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1. On Kernel Method–Based Connectionist Models and Supervised Deep Learning Without Backpropagation

   https://doi.org/10.1162/neco_a_01250  

   Duan, Shiyu ; Yu, Shujian ; Chen, Yunmei ; Principe, Jose ( January 2020 , Neural computation)

   We propose a novel family of connectionist models based on kernel machines and consider the problem of learning layer by layer a compositional hypothesis class (i.e., a feedforward, multilayer architecture) in a supervised setting. In terms of the models, we present a principled method to “kernelize” (partly or completely) any neural network (NN). With this method, we obtain a counterpart of any given NN that is powered by kernel machines instead of neurons. In terms of learning, when learning a feedforward deep architecture in a supervised setting, one needs to train all the components simultaneously using backpropagation (BP) since there are no explicit targets for the hidden layers (Rumelhart, Hinton, & Williams, 1986). We consider without loss of generality the two-layer case and present a general framework that explicitly characterizes a target for the hidden layer that is optimal for minimizing the objective function of the network. This characterization then makes possible a purely greedy training scheme that learns one layer at a time, starting from the input layer. We provide instantiations of the abstract framework under certain architectures and objective functions. Based on these instantiations, we present a layer-wise training algorithm for an l-layer feedforward network for classification, wheremore »l≥2 can be arbitrary. This algorithm can be given an intuitive geometric interpretation that makes the learning dynamics transparent. Empirical results are provided to complement our theory. We show that the kernelized networks, trained layer-wise, compare favorably with classical kernel machines as well as other connectionist models trained by BP. We also visualize the inner workings of the greedy kernelized models to validate our claim on the transparency of the layer-wise algorithm.« less
2. (Digital Presentation) Investigation of Top Electrodes Impact on Performance of Transparent Amorphous Indium Gallium Zinc Oxide (a-InGaZnO) Based Resistive Random Access Memory

   https://doi.org/10.1149/MA2022-01191075mtgabs  

   Qin, Fei ; Lee, Sunghwan ( July 2022 , ECS Meeting Abstracts)

   The traditional von Neumann architecture limits the increase in computing efficiency and results in massive power consumption in modern computers due to the separation of storage and processing units. The novel neuromorphic computation system, an in-memory computing architecture with low power consumption, is aimed to break the bottleneck and meet the needs of the next generation of artificial intelligence (AI) systems. Thus, it is urgent to find a memory technology to implement the neuromorphic computing nanosystem. Nowadays, the silicon-based flash memory dominates non-volatile memory market, however, it is facing challenging issues to achieve the requirements of future data storage device development due to the drawbacks, such as scaling issue, relatively slow operation speed, and high voltage for program/erase operations. The emerging resistive random-access memory (RRAM) has prompted extensive research as its simple two-terminal structure, including top electrode (TE) layer, bottom electrode (BE) layer, and an intermediate resistive switching (RS) layer. It can utilize a temporary and reversible dielectric breakdown to cause the RS phenomenon between the high resistance state (HRS) and the low resistance state (LRS). RRAM is expected to outperform conventional memory device with the advantages, notably its low-voltage operation, short programming time, great cyclic stability, and good scalability.more »Among the materials for RS layer, indium gallium zinc oxide (IGZO) has shown attractive prospects in abundance and high atomic diffusion property of oxygen atoms, transparency. Additionally, its electrical properties can be easily modulated by controlling the stoichiometric ratio of indium and gallium as well as oxygen potential in the sputter gas. Moreover, since the IGZO can be applied to both the thin-film transistor (TFT) channel and RS layer, it has a great potential for fully integrated transparent electronics application. In this work, we proposed amorphous transparent IGZO-based RRAMs and investigated switching behaviors of the memory cells prepared with different top electrodes. First, ITO was choosing to serve as both TE and BE to achieve high transmittance. A multi-target magnetron sputtering system was employed to deposit all three layers (TE, RS, BE layers) on glass substrate. I-V characteristics were evaluated by a semiconductor parameter analyzer, and the bipolar RS feature of our RRAM devices was demonstrated by typical butterfly curves. The optical transmission analysis was carried out via a UV-Vis spectrometer and the average transmittance was around 80% out of entire devices in the visible-light wavelength range, implying high transparency. We adjusted the oxygen partial pressure during the sputtering of IGZO to optimize the property because the oxygen vacancy concentration governs the RS performance. Electrode selection is crucial and can impact the performance of the whole device. Thus, Cu TE was chosen for our second type of device because the diffusion of Cu ions can be beneficial for the formation of the conductive filament (CF). A ~5 nm SiO 2 barrier layer was employed between TE and RS layers to confine the diffusion of Cu into the RS layer. At the same time, this SiO 2 inserting layer can provide an additional interfacial series resistance in the device to lower the off current, consequently, improve the on/off ratio and whole performance. Finally, an oxygen affinity metal Ti was selected as the TE for our third type of device because the concentration of the oxygen atoms can be shifted towards the Ti electrode, which provides an oxygengettering activity near the Ti metal. This process may in turn lead to the formation of a sub-stoichiometric region in the neighboring oxide that is believed to be the origin of better performance. In conclusion, the transparent amorphous IGZO-based RRAMs were established. To tune the property of RS layer, the sputtering conditions of RS were varied. To investigate the influence of TE selections on switching performance of RRAMs, we integrated a set of TE materials, and a barrier layer on IGZO-based RRAM and compared the switch characteristics. Our encouraging results clearly demonstrate that IGZO is a promising material in RRAM applications and breaking the bottleneck of current memory technologies.« less
3. Florida mangrove saltmarsh reference surface soils

   https://doi.org/10.6073/pasta/0e08cbe07c84488cb7b9dd16669946d0  

   Lewis, David Bruce ( January 2021 )

   Abstract

   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.
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4. MAGIC: Multitask Automated Generation of Inter-modal CT Perfusion Maps via Generative Adversarial Network

   Fullerton, Garrett ; Kato, Simon ; Fang, Ruogu ( October 2021 , Biomedical Engineering Society Annual Meeting)

   Introduction: Computed tomography perfusion (CTP) imaging requires injection of an intravenous contrast agent and increased exposure to ionizing radiation. This process can be lengthy, costly, and potentially dangerous to patients, especially in emergency settings. We propose MAGIC, a multitask, generative adversarial network-based deep learning model to synthesize an entire CTP series from only a non-contrasted CT (NCCT) input. Materials and Methods: NCCT and CTP series were retrospectively retrieved from 493 patients at UF Health with IRB approval. The data were deidentified and all images were resized to 256x256 pixels. The collected perfusion data were analyzed using the RapidAI CT Perfusion analysis software (iSchemaView, Inc. CA) to generate each CTP map. For each subject, 10 CTP slices were selected. Each slice was paired with one NCCT slice at the same location and two NCCT slices at a predefined vertical offset, resulting in 4.3K CTP images and 12.9K NCCT images used for training. The incorporation of a spatial offset into the NCCT input allows MAGIC to more accurately synthesize cerebral perfusive structures, increasing the quality of the generated images. The studies included a variety of indications, including healthy tissue, mild infarction, and severe infarction. The proposed MAGIC model incorporates a novel multitaskmore »architecture, allowing for the simultaneous synthesis of four CTP modalities: mean transit time (MTT), cerebral blood flow (CBF), cerebral blood volume (CBV), and time to peak (TTP). We propose a novel Physicians-in-the-loop module in the model's architecture, acting as a tunable layer that allows physicians to manually adjust the amount of anatomic detail present in the synthesized CTP series. Additionally, we propose two novel loss terms: multi-modal connectivity loss and extrema loss. The multi-modal connectivity loss leverages the multi-task nature to assert that the mathematical relationship between MTT, CBF, and CBV is satisfied. The extrema loss aids in learning regions of elevated and decreased activity in each modality, allowing for MAGIC to accurately learn the characteristics of diagnostic regions of interest. Corresponding NCCT and CTP slices were paired along the vertical axis. The model was trained for 100 epochs on a NVIDIA TITAN X GPU. Results and Discussion: The MAGIC model’s performance was evaluated on a sample of 40 patients from the UF Health dataset. Across all CTP modalities, MAGIC was able to accurately produce images with high structural agreement between the entire synthesized and clinical perfusion images (SSIMmean=0.801 , UQImean=0.926). MAGIC was able to synthesize CTP images to accurately characterize cerebral circulatory structures and identify regions of infarct tissue, as shown in Figure 1. A blind binary evaluation was conducted to assess the presence of cerebral infarction in both the synthesized and clinical perfusion images, resulting in the synthesized images correctly predicting the presence of cerebral infarction with 87.5% accuracy. Conclusions: We proposed a MAGIC model whose novel deep learning structures and loss terms enable high-quality synthesis of CTP maps and characterization of circulatory structures solely from NCCT images, potentially eliminating the requirement for the injection of an intravenous contrast agent and elevated radiation exposure during perfusion imaging. This makes MAGIC a beneficial tool in a clinical scenario increasing the overall safety, accessibility, and efficiency of cerebral perfusion and facilitating better patient outcomes. Acknowledgements: This work was partially supported by the National Science Foundation, IIS-1908299 III: Small: Modeling Multi-Level Connectivity of Brain Dynamics + REU Supplement, to the University of Florida.« less
5. Willump: A Statistically-Aware End-to-end Optimizer for Machine Learning Inference

   Kraft, Peter ; Kang, Daniel ; Narayanan, Deepak ; Palkar, Shoumik ; Bailis, Peter ; and Zaharia, Matei. ( April 2020 , MLSys 2020)

   Systems for ML inference are widely deployed today, but they typically optimize ML inference workloads using techniques designed for conventional data serving workloads and miss critical opportunities to leverage the statistical nature of ML. In this paper, we present WILLUMP, an optimizer for ML inference that introduces two statistically-motivated optimizations targeting ML applications whose performance bottleneck is feature computation. First, WILLUMP automatically cascades feature computation for classification queries: WILLUMP classifies most data inputs using only high-value, low-cost features selected through empirical observations of ML model performance, improving query performance by up to 5× without statistically significant accuracy loss. Second, WILLUMP accurately approximates ML top-K queries, discarding low-scoring inputs with an automatically constructed approximate model and then ranking the remainder with a more powerful model, improving query performance by up to 10× with minimal accuracy loss. WILLUMP automatically tunes these optimizations’ parameters to maximize query performance while meeting an accuracy target. Moreover, WILLUMP complements these statistical optimizations with compiler optimizations to automatically generate fast inference code for ML applications. We show that WILLUMP improves the end-to-end performance of real-world ML inference pipelines curated from major data science competitions by up to 16× without statistically significant loss of accuracy.