (Woodroffe, 2002, "Coasts: Form, Process and Evolution", Cambridge University Press), given their conspicuous semi-diurnal tides. There was nevertheless some geomorphic variation, as some plot pairs were directly open to the Gulf of Mexico while others sat behind keys and spits or along small tidal creeks. Our use of a plot-pair approach is intended to control for this geomorphic variation. Plot center elevations (cm above mean sea level, NAVD 88) were estimated by overlaying the plot locations determined with a global positioning system (Garmin GPS 60, Olathe, KS, USA) on a LiDAR-derived bare-earth digital elevation model (Dewberry, Inc., 2019). The digital elevation model had a vertical accuracy of ± 10 cm (95 % CI) and a horizontal accuracy of ± 116 cm (95 % CI). Soil samples were collected via coring at low tide in June 2011. From each plot, we collected a composite soil sample consisting of three discrete 5.1 cm diameter soil cores taken at equidistant points to 7.6 cm depth. Cores were taken by tapping a sleeve into the soil until its top was flush with the soil surface, sliding a hand under the core, and lifting it up. Cores were then capped and transferred on ice to our laboratory at the University of South Florida (Tampa, Florida, USA), where they were combined in plastic zipper bags, and homogenized by hand into plot-level composite samples on the day they were collected. A damp soil subsample was immediately taken from each composite sample to initiate 1 y incubations for determination of active C and N (see below). The remainder of each composite sample was then placed in a drying oven (60 °C) for 1 week with frequent mixing of the soil to prevent aggregation and liberate water. Organic wetland soils are sometimes dried at 70 °C, however high drying temperatures can volatilize non-water liquids and oxidize and decompose organic matter, so 50 °C is also a common drying temperature for organic soils (Gardner 1986, "Methods of Soil Analysis: Part 1", Soil Science Society of America); we accordingly chose 60 °C as a compromise between sufficient water removal and avoidance of non-water mass loss. Bulk density was determined as soil dry mass per core volume (adding back the dry mass equivalent of the damp subsample removed prior to drying). Dried subsamples were obtained for determination of soil organic matter (SOM), mineral texture composition, and extractable and total carbon (C) and nitrogen (N) within the following week. Sample analyses. A dried subsample was apportioned from each composite sample to determine SOM as mass loss on ignition at 550 °C for 4 h. After organic matter was removed from soil via ignition, mineral particle size composition was determined using a combination of wet sieving and density separation in 49 mM (3 %) sodium hexametaphosphate ((NaPO_3)_6) following procedures in Kettler et al. (2001, Soil Science Society of America Journal 65, 849-852). The percentage of dry soil mass composed of silt and clay particles (hereafter, fines) was calculated as the mass lost from dispersed mineral soil after sieving (0.053 mm mesh sieve). Fines could have been slightly underestimated if any clay particles were burned off during the preceding ignition of soil. An additional subsample was taken from each composite sample to determine extractable N and organic C concentrations via 0.5 M potassium sulfate (K_2SO_4) extractions. We combined soil and extractant (ratio of 1 g dry soil:5 mL extractant) in plastic bottles, reciprocally shook the slurry for 1 h at 120 rpm, and then gravity filtered it through Fisher G6 (1.6 μm pore size) glass fiber filters, followed by colorimetric detection of nitrite (NO_2^-) + nitrate (NO_3^-) and ammonium (NH_4^+) in the filtrate (Hood Nowotny et al., 2010,Soil Science Society of America Journal 74, 1018-1027) using a microplate spectrophotometer (Biotek Epoch, Winooski, VT, USA). Filtrate was also analyzed for dissolved organic C (referred to hereafter as extractable organic C) and total dissolved N via combustion and oxidation followed by detection of the evolved CO_2 and N oxide gases on a Formacs HT TOC/TN analyzer (Skalar, Breda, The Netherlands). Extractable organic N was then computed as total dissolved N in filtrate minus extractable mineral N (itself the sum of extractable NH_4-N and NO_2-N + NO_3-N). We determined soil total C and N from dried, milled subsamples subjected to elemental analysis (ECS 4010, Costech, Inc., Valencia, CA, USA) at the University of South Florida Stable Isotope Laboratory. Median concentration of inorganic C in unvegetated surface soil at our sites is 0.5 % of soil mass (Anderson, 2019, Univ. of South Florida M.S. thesis via methods in Wang et al., 2011, Environmental Monitoring and Assessment 174, 241-257). Inorganic C concentrations are likely even lower in our samples from under vegetation, where organic matter would dilute the contribution of inorganic C to soil mass. Nevertheless, the presence of a small inorganic C pool in our soils may be counted in the total C values we report. Extractable organic C is necessarily of organic C origin given the method (sparging with HCl) used in detection. Active C and N represent the fractions of organic C and N that are mineralizable by soil microorganisms under aerobic conditions in long-term soil incubations. To quantify active C and N, 60 g of field-moist soil were apportioned from each composite sample, placed in a filtration apparatus, and incubated in the dark at 25 °C and field capacity moisture for 365 d (as in Lewis et al., 2014, Ecosphere 5, art59). Moisture levels were maintained by frequently weighing incubated soil and wetting them up to target mass. Daily CO_2 flux was quantified on 29 occasions at 0.5-3 week intervals during the incubation period (with shorter intervals earlier in the incubation), and these per day flux rates were integrated over the 365 d period to compute an estimate of active C. Observations of per day flux were made by sealing samples overnight in airtight chambers fitted with septa and quantifying headspace CO_2 accumulation by injecting headspace samples (obtained through the septa via needle and syringe) into an infrared gas analyzer (PP Systems EGM 4, Amesbury, MA, USA). To estimate active N, each incubated sample was leached with a C and N free, 35 psu solution containing micronutrients (Nadelhoffer, 1990, Soil Science Society of America Journal 54, 411-415) on 19 occasions at increasing 1-6 week intervals during the 365 d incubation, and then extracted in 0.5 M K_2SO_4 at the end of the incubation in order to remove any residual mineral N. Active N was then quantified as the total mass of mineral N leached and extracted. Mineral N in leached and extracted solutions was detected as NH_4-N and NO_2-N + NO_3-N via colorimetry as above. This incubation technique precludes new C and N inputs and persistently leaches mineral N, forcing microorganisms to meet demand by mineralizing existing pools, and thereby directly assays the potential activity of soil organic C and N pools present at the time of soil sampling. Because this analysis commences with disrupting soil physical structure, it is biased toward higher estimates of active fractions. Calculations. Non-mobile C and N fractions were computed as total C and N concentrations minus the extractable and active fractions of each element. This data package reports surface-soil constituents (moisture, fines, SOM, and C and N pools and fractions) in both gravimetric units (mass constituent / mass soil) and areal units (mass constituent / soil surface area integrated through 7.6 cm soil depth, the depth of sampling). Areal concentrations were computed as X × D × 7.6, where X is the gravimetric concentration of a soil constituent, D is soil bulk density (g dry soil / cm^3), and 7.6 is the sampling depth in cm.
more »
« less
Coresets for Classification - Simplified and Strengthened
We give relative error coresets for training linear classifiers with a broad class of loss functions, including the logistic loss and hinge loss. Our construction achieves $(1\pm \epsilon)$ relative error with $\tilde O(d \cdot \mu_y(X)^2/\epsilon^2)$ points, where $\mu_y(X)$ is a natural complexity measure of the data matrix $X \in \mathbb{R}^{n \times d}$ and label vector $y \in \{-1,1\}^n$, introduced in Munteanu et al. 2018. Our result is based on subsampling data points with probabilities proportional to their \textit{$\ell_1$ Lewis weights}. It significantly improves on existing theoretical bounds and performs well in practice, outperforming uniform subsampling along with other importance sampling methods. Our sampling distribution does not depend on the labels, so can be used for active learning. It also does not depend on the specific loss function, so a single coreset can be used in multiple training scenarios.
more »
« less
- Award ID(s):
- 2046235
- NSF-PAR ID:
- 10326700
- Date Published:
- Journal Name:
- Advances in neural information processing systems
- ISSN:
- 1049-5258
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
more » « less
Abstract We study the problem of estimating a $k$-sparse signal ${\boldsymbol \beta }_{0}\in{\mathbb{R}}^{p}$ from a set of noisy observations $\mathbf{y}\in{\mathbb{R}}^{n}$ under the model $\mathbf{y}=\mathbf{X}{\boldsymbol \beta }+w$, where $\mathbf{X}\in{\mathbb{R}}^{n\times p}$ is the measurement matrix the row of which is drawn from distribution $N(0,{\boldsymbol \varSigma })$. We consider the class of $L_{q}$-regularized least squares (LQLS) given by the formulation $\hat{{\boldsymbol \beta }}(\lambda )=\text{argmin}_{{\boldsymbol \beta }\in{\mathbb{R}}^{p}}\frac{1}{2}\|\mathbf{y}-\mathbf{X}{\boldsymbol \beta }\|^{2}_{2}+\lambda \|{\boldsymbol \beta }\|_{q}^{q}$, where $\|\cdot \|_{q}$ $(0\le q\le 2)$ denotes the $L_{q}$-norm. In the setting $p,n,k\rightarrow \infty $ with fixed $k/p=\epsilon $ and $n/p=\delta $, we derive the asymptotic risk of $\hat{{\boldsymbol \beta }}(\lambda )$ for arbitrary covariance matrix ${\boldsymbol \varSigma }$ that generalizes the existing results for standard Gaussian design, i.e. $X_{ij}\overset{i.i.d}{\sim }N(0,1)$. The results were derived from the non-rigorous replica method. We perform a higher-order analysis for LQLS in the small-error regime in which the first dominant term can be used to determine the phase transition behavior of LQLS. Our results show that the first dominant term does not depend on the covariance structure of ${\boldsymbol \varSigma }$ in the cases $0\le q\lt 1$ and $1\lt q\le 2,$ which indicates that the correlations among predictors only affect the phase transition curve in the case $q=1$ a.k.a. LASSO. To study the influence of the covariance structure of ${\boldsymbol \varSigma }$ on the performance of LQLS in the cases $0\le q\lt 1$ and $1\lt q\le 2$, we derive the explicit formulas for the second dominant term in the expansion of the asymptotic risk in terms of small error. Extensive computational experiments confirm that our analytical predictions are consistent with numerical results.
-
Abstract Kernelized Gram matrix $W$ constructed from data points $\{x_i\}_{i=1}^N$ as $W_{ij}= k_0( \frac{ \| x_i - x_j \|^2} {\sigma ^2} ) $ is widely used in graph-based geometric data analysis and unsupervised learning. An important question is how to choose the kernel bandwidth $\sigma $, and a common practice called self-tuned kernel adaptively sets a $\sigma _i$ at each point $x_i$ by the $k$-nearest neighbor (kNN) distance. When $x_i$s are sampled from a $d$-dimensional manifold embedded in a possibly high-dimensional space, unlike with fixed-bandwidth kernels, theoretical results of graph Laplacian convergence with self-tuned kernels have been incomplete. This paper proves the convergence of graph Laplacian operator $L_N$ to manifold (weighted-)Laplacian for a new family of kNN self-tuned kernels $W^{(\alpha )}_{ij} = k_0( \frac{ \| x_i - x_j \|^2}{ \epsilon \hat{\rho }(x_i) \hat{\rho }(x_j)})/\hat{\rho }(x_i)^\alpha \hat{\rho }(x_j)^\alpha $, where $\hat{\rho }$ is the estimated bandwidth function by kNN and the limiting operator is also parametrized by $\alpha $. When $\alpha = 1$, the limiting operator is the weighted manifold Laplacian $\varDelta _p$. Specifically, we prove the point-wise convergence of $L_N f $ and convergence of the graph Dirichlet form with rates. Our analysis is based on first establishing a $C^0$ consistency for $\hat{\rho }$ which bounds the relative estimation error $|\hat{\rho } - \bar{\rho }|/\bar{\rho }$ uniformly with high probability, where $\bar{\rho } = p^{-1/d}$ and $p$ is the data density function. Our theoretical results reveal the advantage of the self-tuned kernel over the fixed-bandwidth kernel via smaller variance error in low-density regions. In the algorithm, no prior knowledge of $d$ or data density is needed. The theoretical results are supported by numerical experiments on simulated data and hand-written digit image data.more » « less
-
We consider the problem of designing sublinear time algorithms for estimating the cost of minimum] metric traveling salesman (TSP) tour. Specifically, given access to a n × n distance matrix D that specifies pairwise distances between n points, the goal is to estimate the TSP cost by performing only sublinear (in the size of D) queries. For the closely related problem of estimating the weight of a metric minimum spanning tree (MST), it is known that for any epsilon > 0, there exists an O^~(n/epsilon^O(1))-time algorithm that returns a (1+epsilon)-approximate estimate of the MST cost. This result immediately implies an O^~(n/epsilon^O(1)) time algorithm to estimate the TSP cost to within a (2 + epsilon) factor for any epsilon > 0. However, no o(n^2)-time algorithms are known to approximate metric TSP to a factor that is strictly better than 2. On the other hand, there were also no known barriers that rule out existence of (1 + epsilon)-approximate estimation algorithms for metric TSP with O^~ (n) time for any fixed epsilon > 0. In this paper, we make progress on both algorithms and lower bounds for estimating metric TSP cost. On the algorithmic side, we first consider the graphic TSP problem where the metric D corresponds to shortest path distances in a connected unweighted undirected graph. We show that there exists an O^~(n) time algorithm that estimates the cost of graphic TSP to within a factor of (2 − epsilon_0) for some epsilon_0 > 0. This is the first sublinear cost estimation algorithm for graphic TSP that achieves an approximation factor less than 2. We also consider another well-studied special case of metric TSP, namely, (1, 2)-TSP where all distances are either 1 or 2, and give an O^~(n ^ 1.5) time algorithm to estimate optimal cost to within a factor of 1.625. Our estimation algorithms for graphic TSP as well as for (1, 2)-TSP naturally lend themselves to O^~(n) space streaming algorithms that give an 11/6-approximation for graphic TSP and a 1.625-approximation for (1, 2)-TSP. These results motivate the natural question if analogously to metric MST, for any epsilon > 0, (1 + epsilon)-approximate estimates can be obtained for graphic TSP and (1, 2)-TSP using O^~ (n) queries. We answer this question in the negative – there exists an epsilon_0 > 0, such that any algorithm that estimates the cost of graphic TSP ((1, 2)-TSP) to within a (1 + epsilon_0)-factor, necessarily requires (n^2) queries. This lower bound result highlights a sharp separation between the metric MST and metric TSP problems. Similarly to many classical approximation algorithms for TSP, our sublinear time estimation algorithms utilize subroutines for estimating the size of a maximum matching in the underlying graph. We show that this is not merely an artifact of our approach, and that for any epsilon > 0, any algorithm that estimates the cost of graphic TSP or (1, 2)-TSP to within a (1 + epsilon)-factor, can also be used to estimate the size of a maximum matching in a bipartite graph to within an epsilon n additive error. This connection allows us to translate known lower bounds for matching size estimation in various models to similar lower bounds for metric TSP cost estimation.more » « less
-
We study the $\ell_p$ regression problem, which requires finding $\mathbf{x}\in\mathbb R^{d}$ that minimizes $\|\mathbf{A}\mathbf{x}-\mathbf{b}\|_p$ for a matrix $\mathbf{A}\in\mathbb R^{n \times d}$ and response vector $\mathbf{b}\in\mathbb R^{n}$. There has been recent interest in developing subsampling methods for this problem that can outperform standard techniques when $n$ is very large. However, all known subsampling approaches have run time that depends exponentially on $p$, typically, $d^{\mathcal{O}(p)}$, which can be prohibitively expensive. We improve on this work by showing that for a large class of common \emph{structured matrices}, such as combinations of low-rank matrices, sparse matrices, and Vandermonde matrices, there are subsampling based methods for $\ell_p$ regression that depend polynomially on $p$. For example, we give an algorithm for $\ell_p$ regression on Vandermonde matrices that runs in time $\mathcal{O}(n\log^3 n+(dp^2)^{0.5+\omega}\cdot\text{polylog}\,n)$, where $\omega$ is the exponent of matrix multiplication. The polynomial dependence on $p$ crucially allows our algorithms to extend naturally to efficient algorithms for $\ell_\infty$ regression, via approximation of $\ell_\infty$ by $\ell_{\mathcal{O}(\log n)}$. Of practical interest, we also develop a new subsampling algorithm for $\ell_p$ regression for arbitrary matrices, which is simpler than previous approaches for $p \ge 4$.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- The DOI is not currently available.
