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Multiclass Disease Classification from Microbial Whole-Community Metagenomes
2020
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
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We compared three different machine learning models: random forests, deep neural nets, and a novel graph convolutional architecture which exploits the graph structure of phylogenetic trees as its input ...
The microbiome, the community of microorganisms living within an individual, is a promising avenue for developing non-invasive methods for disease screening and diagnosis. ...
Here, we quantify the performance of three machine learning approaches to address this problem: random forests due to their popularity and ease-of-use, deep neural networks as a baseline for a deep-learning ...
pmid:31797586
pmcid:PMC7120658
fatcat:nvmoyhcn7vgxfbdb25pwohuyva
Non-linear Dimensionality Reduction on Extracellular Waveforms Reveals Physiological, Functional, and Laminar Diversity in Premotor Cortex
[article]
2021
bioRxiv
pre-print
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Using WaveMAP, we robustly establish eight waveform clusters and show that these clusters recapitulate previously identified narrow- and broad-spiking types while also revealing undocumented diversity. ...
These clusters exhibit distinct laminar distributions, characteristic firing rate patterns, and decision-related dynamics. ...
A learned manifold could be used in future experiments to 571 identify cell types in real-time without opto-tagging. ...
doi:10.1101/2021.02.07.430135
fatcat:t5d6h732rbbyxma4dkumoqiv3y
Integrating Biodiversity, Remote Sensing, and Auxiliary Information for the Study of Ecosystem Functioning and Conservation at Large Spatial Scales
[chapter]
2020
Remote Sensing of Plant Biodiversity
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Thus, the combination of RS, in-situ and other auxiliary data, provides the most powerful approach to assessing ecosystem functioning and conservation at large spatial scales. ...
However, RS data comes with limitation of their own, and despite of the many opportunities offered by RS data, certain aspects and scales of biodiversity are currently not measurable using RS technology ...
We thank Nathalie Pettorelli for useful discussions and suggestions. CW acknowledges support from the British Geological Survey. ...
doi:10.1007/978-3-030-33157-3_17
fatcat:f3qfvseedjdqhgs7xzpc3wf6u4
Inference and differential analysis of Extended Core Networks: A way to study anti-sense regulation
2016
2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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Jerry Hoogenboom, Yuanhao Guo, Fuyu Cai, and Fons Verbeek
Regular
B465 "A Modified Rough-Fuzzy Clustering Algorithm with Spatial Information for HEp-2 Cell
Image Segmentation"
Pradipta Maji and ...
Short
B268 "Robust Retinal Vessel Segmentation via Clustering-Based Patch Mapping Functions"
haiying xia, shuaifei deng, Minqi Li, and frank jiang
Session 17 Phylogeny
Invited
Talk 5
Regular ...
doi:10.1109/bibm.2016.7822532
dblp:conf/bibm/LegeayDR16
fatcat:k33tacfd25flplfykeqfwkmzg4
Image splicing detection with local illumination estimation
2015
2015 IEEE International Conference on Image Processing (ICIP)
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A brief introduction will be given to the current state-of-the-art in this area and how these ideas are motivated the point of view of geometry (manifold learning) and the discovery of underlying causal ...
74 | ICIP 2015 -Technical Program COI-P1.4 -MULTILAYER MANIFOLD AND SPARSITY CONSTRAINTED NONNEGATIVE MATRIXFACTORIZATION FOR HYPERSPECTRAL UNMIXING Shu ZHENQIU, Nanjing University of Science and Technology ...
Concluding the Show & Tell session will be a section concentrating on why the sensory gap is important to consider for practical applications, such as annotation tools, and image learning and mining systems ...
doi:10.1109/icip.2015.7351341
dblp:conf/icip/FanCF15
fatcat:7ja5gjnp5rafvedc2nman7xcru
Detection and Evaluation of Clusters within Sequential Data
[article]
2022
arXiv
pre-print
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Clustering algorithms for Block Markov Chains possess theoretical optimality guarantees and can be deployed in sparse data regimes. ...
These tools include benchmarking, spectral noise analysis and statistical model selection tools. ...
We would finally like to thank Mike van Santvoort for useful discussions while writing this paper. ...
arXiv:2210.01679v1
fatcat:jgoimy2edbb35ih4cjwjkveexy
Perceptual-cognitive universals as reflections of the world
2001
Behavioral and Brain Sciences
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fullest and simplest way when represented as points and connecting geodesic paths in the six-dimensional manifold jointly determined by the Euclidean group of three-dimensional space and the symmetry ...
with respect to the abstract spaces appropriate for the representation of biologically significant objects and their properties. (1) Positions and motions of objects conserve their shapes in the geometrically ...
leave during 2000 -2001, and to the Department of Philosophy, Monash University, for its hospitality, intellectual stimulation, and support. ...
pmid:12048942
fatcat:q7istgyd4zfo5ewh5u4susudf4
Selected abstracts of "Bioinformatics: from Algorithms to Applications 2020" conference
2020
BMC Bioinformatics
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The research was supported by the Russian Science Foundation Grant 18-11-00100 and a grant from Jet-Brains Research. ...
Acknowledgements This study was supported by the grant from the RFBR, the project № 18-05-60203_Arctica and 19-05-50107. ...
incorrectly guessed contacts for each image. ...
doi:10.1186/s12859-020-03838-2
pmid:33327929
fatcat:2t65jee32rgsnohhdwd7vbwj74
Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse
[article]
2020
biorxiv/medrxiv
pre-print
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The primary motor cortex (M1) is essential for voluntary fine motor control and is functionally conserved across mammals. ...
These findings highlight the robust molecular underpinnings of cell type diversity in M1 across mammals and point to the genes and regulatory pathways responsible for the functional identity of cell types ...
Briefly, for each cluster NS-1342 Forest produces a Random Forest (RF) model using a one vs all binary classification approach. ...
doi:10.1101/2020.03.31.016972
fatcat:yv64otyesjf33cf5q3zmb3e2oa
176 New Discoveries Regarding the Benthic Marine Algal Flora of the Sultanate of Oman
2003
Journal of Phycology
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This product is designed for use in undergraduate classes; however, our testing has shown that it provides an exciting and interactive learning experience appropriate for Grades 7 and higher. ...
Data retrieved includes JPG image, cataloged data, map regions, synonyms, and illustrated microscopic, cross section and surface view for some species. ...
For each dark bottle, chl-a, particulate carbon, phosphorus and nitrogen, trichome count and fluorescence parameters were measured daily. ...
doi:10.1111/j.0022-3646.2003.03906002_176.x
fatcat:xprvfzupgnhutejjhahvnefgyu
Abstracts from the Second Astrobiology Science Conference
2002
International Journal of Astrobiology
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Here we recommend wavelength ranges and spectral features for these missions. We assess known spectroscopic features of Earth, Venus and Mars in the context of putative extrasolar analogs. ...
For the mid-IR and the visible to near-IR, the preferred wavelength ranges are 7-25 microns and 0n5 to about 1n1 microns, respectively. ...
The reflective imaging slicers enable us to collect spectral information from the Mars surface in 3-D form -two spatial dimensions and one spectral dimension. ...
doi:10.1017/s147355040200112x
fatcat:csnt46qubrce5gwltddgsexgk4
A Model of Selective Advantage for the Efficient Inference of Cancer Clonal Evolution
[article]
2016
arXiv
pre-print
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The motivations are manifold: (i) growing NGS and single cell data from cancer patients, (ii) need for novel Data Science and Machine Learning algorithms to infer models of cancer progression, and (iii ...
The approach derives its power from several fields including algorithms in machine learning, theory of causality and cancer biology. ...
Many common approaches cluster expression profiles [119] by relying on non-negative matrix factorization techniques [59] or earlier approaches such as k-means, Gaussians mixtures or hierarchical/spectral ...
arXiv:1602.07614v1
fatcat:3mdqck6ztnav7eea2xz4hl5xue
Program of the 89th Annual Meeting of the American Association of Physical Anthropologists
2020
American Journal of Physical Anthropology
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We used data derived from the 16-year dataset of forest phenology and orangutan diet at Tuanan in Central Kalimantan, Indonesia. ...
neuro bromas), macrocephaly, short stature, heat intolerance, learning disabilities (involving speech, spatial reasoning, executive functioning, and musicality), and resistance to obesity, diabetes, alcoholism ...
This research was supported by National Science Foundation (BCS-1341174), Animal Behavior Society, The Society for Integrative and Comparative Biology, Tinker Foundation, and The Ohio State University ...
doi:10.1002/ajpa.24023
pmid:32058585
fatcat:gulriykcvbgdbikcya2xflv73a
Modeling tropical montane forest biodiversity – The potential of multispectral remote sensing
2019
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The robustness of multispectral image textures as an important driver of taxonomic and functional diversity should therefore be further investigated. ...
For this purpose (i) different taxonomic groups and diversity measures (e.g. alpha/beta diversity) were investigated, (ii) a comparison to topographic metrics was made, and (iii) sensor data with high ...
Special thanks go to Roman Link, Greta Weitmann, Stefanie Lorenz, Philipp Obst and Nixon Cumbicus for field assistance (forest inventories and leaf trait sampling). ...
doi:10.17192/z2019.0058
fatcat:hwbjolkpz5gb7jdtfcjeiskr4a
Management and Administration
[chapter]
2012
Advances in Police Theory and Practice
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Planned research and new directions We are currently working on automating high content imaging. ...
Acquisition can be guided by image analysis: during a low resolution scan of the 96 well plate positions of interesting cells can be identified for high content imaging. ...
On A1R resonant mode and simultaneous photactivation and imaging as well as spectral detector are available. ...
doi:10.1201/b12530-8
fatcat:mkscpdo24nbznpk3xdhp4i6pdm
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