Kernel Spectral Clustering and applications

In this chapter we review the main literature related to kernel spectral clustering (KSC), an approach to clustering cast within a kernel-based optimization setting. KSC represents a least-squares support vector machine based formulation of spectral clustering described by a weighted kernel PCA objective. Just as in the classifier case, the binary clustering model is expressed by a hyperplane in a high dimensional space induced by a kernel. In addition, the multi-way clustering can be obtained by combining a set of binary decision functions via an Error Correcting Output Codes (ECOC) encoding scheme. Because of its model-based nature, the KSC method encompasses three main steps: training, validation, testing. In the validation stage model selection is performed to obtain tuning parameters, like the number of clusters present in the data. This is a major advantage compared to classical spectral clustering where the determination of the clustering parameters is unclear and relies on heuristics. Once a KSC model is trained on a small subset of the entire data, it is able to generalize well to unseen test points. Beyond the basic formulation, sparse KSC algorithms based on the Incomplete Cholesky Decomposition (ICD) and $L_0$, $L_1, L_0 + L_1$, Group Lasso regularization are reviewed. In that respect, we show how it is possible to handle large scale data. Also, two possible ways to perform hierarchical clustering and a soft clustering method are presented. Finally, real-world applications such as image segmentation, power load time-series clustering, document clustering and big data learning are considered.Comment: chapter contribution to the book "Unsupervised Learning Algorithms

Translating tumor biology into personalized treatment planning: analytical performance characteristics of the Oncotype DX® Colon Cancer Assay

<p>Abstract</p> <p>Background</p> <p>The Onco<it>type </it>DX^®Colon Cancer Assay is a new diagnostic test for determining the likelihood of recurrence in stage II colon cancer patients after surgical resection using fixed paraffin embedded (FPE) primary colon tumor tissue. Like the Onco<it>type </it>DX Breast Cancer Assay, this is a high complexity, multi-analyte, reverse transcription (RT) polymerase chain reaction (PCR) assay that measures the expression levels of specific cancer-related genes. By capturing the biology underlying each patient's tumor, the Onco<it>type </it>DX Colon Cancer Assay provides a Recurrence Score (RS) that reflects an individualized risk of disease recurrence. Here we describe its analytical performance using pre-determined performance criteria, which is a critical component of molecular diagnostic test validation.</p> <p>Results</p> <p>All analytical measurements met pre-specified performance criteria. PCR amplification efficiency for all 12 assays was high, ranging from 96% to 107%, while linearity was demonstrated over an 11 log₂concentration range for all assays. Based on estimated components of variance for FPE RNA pools, analytical reproducibility and precision demonstrated low SDs for individual genes (0.16 to 0.32 C_Ts), gene groups (≤0.05 normalized/aggregate C_Ts) and RS (≤1.38 RS units).</p> <p>Conclusions</p> <p>Analytical performance characteristics shown here for both individual genes and gene groups in the Onco<it>type </it>DX Colon Cancer Assay demonstrate consistent translation of specific biology of individual tumors into clinically useful diagnostic information. The results of these studies illustrate how the analytical capability of the Onco<it>type </it>DX Colon Cancer Assay has enabled clinical validation of a test to determine individualized recurrence risk after colon cancer surgery.</p

Particle Fluxes and Transport Proceses Along the Continental Margins and in Deep Sea Environments.

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U-Th-Pb &#8220;multi-phase&#8221; approach to the study of crystalline basement: application to the northernmost sector of the Ivrea-Verbano Zone (Alps)

In situ U-Pb geochronology was carried out on amphibolites and siliciclastic metasediments of the Kinzigite Formation exposed in the northernmost sector of the Ivrea-Verbano Zone (Finero area). The aim is to shed light on the tectono-metamorphic evolution of this intermediate-lower crustal section and its bearing with the evolution of the southern and better known sectors of the Ivrea-Verbano Zone. Based on eld observation and petrography, a metamorphic gradient gently increasing from amphibolite to upper amphibolite facies (from SE to NW) characterizes the whole metamorphic sequence. Granulite facies conditions are reached only by the slivers (septa) of the Kinzigite Formation into the External Gabbro unit of the Finero Ma c Complex. Metapelites consist mainly of biotite, quartz, plagioclase, garnet, and brolitic to prismatic sillimanite; muscovite progressively disappears as K-feldspar appears and becomes abundant. Amphibolites are made of green-brown hornblende and plagioclase and may contain clinopyroxene de ning thin layers together with plagioclase and titanite. Both metapelites and amphibolites show mylonitic deformation which is more intense towards NW, i.e. towards the lower structural levels. The mylonitic deformation strongly affected the lower crustal metabasic rocks of External Gabbro unit (Finero Ma c Complex). Zircon, monazite and titanite U-Pb geochronology was carried out with laser ablation (LA)- ICP-MS on amphibolites, migmatitic paragneiss and septa. The multi-chronological approach allowed recognizing three discrete tectono-metamorphic events, at Permian, Triassic and Jurassic. Zircon and monazite yielded Permian ages suggesting (re)crystallization during an high temperature event characterized by both metamorphism and magmatism. Titanite dating provided Triassic and Jurassic ages, that were interpreted as U-Pb resetting ages. A Triassic perturbation of the U-Pb system was also recorded by zircon and monazite as rare domains. The tectono-metamorphic reconstruction of the evolution of the northernmost Ivrea- Verbano Zone, as revealed by the new geochronological data, is only partially in agreement with the temperature-time evolutions depicted for the southern sectors of the Ivrea-VerbanoZone. Permian ages indicating magmatism and high temperature metamorphism are common throughout the Ivrea-Verbano Zone, as well as the Jurassic ages related to local thermal pulses likely related to lithospheric thinning and associated lithospheric advection. Conversely, the occurrence of Triassic ages is peculiar of the Finero area. Two possible explanations may account for this Triassic event: Triassic ages are possibly related to the thermal effect and uid circulation during the emplacement of the External Gabbro unit; or alternatively, they are the response to the ductile deformation largely recognized in the whole area. This study is a further evidence of the necessity of approaching crystalline basement with multiple geochronometers in order to unravel the complete tectono-metamorphic evolution

The Identity of the Crackling, Luminescent Frog of Suriname (\u3cem\u3eRana typhonia\u3c/em\u3e Linnaeus, 1758) (Amphibia, Anura)

Review of the literature and recently available field notes from the collector of the type allows a reconsideration of the identity of the Linnaean name Rana typhonia. We provide evidence to demonstrate that the Linnaean species is neither a bufonid nor an Asiatic ranid, but a Neotropical hylid. Subsequently, we consider Rana typhonia as an older synonym of Rana venulosa Laurenti, 1768, redescribing its holotype under the new combination, Trachycephalus typhonius (Linnaeus, 1758)

Influence of distributary channels on sediment and organic matter supply in event-dominated coastal margins: the Po prodelta as a study case

From November 2008 through May 2009, the Po river (Italy) experienced several floods exceeding 5000 m&lt;sup&gt;3&lt;/sup&gt; s&lt;sup&gt;−1&lt;/sup&gt;. This long series of events ended with a large flood in early May 2009 (~8000 m&lt;sup&gt;3&lt;/sup&gt; s&lt;sup&gt;−1&lt;/sup&gt;). An event-response sampling was carried out in the Po prodelta in April–May 2009 to characterize the preservation of this series of floods in the sediment record and to describe the event-supply and deposition of riverborne particulate material during the May 2009 flood. The water sampling was carried out early in the event under conditions of moderate river flow (~5000 m&lt;sup&gt;3&lt;/sup&gt; s&lt;sup&gt;−1&lt;/sup&gt;) and 24 h later during the peak discharge (~8000 m&lt;sup&gt;3&lt;/sup&gt; s&lt;sup&gt;−1&lt;/sup&gt;). Sediment cores were collected in the prodelta before and after the peak flood. At each station, profiles of conductivity, transmittance, and fluorescence were acquired. Surface and bottom waters were sampled to collect sediments in suspension. In addition, a few days before the May 2009 event, suspended sediments were collected at Pontelagoscuro gauging station, ~90 km upstream from the coast. Biogeochemical compositions and sedimentological characteristics of suspended and sediment samples were investigated using bulk and biomarker analyses. Furthermore, &lt;sup&gt;7&lt;/sup&gt;Be and radiographs were used to analyze the internal stratigraphy of sediment cores. &lt;br&gt;&lt;br&gt; During moderate flow, the water column did not show evidence of plume penetration. Stations re-occupied 24 h later exhibited marked physical and biogeochemical changes during the peak flood. However, the concentration of terrestrially-derived material in surface waters was still less than expected. These results suggested that, since material enters the Adriatic as buoyancy-driven flow with a reduced transport capacity, settling and flocculation processes result in trapping a significant fraction of land-derived material in shallow sediments and/or within distributary channels. &lt;br&gt;&lt;br&gt; Although numerous discharge peaks occurred from November 2008 through April 2009 (4000–6000 m&lt;sup&gt;3&lt;/sup&gt; s&lt;sup&gt;−1&lt;/sup&gt;), sediment cores collected in late April 2009 showed lack of event-strata preservation and reduced &lt;sup&gt;7&lt;/sup&gt;Be penetrations. This suggested that only a small fraction of the sediment supply during ordinary events reaches the deepest region of the prodelta (12–20 m water depth). As a result, these event-strata have a thickness not sufficient to be preserved in the sediment record because of post-depositional processes that destroy the flood signal. &lt;br&gt;&lt;br&gt; Stations in the northern and central prodelta were re-occupied after the peak of the May 2009 flood. Based on &lt;sup&gt;7&lt;/sup&gt;Be and radiographs, we estimated event layers of 17 and 6 cm thickness, respectively. Selective trapping of coarse material occurred in the central prodelta likely because of the geomorphologic setting of the central outlet characterized by an estuary-like mouth. Despite these settling processes, lignin-based parameters indicated that the composition of the terrigenous OC was fairly homogenous throughout the network of channels and between size-fractions

Towards a Southern European Tethyan Palaeomargin provenance signature: sandstone detrital modes and detrital zircon U–Pb age distribution of the Upper Cretaceous–Paleocene Monte Bignone Sandstones (Ligurian Alps, NW Italy)

Constraining the source terranes of Alpine siliciclastic flysch sequences is crucial for building a clearer picture of the palaeogeography and geodynamic evolution of the Western Tethys in the framework of impending continental collision. This paper presents an integrated study that involves palaeocurrent dispersal analysis, sandstone petrography and detrital zircon geochronology of the Upper Cretaceous–Paleocene Monte Bignone Sandstones, a siliciclastic turbidite system deposited during the pre-collisional evolution of the Ligurian Alps. Palaeocurrent analysis illustrates an overall eastward transport of the proximal sediments in the present configuration. Considering the ca. 45°–50° counter-clockwise rotation of the Tertiary Piedmont Basin and of the Corsica–Sardinia block in the late Paleogene, this indicates the derivation of the sediments from the northern margin of the Piedmont–Ligurian Ocean. Sandstone petrography records a stratigraphic evolution from quartzose sandstones towards lithic and then to lithic sub-arkosic composition. This trend is interpreted to reflect the gradual unroofing of the provenance terrane. The lithotypes of the recycled sedimentary rock fragments and the up-section increase in dolostone and carbonate clast proportions suggest the erosion of the sedimentary cover of the southern European palaeo-margin. New geochronological data (U–Pb detrital zircon ages) correspond to the pre-Alpine stages of crustal growth recorded in the Variscan Maures-Tanneron Massif, and therewith confirm the derivation of the sediments from the passive palaeo-European margin. This conclusion highlights the importance of the lower plate in providing the source of coarse-clastic deep-water successions during pre-collisional convergent steps. Results from this multi-proxy provenance analysis contribute to better defining the detrital signatures associated to the continental micro-fragments that constituted the palaeo-European plate as it supplied deep-sea siliciclastic sediments into the Piedmont–Ligurian Ocean prior to continental collision

Early cretaceous plume–ridge interaction recorded in the band-e-zeyarat ophiolite (North Makran, Iran): New constraints from petrological, mineral chemistry, and geochronological data

The North Makran domain (southeast Iran) is part of the Makran accretionary wedge and consists of an imbricate stack of continental and Neo-Tethyan oceanic tectonic units. Among these, the Band-e-Zeyarat ophiolite consists of (from bottom to top): ultramafic cumulates, layered gabbros, isotropic gabbros, a sheeted dyke complex, and a volcanic sequence. Sheeted dykes and volcanic rocks are mainly represented by basalts and minor andesites and rhyolites showing either normal-type (N) or enriched-type (E) mid-ocean ridge basalt affinities (MORB). These conclusions are also supported by mineral chemistry data. In addition, E-MORBs can be subdivided in distinct subtypes based on slightly different but significant light rare earth elements, Th, Nb, TiO2, and Ta contents. These chemical differences point out for different partial melting conditions of their mantle sources, in terms of source composition, partial melting degrees, and melting depths. U-Pb geochronological data on zircons from intrusive rocks gave ages ranging from 122 to 129 Ma. We suggest that the Band-e-Zeyarat ophiolite represents an Early Cretaceous chemical composite oceanic crust formed in a mid-ocean ridge setting by partial melting of a depleted suboceanic mantle variably metasomatized by plume-type components. This ophiolite records, therefore, an Early Cretaceous plume–ridge interaction in the Makran Neo-Tethys