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Seed classification with random forest models

Premise: To improve forest conservation monitoring, we developed a protocol to automatically count and identify the seeds of plant species with minimal resource requirements, making the process more efficient and less dependent on human operators. Methods and Results: Seeds from six North American conifer tree species were separated from leaf litter and imaged on a flatbed scanner. In the most successful species-classification approach, an ImageJ macro automatically extracted measurements for random forest classification in the software R. The method allows for good classification accuracy, and the same process can be used to train the model on other species. Conclusions: This protocol is an adaptable tool for efficient and consistent identification of seed species or potentially other objects. Automated seed classification is efficient and inexpensive, making it a practical solution that enhances the feasibility of large-scale monitoring projects in conservation biology.

59 BASIC BIOLOGICAL SCIENCES

Protein Kinase Classification with 2866 Hidden Markov Models and One Support Vector Machine

The main application considered in this paper is predicting true kinases from randomly permuted kinases that share the same length and amino acid distributions as the true kinases. Numerous methods already exist for this classification task, such as HMMs, motif-matchers, and sequence comparison algorithms. We build on some of these efforts by creating a vector from the output of thousands of structurally based HMMs, created offline with Pfam-A seed alignments using SAM-T99, which then must be combined into an overall classification for the protein. Then we use a Support Vector Machine for classifying this large ensemble Pfam-Vector, with a polynomial and chisquared kernel. In particular, the chi-squared kernel SVM performs better than the HMMs and better than the BLAST pairwise comparisons, when predicting true from false kinases in some respects, but no one algorithm is best for all purposes or in all instances so we consider the particular strengths and weaknesses of each.

Weber, Ryan

User oriented ERTS-1 images

Photographic reproduction of ERTS-1 images are capable of displaying only a portion of the total information available from the multispectral scanner. Methods are being developed to generate ERTS-1 images oriented towards special users such as agriculturists, foresters, and hydrologists by applying image enhancement techniques and interactive statistical classification schemes. Spatial boundaries and linear features can be emphasized and delineated using simple filters. Linear and nonlinear transformations can be applied to the spectral data to emphasize certain ground information. An automatic classification scheme was developed to identify particular ground cover classes such as fallow, grain, rape seed or various vegetation covers. The scheme applies the maximum likelihood decision rule to the spectral information and classifies the ERTS-1 image on a pixel by pixel basis. Preliminary results indicate that the classifier has limited success in distinguishing crops, but is well adapted for identifying different types of vegetation.

Shlien, S.

Multiple Spectral-Spatial Classification Approach for Hyperspectral Data

A .new multiple classifier approach for spectral-spatial classification of hyperspectral images is proposed. Several classifiers are used independently to classify an image. For every pixel, if all the classifiers have assigned this pixel to the same class, the pixel is kept as a marker, i.e., a seed of the spatial region, with the corresponding class label. We propose to use spectral-spatial classifiers at the preliminary step of the marker selection procedure, each of them combining the results of a pixel-wise classification and a segmentation map. Different segmentation methods based on dissimilar principles lead to different classification results. Furthermore, a minimum spanning forest is built, where each tree is rooted on a classification -driven marker and forms a region in the spectral -spatial classification: map. Experimental results are presented for two hyperspectral airborne images. The proposed method significantly improves classification accuracies, when compared to previously proposed classification techniques.

Tarabalka, Yuliya

Seeding materials: Health and safety considerations

The choice of a proper seeding material for laser velocimeters must include health and safety considerations. Failure to do so can lead to catastrophic results. All materials are toxic, and laser velocimeter seeding materials are no exception. Toxicity may be considered an inherent property of a given material. The manifestation of that property or the physiological response to the material is dependent on dose and exposure conditions. An approximate physiological classification of toxicity is given in tablular form. Toxicity in some situations is not necessarily the most restrictive factor in selection of materials. It is also very important to consider how the material is used so that actual exposure to the material in a damaging form can result. For example, nickel and cadmium are both extremely toxic as systemic poisons and in the case of nickel as a carcinogen. Seeding materials are dispersed in air under conditions that favor personnel exposure. Dispersal equipment is frequently if not normally manned, and personnel are often required to make frequent adjustments to assure proper operations.

Brown, R. D.

Spectral reflectance of hydrophytes

Identification of hydrophytes will improve the delineation and classification of wetlands on remotely sensed imagery. Spectral reflectance measurements of 10 species of hydrophytes were made with an Exotech radiometer during three phenological stages, flowering and early seed, senescent, and early emergent. Reflectance data were analyzed to determine significant (P not greater than 0.5) differences between species in each of four spectral regions during each phenological stage. Eight species had significantly (P not greater than 0.05) different reflectances during the flower and early seed stage. Among the ten species only one could not be spectrally isolated during at least 1 phenological stage. The results indicate that films sensitive to both visible and infrared spectra (e.g., Ektachrome infrared) should enable recognition of different species of hydrophytes.

Best, R. G.

Collaborative Supervised Learning for Sensor Networks

Collaboration methods for distributed machine-learning algorithms involve the specification of communication protocols for the learners, which can query other learners and/or broadcast their findings preemptively. Each learner incorporates information from its neighbors into its own training set, and they are thereby able to bootstrap each other to higher performance. Each learner resides at a different node in the sensor network and makes observations (collects data) independently of the other learners. After being seeded with an initial labeled training set, each learner proceeds to learn in an iterative fashion. New data is collected and classified. The learner can then either broadcast its most confident classifications for use by other learners, or can query neighbors for their classifications of its least confident items. As such, collaborative learning combines elements of both passive (broadcast) and active (query) learning. It also uses ideas from ensemble learning to combine the multiple responses to a given query into a single useful label. This approach has been evaluated against current non-collaborative alternatives, including training a single classifier and deploying it at all nodes with no further learning possible, and permitting learners to learn from their own most confident judgments, absent interaction with their neighbors. On several data sets, it has been consistently found that active collaboration is the best strategy for a distributed learner network. The main advantages include the ability for learning to take place autonomously by collaboration rather than by requiring intervention from an oracle (usually human), and also the ability to learn in a distributed environment, permitting decisions to be made in situ and to yield faster response time.

Wagstaff, Kiri L.

Analysis of the Westland Data Set

The "Westland" set of empirical accelerometer helicopter data with seeded and labeled faults is analyzed with the aim of condition monitoring. The autoregressive (AR) coefficients from a simple linear model encapsulate a great deal of information in a relatively few measurements; and it has also been found that augmentation of these by harmonic and other parameters call improve classification significantly. Several techniques have been explored, among these restricted Coulomb energy (RCE) networks, learning vector quantization (LVQ), Gaussian mixture classifiers and decision trees. A problem with these approaches, and in common with many classification paradigms, is that augmentation of the feature dimension can degrade classification ability. Thus, we also introduce the Bayesian data reduction algorithm (BDRA), which imposes a Dirichlet prior oil training data and is thus able to quantify probability of error in all exact manner, such that features may be discarded or coarsened appropriately.

Wen, Fang

Integration of environmental and spectral data for sunflower stress determination

Stress in sunflowers was assessed in western and northwestern Minnesota. Weekly ground observations (acquired in 1980 and 1981) were analyzed in concert with large scale aerial photography and concurrent LANDSAT data. Using multidate supervised and unsupervised classification procedures, it was found that all crops grown in association with sunflowers in the study area are spectrally separable from one another. Under conditions of extreme drought, severely stressed plants were differentiable from those not severely stressed, but between-crop separation was not possible. Initial regression analyses to estimate sunflower seed yield showed a sensitivity to environmental stress during the flowering and seed development stages. One of the most important biological factors related to sunflower production in the Red River Valley area was found to be the extent and severity of insect infestations.

Lillesand, T.

Populating a Graph Database to Run a Usage-Based Discovery Tool

Most dataset discovery tools for Earth Observation data rely on descriptions and other metadata of the datasets, using keyword searches or attribute filtering to determine relevance. However, these descriptions often do not include the potential uses of the data. Thus, a user working on floods will rarely see few if any rainfall datasets show up in such a search. The Usage Based Discovery tool, on the other hand, offers usage instances to the user, either research articles or applications, along with the datasets that those usage instances used. This allows a user, particularly one new to the world of Earth Observation data, to investigate which datasets are used in similar cases. The information that powers Usage-Based Discovery is a graph database of relationships of usage to dataset and usage to topic, allowing the user to narrow their search for similar cases. In order to scale out to a graph database rich enough to provide a satisfactory user experience, we combine manual and automated processes to populate the graph. The initial content of the graph has been seeded primarily via human-aided data curation methods, using sites like Google Scholar. To scale up this effort, we’ve employed crowdsourcing. It is easy for anyone to contribute to our graph using their Open Researcher and Contributor Identifier for authorization. We’re now experimenting with Machine Learning and Natural Language Processing to help automate population of the graph, starting with the classification of research articles by topic. Finding adequate training data in the absence of a comprehensive and open research article API continues to be a significant challenge.

Vincent Inverso

Autonomous Information Unit for Fine-Grain Data Access Control and Information Protection in a Net-Centric System

As communication and networking technologies advance, networks will become highly complex and heterogeneous, interconnecting different network domains. There is a need to provide user authentication and data protection in order to further facilitate critical mission operations, especially in the tactical and mission-critical net-centric networking environment. The Autonomous Information Unit (AIU) technology was designed to provide the fine-grain data access and user control in a net-centric system-testing environment to meet these objectives. The AIU is a fundamental capability designed to enable fine-grain data access and user control in the cross-domain networking environments, where an AIU is composed of the mission data, metadata, and policy. An AIU provides a mechanism to establish trust among deployed AIUs based on recombining shared secrets, authentication and verify users with a username, X.509 certificate, enclave information, and classification level. AIU achieves data protection through (1) splitting data into multiple information pieces using the Shamir's secret sharing algorithm, (2) encrypting each individual information piece using military-grade AES-256 encryption, and (3) randomizing the position of the encrypted data based on the unbiased and memory efficient in-place Fisher-Yates shuffle method. Therefore, it becomes virtually impossible for attackers to compromise data since attackers need to obtain all distributed information as well as the encryption key and the random seeds to properly arrange the data. In addition, since policy can be associated with data in the AIU, different user access and data control strategies can be included. The AIU technology can greatly enhance information assurance and security management in the bandwidth-limited and ad hoc net-centric environments. In addition, AIU technology can be applicable to general complex network domains and applications where distributed user authentication and data protection are necessary. AIU achieves fine-grain data access and user control, reducing the security risk significantly, simplifying the complexity of various security operations, and providing the high information assurance across different network domains.

Chow, Edward T.

Predicting U 3 O 8 powder processing conditions: An AI/ML approach analyzing deep learning embeddings of SEM micrographs

High-resolution SEM images of uranium-oxide powders encode micro- and nanoscale clues to their synthesis route and calcination temperature. We trained a ResNet-50 model on 11 commercial-scale U₃O₈ classes, ammonium diuranate (ADU) or uranyl peroxide (H₂O₂) precursors calcined at temperatures ranging from 400 to 750 °C and added a 256-D projection head before the classifier to analyze the learned representation. The best of eight seeds reached 92.4 % accuracy on reserved testing data, but our focus is the structure of the embedding space rather than the accuracy and labels. We quantify class relatedness in the original 256-D space using centroid similarity and distributional distances, and we use Uniform Manifold Approximation Projection (UMAP) for visualization. ‘Unknown’ images from different preparation methods, SEM operators, and from the literature localized near the expected classes under a nearest-centroid analysis without retraining, as well as clustered in similar UMAP space. In conclusion, this embedding-centered workflow complements black-box classification by providing quantitative, similarity-based comparisons of U₃O₈ morphologies and reduces storage space by up to 98 % for image data used in millisecond vector search comparisons.

36 MATERIALS SCIENCE

PAIReD jet: A multi-pronged resonance tagging strategy across all Lorentz boosts

We propose a new approach of jet-based event reconstruction that aims to optimally exploit correlations between the products of a hadronic multi-pronged decay across all Lorentz boost regimes. The new approach utilizes clustered small-radius jets as seeds to define unconventional jets, referred to as PAIReD jets. The constituents of these jets are subsequently used as inputs to machine learning-based algorithms to identify the flavor content of the jet. We demonstrate that this approach achieves higher efficiencies in the reconstruction of signal events containing heavy-flavor jets compared to other event reconstruction strategies at all Lorentz boost regimes. Classifiers trained on PAIReD jets also have significantly better background rejections compared to those based on traditional event reconstruction approaches using small-radius jets at low Lorentz boost regimes. The combined effect of a higher signal reconstruction efficiency and better classification performance results in a two to four times stronger rejection of light-flavor jets compared to conventional strategies at low Lorentz-boosts, and rejection rates similar to classifiers based on large-radius multi-pronged jets at high Lorentz-boost regimes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS