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2016


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Autofocusing-based correction of B0 fluctuation-induced ghosting

Loktyushin, A., Ehses, P., Schölkopf, B., Scheffler, K.

24th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), May 2016 (poster)

link (url) [BibTex]

2016

link (url) [BibTex]


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PGO wave-triggered functional MRI: mapping the networks underlying synaptic consolidation

Logothetis, N. K., Murayama, Y., Ramirez-Villegas, J. F., Besserve, M., Evrard, H.

47th Annual Meeting of the Society for Neuroscience (Neuroscience), 2016 (poster)

[BibTex]

[BibTex]


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Statistical source separation of rhythmic LFP patterns during sharp wave ripples in the macaque hippocampus

Ramirez-Villegas, J. F., Logothetis, N. K., Besserve, M.

47th Annual Meeting of the Society for Neuroscience (Neuroscience), 2016 (poster)

[BibTex]

[BibTex]


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Hippocampal neural events predict ongoing brain-wide BOLD activity

Besserve, M., Logothetis, N. K.

47th Annual Meeting of the Society for Neuroscience (Neuroscience), 2016 (poster)

[BibTex]

[BibTex]

2015


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Diversity of sharp wave-ripples in the CA1 of the macaque hippocampus and their brain wide signatures

Ramirez-Villegas, J. F., Logothetis, N. K., Besserve, M.

45th Annual Meeting of the Society for Neuroscience (Neuroscience 2015), October 2015 (poster)

link (url) [BibTex]

2015

link (url) [BibTex]


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Causal Inference for Empirical Time Series Based on the Postulate of Independence of Cause and Mechanism

Besserve, M.

53rd Annual Allerton Conference on Communication, Control, and Computing, September 2015 (talk)

[BibTex]

[BibTex]


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Retrospective rigid motion correction of undersampled MRI data

Loktyushin, A., Babayeva, M., Gallichan, D., Krueger, G., Scheffler, K., Kober, T.

23rd Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine, ISMRM, June 2015 (poster)

[BibTex]

[BibTex]


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Improving Quantitative Susceptibility and R2* Mapping by Applying Retrospective Motion Correction

Feng, X., Loktyushin, A., Deistung, A., Reichenbach, J. R.

23rd Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine, ISMRM, June 2015 (poster)

[BibTex]

[BibTex]


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Independence of cause and mechanism in brain networks

Besserve, M.

DALI workshop on Networks: Processes and Causality, April 2015 (talk)

[BibTex]

[BibTex]


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Increasing the sensitivity of Kepler to Earth-like exoplanets

Foreman-Mackey, D., Hogg, D., Schölkopf, B., Wang, D.

Workshop: 225th American Astronomical Society Meeting 2015 , pages: 105.01D, 2015 (poster)

Web link (url) [BibTex]

Web link (url) [BibTex]


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Information-Theoretic Implications of Classical and Quantum Causal Structures

Chaves, R., Majenz, C., Luft, L., Maciel, T., Janzing, D., Schölkopf, B., Gross, D.

18th Conference on Quantum Information Processing (QIP), 2015 (talk)

Web link (url) [BibTex]

Web link (url) [BibTex]


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Calibrating the pixel-level Kepler imaging data with a causal data-driven model

Wang, D., Foreman-Mackey, D., Hogg, D., Schölkopf, B.

Workshop: 225th American Astronomical Society Meeting 2015 , pages: 258.08, 2015 (poster)

Web link (url) [BibTex]

Web link (url) [BibTex]


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Disparity estimation from a generative light field model

Köhler, R., Schölkopf, B., Hirsch, M.

IEEE International Conference on Computer Vision (ICCV 2015), Workshop on Inverse Rendering, 2015, Note: This work has been presented as a poster and is not included in the workshop proceedings. (poster)

[BibTex]

[BibTex]


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The search for single exoplanet transits in the Kepler light curves

Foreman-Mackey, D., Hogg, D. W., Schölkopf, B.

IAU General Assembly, 22, pages: 2258352, 2015 (talk)

link (url) [BibTex]

link (url) [BibTex]

2011


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Combined whole-body PET/MR imaging: MR contrast agents do not affect the quantitative accuracy of PET following attenuation correction

Lois, C., Kupferschläger, J., Bezrukov, I., Schmidt, H., Werner, M., Mannheim, J., Pichler, B., Schwenzer, N., Beyer, T.

(SST15-05 ), 97th Scientific Assemble and Annual Meeting of the Radiological Society of North America (RSNA), December 2011 (talk)

Abstract
PURPOSE Combined PET/MR imaging entails the use of MR contrast agents (MRCA) as part of integrated protocols. We assess additional attenuation of the PET emission signals in the presence of oral and intraveneous (iv) MRCA made up of iron oxide and Gd-chelates, respectively. METHOD AND MATERIALS Phantom scans were performed on a clinical PET/CT (Biograph HiRez16, Siemens) and integrated whole-body PET/MR (Biograph mMR, Siemens) using oral (Lumirem) and intraveneous (Gadovist) MRCA. Reference PET attenuation values were determined on a small-animal PET (Inveon, Siemens) using standard PET transmission imaging (TX). Seven syringes of 5mL were filled with (a) Water, (b) Lumirem_100 (100% conc.), (c) Gadovist_100 (100%), (d) Gadovist_18 (18%), (e) Gadovist_02 (0.2%), (f) Imeron-400 CT iv-contrast (100%) and (g) Imeron-400 (2.4%). The same set of syringes was scanned on CT (Sensation16, Siemens) at 120kVp and 160mAs. The effect of MRCA on the attenuation of PET emission data was evaluated using a 20cm cylinder filled uniformly with [18F]-FDG (FDG) in water (BGD). Three 4.5cm diameter cylinders were inserted into the phantom: (C1) Teflon, (C2) Water+FDG (2:1) and (C3) Lumirem_100+FDG (2:1). Two 50mL syringes filled with Gadovist_02+FDG (Sy1) and water+FDG (Sy2) were attached to the sides of (C1) to mimick the effects of iv-contrast in vessels near bone. Syringe-to-background activity ratio was 4-to-1. PET emission data were acquired for 10min each using the PET/CT and the PET/MR. Images were reconstructed using CT- and MR-based attenuation correction. RESULTS Mean linear PET attenuation (cm-1) on TX was (a) 0.098, (b) 0.098, (c) 0.300, (d) 0.134, (e) 0.095, (f) 0.397 and (g) 0.105. Corresponding CT attenuation (HU) was: (a) 5, (b) 14, (c) 3070, (d) 1040, (e) 13, (f) 3070 and (g) 347. Lumirem had little effect on PET attenuation with (C3) being 13% and 10% higher than (C2) on PET/CT and PET/MR, respectively. Gadovist_02 had even smaller effects with (Sy1) being 2.5% lower than (Sy2) on PET/CT and 1.2% higher than (Sy2) on PET/MR. CONCLUSION MRCA in high and clinically relevant concentrations have attenuation values similar to that of CT contrast and water, respectively. In clinical PET/MR scenarios MRCA are not expected to lead to significant attenuation of the PET emission signals.

Web [BibTex]

2011

Web [BibTex]


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Spatiotemporal mapping of rhythmic activity in the inferior convexity of the macaque prefrontal cortex

Panagiotaropoulos, T., Besserve, M., Crocker, B., Kapoor, V., Tolias, A., Panzeri, S., Logothetis, N.

41(239.15), 41st Annual Meeting of the Society for Neuroscience (Neuroscience), November 2011 (poster)

Abstract
The inferior convexity of the macaque prefrontal cortex (icPFC) is known to be involved in higher order processing of sensory information mediating stimulus selection, attention and working memory. Until now, the vast majority of electrophysiological investigations of the icPFC employed single electrode recordings. As a result, relatively little is known about the spatiotemporal structure of neuronal activity in this cortical area. Here we study in detail the spatiotemporal properties of local field potentials (LFP's) in the icPFC using multi electrode recordings during anesthesia. We computed the LFP-LFP coherence as a function of frequency for thousands of pairs of simultaneously recorded sites anterior to the arcuate and inferior to the principal sulcus. We observed two distinct peaks of coherent oscillatory activity between approximately 4-10 and 15-25 Hz. We then quantified the instantaneous phase of these frequency bands using the Hilbert transform and found robust phase gradients across recording sites. The dependency of the phase on the spatial location reflects the existence of traveling waves of electrical activity in the icPFC. The dominant axis of these traveling waves roughly followed the ventral-dorsal plane. Preliminary results show that repeated visual stimulation with a 10s movie had no dramatic effect on the spatial structure of the traveling waves. Traveling waves of electrical activity in the icPFC could reflect highly organized cortical processing in this area of prefrontal cortex.

Web [BibTex]

Web [BibTex]


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Cooperative Cuts: a new use of submodularity in image segmentation

Jegelka, S.

Second I.S.T. Austria Symposium on Computer Vision and Machine Learning, October 2011 (talk)

Web [BibTex]

Web [BibTex]


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Effect of MR Contrast Agents on Quantitative Accuracy of PET in Combined Whole-Body PET/MR Imaging

Lois, C., Bezrukov, I., Schmidt, H., Schwenzer, N., Werner, M., Pichler, B., Kupferschläger, J., Beyer, T.

2011(MIC3-3), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (talk)

Abstract
Combined whole-body PET/MR systems are being tested in clinical practice today. Integrated imaging protocols entail the use of MR contrast agents (MRCA) that could bias PET attenuation correction. In this work, we assess the effect of MRCA in PET/MR imaging. We analyze the effect of oral and intravenous MRCA on PET activity after attenuation correction. We conclude that in clinical scenarios, MRCA are not expected to lead to significant attenuation of PET signals, and that attenuation maps are not biased after the ingestion of adequate oral contrasts.

Web [BibTex]

Web [BibTex]


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First Results on Patients and Phantoms of a Fully Integrated Clinical Whole-Body PET/MRI

Schmidt, H., Schwenzer, N., Bezrukov, I., Kolb, A., Mantlik, F., Kupferschläger, J., Lois, C., Sauter, A., Brendle, C., Pfannenberg, C., Pichler, B.

2011(J2-8), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (talk)

Abstract
First clinical fully integrated whole-body PET/MR scanners are just entering the field. Here, we present studies toward quantification accuracy and variation within the PET field of view of small lesions from our BrainPET/MRI, a dedicated clinical brain scanner which was installed three years ago in Tbingen. Also, we present first results for patient and phantom scans of a fully integral whole-body PET/MRI, which was installed two months ago at our department. The quantification accuracy and homogeneity of the BrainPET-Insert (Siemens Medical Solutions, Germany) installed inside the magnet bore of a clinical 3T MRI scanner (Magnetom TIM Trio, Siemens Medical Solutions, Germany) was evaluated by using eight hollow spheres with inner diameters from 3.95 to 7.86 mm placed at different positions inside a homogeneous cylinder phantom with an 9:1 and 6:1 sphere to background ratio. The quantification accuracy for small lesions at different positions in the PET FoV shows a standard deviation of up to 11% and is acceptable for quantitative brain studies where the homogeneity of quantification on the entire FoV is essental. Image quality and resolution of the new Siemens whole-body PET/MR system (Biograph mMR, Siemens Medical Solutions, Germany) was evaluated according to the NEMA NU2 2007 protocol using a body phantom containing six spheres with inner diameter from 10 to 37 mm at sphere to background ratios of 8:1 and 4:1 and the F-18 point sources located at different positions inside the PET FoV, respectively. The evaluation of the whole-body PET/MR system reveals a good PET image quality and resolution comparable to state-of-the-art clinical PET/CT scanners. First images of patient studies carried out at the whole-body PET/MR are presented highlighting the potency of combined PET/MR imaging.

Web [BibTex]

Web [BibTex]


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Evaluation and Optimization of MR-Based Attenuation Correction Methods in Combined Brain PET/MR

Mantlik, F., Hofmann, M., Bezrukov, I., Schmidt, H., Kolb, A., Beyer, T., Reimold, M., Schölkopf, B., Pichler, B.

2011(MIC18.M-96), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (poster)

Abstract
Combined PET/MR provides simultaneous molecular and functional information in an anatomical context with unique soft tissue contrast. However, PET/MR does not support direct derivation of attenuation maps of objects and tissues within the measured PET field-of-view. Valid attenuation maps are required for quantitative PET imaging, specifically for scientific brain studies. Therefore, several methods have been proposed for MR-based attenuation correction (MR-AC). Last year, we performed an evaluation of different MR-AC methods, including simple MR thresholding, atlas- and machine learning-based MR-AC. CT-based AC served as gold standard reference. RoIs from 2 anatomic brain atlases with different levels of detail were used for evaluation of correction accuracy. We now extend our evaluation of different MR-AC methods by using an enlarged dataset of 23 patients from the integrated BrainPET/MR (Siemens Healthcare). Further, we analyze options for improving the MR-AC performance in terms of speed and accuracy. Finally, we assess the impact of ignoring BrainPET positioning aids during the course of MR-AC. This extended study confirms the overall prediction accuracy evaluation results of the first evaluation in a larger patient population. Removing datasets affected by metal artifacts from the Atlas-Patch database helped to improve prediction accuracy, although the size of the database was reduced by one half. Significant improvement in prediction speed can be gained at a cost of only slightly reduced accuracy, while further optimizations are still possible.

Web [BibTex]

Web [BibTex]


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Atlas- and Pattern Recognition Based Attenuation Correction on Simultaneous Whole-Body PET/MR

Bezrukov, I., Schmidt, H., Mantlik, F., Schwenzer, N., Hofmann, M., Schölkopf, B., Pichler, B.

2011(MIC18.M-116), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (poster)

Abstract
With the recent availability of clinical whole-body PET/MRI it is possible to evaluate and further develop MR-based attenuation correction methods using simultaneously acquired PET/MR data. We present first results for MRAC on patient data acquired on a fully integrated whole-body PET/MRI (Biograph mMR, Siemens) using our method that applies atlas registration and pattern recognition (ATPR) and compare them to the segmentation-based (SEG) method provided by the manufacturer. The ATPR method makes use of a database of previously aligned pairs of MR-CT volumes to predict attenuation values on a continuous scale. The robustness of the method in presence of MR artifacts was improved by location and size based detection. Lesion to liver and lesion to blood ratios (LLR and LBR) were compared for both methods on 29 iso-contour ROIs in 4 patients. ATPR showed >20% higher LBR and LLR for ROIs in and >7% near osseous tissue. For ROIs in soft tissue, both methods yielded similar ratios with max. differences <6% . For ROIs located within metal artifacts in the MR image, ATPR showed >190% higher LLR and LBR than SEG, where ratios <0.1 occured. For lesions in the neighborhood of artifacts, both ratios were >15% higher for ATPR. If artifacts in MR volumes caused by metal implants are not accounted for in the computation of attenuation maps, they can lead to a strong decrease of lesion to background ratios, even to disappearance of hot spots. Metal implants are likely to occur in the patient collective receiving combined PET/MR scans, of our first 10 patients, 3 had metal implants. Our method is currently able to account for artifacts in the pelvis caused by prostheses. The ability of the ATPR method to account for bone leads to a significant increase of LLR and LBR in osseous tissue, which supports our previous evaluations with combined PET/CT and PET/MR data. For lesions within soft tissue, lesion to background ratios of ATPR and SEG were comparable.

Web [BibTex]

Web [BibTex]


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Retrospective blind motion correction of MR images

Loktyushin, A., Nickisch, H., Pohmann, R.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):498, 28th Annual Scientific Meeting ESMRMB, October 2011 (poster)

Abstract
We present a retrospective method, which significantly reduces ghosting and blurring artifacts due to subject motion. No modifications to the sequence (as in [2, 3]), or the use of additional equipment (as in [1]) are required. Our method iteratively searches for the transformation, that applied to the lines in k-space -- yields the sparsest Laplacian filter output in the spatial domain.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Model based reconstruction for GRE EPI

Blecher, W., Pohmann, R., Schölkopf, B., Seeger, M.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):493-494, 28th Annual Scientific Meeting ESMRMB, October 2011 (poster)

Abstract
Model based nonlinear image reconstruction methods for MRI [3] are at the heart of modern reconstruction techniques (e.g.compressed sensing [6]). In general, models are expressed as a matrix equation where y and u are column vectors of k-space and image data, X model matrix and e independent noise. However, solving the corresponding linear system is not tractable. Therefore fast nonlinear algorithms that minimize a function wrt.the unknown image are the method of choice: In this work a model for gradient echo EPI, is proposed that incorporates N/2 Ghost correction and correction for field inhomogeneities. In addition to reconstruction from full data, the model allows for sparse reconstruction, joint estimation of image, field-, and relaxation-map (like [5,8] for spiral imaging), and improved N/2 ghost correction.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Effect of MR contrast agents on quantitative accuracy of PET in combined whole-body PET/MR imaging

Lois, C., Kupferschläger, J., Bezrukov, I., Schmidt, H., Werner, M., Mannheim, J., Pichler, B., Schwenzer, N., Beyer, T.

(OP314), Annual Congress of the European Association of Nuclear Medicine (EANM), October 2011 (talk)

Abstract
PURPOSE:Combined PET/MR imaging entails the use of MR contrast agents (MRCA) as part of integrated protocols. MRCA are made up of iron oxide and Gd-chelates for oral and intravenous (iv) application, respectively. We assess additional attenuation of the PET emission signals in the presence of oral and iv MRCA.MATERIALS AND METHODS:Phantom scans were performed on a clinical PET/CT (Biograph HiRez16, Siemens) and an integrated whole-body PET/MR (Biograph mMR, Siemens). Two common MRCA were evaluated: Lumirem (oral) and Gadovist (iv).Reference PET attenuation values were determined on a dedicated small-animal PET (Inveon, Siemens) using equivalent standard PET transmission source imaging (TX). Seven syringes of 5mL were filled with (a) Water, (b) Lumirem_100 (100% concentration), (c) Gadovist_100 (100%), (d) Gadovist_18 (18%), (e) Gadovist_02 (0.2%), (f) Imeron-400 CT iv-contrast (100%) and (g) Imeron-400 (2.4%). The same set of syringes was scanned on CT (Sensation16, Siemens) at 120kVp and 160mAs.The effect of MRCA on the attenuation of PET emission data was evaluated using a 20cm cylinder filled uniformly with [18F]-FDG (FDG) in water (BGD). Three 4.5cm diameter cylinders were inserted into the phantom: (C1) Teflon, (C2) Water+FDG (2:1) and (C3) Lumirem_100+FDG (2:1). Two 50mL syringes filled with Gadovist_02+FDG (Sy1) and water+FDG (Sy2) were attached to the sides of (C1) to mimick the effects of iv-contrast in vessels near bone. Syringe-to-background activity ratio was 4-to-1.PET emission data were acquired for 10min each using the PET/CT and the PET/MR. Images were reconstructed using CT- and MR-based attenuation correction (AC). Since Teflon is not correctly identified on MR, PET(/MR) data were reconstructed using MR-AC and CT-AC.RESULTS:Mean linear PET attenuation (cm-1) on TX was (a) 0.098, (b) 0.098, (c) 0.300, (d) 0.134, (e) 0.095, (f) 0.397 and (g) 0.105. Corresponding CT attenuation (HU) was: (a) 5, (b) 14, (c) 3070, (d) 1040, (e) 13, (f) 3070 and (g) 347.Lumirem had little effect on PET attenuation with (C3) being 13%, 10% and 11% higher than (C2) on PET/CT, PET/MR with MR-AC, and PET/MR with CT-AC, respectively. Gadovist_02 had even smaller effects with (Sy1) being 2.5% lower, 1.2% higher, and 3.5% lower than (Sy2) on PET/CT, PET/MR with MR-AC and PET/MR with CT-AC, respectively.CONCLUSION:MRCA in high and clinically relevant concentrations have attenuation values similar to that of CT contrast and water, respectively. In clinical PET/MR scenarios MRCA are not expected to lead to significant attenuation of the PET emission signals.

Web [BibTex]

Web [BibTex]


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Simultaneous multimodal imaging of patients with bronchial carcinoma in a whole body MR/PET system

Brendle, C., Sauter, A., Schmidt, H., Schraml, C., Bezrukov, I., Martirosian, P., Hetzel, J., Müller, M., Claussen, C., Schwenzer, N., Pfannenberg, C.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):141, 28th annual scientific meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRB), October 2011 (poster)

Abstract
Purpose/Introduction: Lung cancer is among the most frequent cancers (1). Exact determination of tumour extent and viability is crucial for adequate therapy guidance. [18F]-FDG-PET allows accurate staging and the evaluation of therapy response based on glucose metabolism. Diffusion weighted MRI (DWI) is another promising tool for the evaluation of tumour viability (2,3). The aim of the study was the simultaneous PET-MR acquisition in lung cancer patients and correlation of PET and MR data. Subjects and Methods: Seven patients (age 38-73 years, mean 61 years) with highly suspected or known bronchial carcinoma were examined. First, a [18F]-FDG-PET/CT was performed (injected dose: 332-380 MBq). Subsequently, patients were examined at the whole-body MR/PET (Siemens Biograph mMR). The MRI is a modified 3T Verio whole body system with a magnet bore of 60 cm (max. amplitude gradients 45 mT/m, max. slew rate 200 T/m/s). Concerning the PET, the whole-body MR/PET system comprises 56 detector cassettes with a 59.4 cm transaxial and 25.8 cm axial FoV. The following parameters for PET acquisition were applied: 2 bed positions, 6 min/bed with an average uptake time of 124 min after injection (range: 110-143 min). The attenuation correction of PET data was conducted with a segmentation-based method provided by the manufacturer. Acquired PET data were reconstructed with an iterative 3D OSEM algorithm using 3 iterations and 21 subsets, Gaussian filter of 3 mm. DWI MR images were recorded simultaneously for each bed using two b-values (0/800 s/mm2). SUVmax and ADCmin were assessed in a ROI analysis. The following ratios were calculated: SUVmax(tumor)/SUVmean(liver) and ADCmin(tumor)/ADCmean(muscle). Correlation between SUV and ADC was analyzed (Pearson’s correlation). Results: Diagnostic scans could be obtained in all patients with good tumour delineation. The spatial matching of PET and DWI data was very exact. Most tumours showed a pronounced FDG-uptake in combination with decreased ADC values. Significant correlation was found between SUV and ADC ratios (r = -0.87, p = 0.0118). Discussion/Conclusion: Simultaneous MR/PET imaging of lung cancer is feasible. The whole-body MR/PET system can provide complementary information regarding tumour viability and cellularity which could facilitate a more profound tumour characterization. Further studies have to be done to evaluate the importance of these parameters for therapy decisions and monitoring

Web DOI [BibTex]

Web DOI [BibTex]


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Multi-parametric Tumor Characterization and Therapy Monitoring using Simultaneous PET/MRI: initial results for Lung Cancer and GvHD

Sauter, A., Schmidt, H., Gueckel, B., Brendle, C., Bezrukov, I., Mantlik, F., Kolb, A., Mueller, M., Reimold, M., Federmann, B., Hetzel, J., Claussen, C., Pfannenberg, C., Horger, M., Pichler, B., Schwenzer, N.

(T110), 2011 World Molecular Imaging Congress (WMIC), September 2011 (talk)

Abstract
Hybrid imaging modalities such as [18F]FDG-PET/CT are superior in staging of e.g. lung cancer disease compared with stand-alone modalities. Clinical PET/MRI systems are about to enter the field of hybrid imaging and offer potential advantages. One added value could be a deeper insight into the tumor metabolism and tumorigenesis due to the combination of PET and dedicated MR methods such as MRS and DWI. Additionally, therapy monitoring of diffucult to diagnose disease such as chronic sclerodermic GvHD (csGvHD) can potentially be improved by this combination. We have applied PET/MRI in 3 patients with lung cancer and 4 patients with csGvHD before and during therapy. All 3 patients had lung cancer confirmed by histology (2 adenocarcinoma, 1 carcinoid). First, a [18F]FDG-PET/CT was performed with the following parameters: injected dose 351.7±25.1 MBq, uptake time 59.0±2.6 min, 3 min/bed. Subsequently, patients were brought to the PET/MRI imaging facility. The whole-body PET/MRI Biograph mMR system comprises 56 detector cassettes with a 59.4 cm transaxial and 25.8 cm axial FoV. The MRI is a modified Verio system with a magnet bore of 60 cm. The following parameters for PET acquisition were applied: uptake time 121.3±2.3 min, 3 bed positions, 6 min/bed. T1w, T2w, and DWI MR images were recorded simultaneously for each bed. Acquired PET data were reconstructed with an iterative 3D OSEM algorithm using 3 iterations and 21 subsets, Gaussian filter of 3 mm. The 4 patients with GvHD were brought to the brainPET/MRI imaging facility 2:10h-2:28h after tracer injection. A 9 min brainPET-acquisition with simultaneous MRI of the lower extremities was accomplished. MRI examination included T1-weighted (pre and post gadolinium) and T2-weighted sequences. Attenuation correction was calculated based on manual bone segmentation and thresholds for soft tissue, fat and air. Soleus muscle (m), crural fascia (f1) and posterior crural intermuscular septum fascia (f2) were surrounded with ROIs based on the pre-treatment T1-weighted images and coregistered using IRW (Siemens). Fascia-to-muscle ratios for PET (f/m), T1 contrast uptake (T1_post-contrast_f-pre-contrast_f/post-contrast_m-pre-contrast_m) and T2 (T2_f/m) were calculated. Both patients with adenocarcinoma show a lower ADC value compared with the carcinoid patient suggesting a higher cellularity. This is also reflected in FDG-PET with higher SUV values. Our initial results reveal that PET/MRI can provide complementary information for a profound tumor characterization and therapy monitoring. The high soft tissue contrast provided by MRI is valuable for the assessment of the fascial inflammation. While in the first patient FDG and contrast uptake as well as edema, represented by T2 signals, decreased with ongoing therapy, all parameters remained comparatively stable in the second patient. Contrary to expectations, an increase in FDG uptake of patient 3 and 4 was accompanied by an increase of the T2 signals, but a decrease in contrast uptake. These initial results suggest that PET/MRI provides complementary information of the complex disease mechanisms in fibrosing disorders.

Web [BibTex]

Web [BibTex]


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Statistical Image Analysis and Percolation Theory

Langovoy, M., Habeck, M., Schölkopf, B.

2011 Joint Statistical Meetings (JSM), August 2011 (talk)

Abstract
We develop a novel method for detection of signals and reconstruction of images in the presence of random noise. The method uses results from percolation theory. We specifically address the problem of detection of multiple objects of unknown shapes in the case of nonparametric noise. The noise density is unknown and can be heavy-tailed. The objects of interest have unknown varying intensities. No boundary shape constraints are imposed on the objects, only a set of weak bulk conditions is required. We view the object detection problem as hypothesis testing for discrete statistical inverse problems. We present an algorithm that allows to detect greyscale objects of various shapes in noisy images. We prove results on consistency and algorithmic complexity of our procedures. Applications to cryo-electron microscopy are presented.

Web [BibTex]

Web [BibTex]


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Cooperative Cuts

Jegelka, S.

COSA Workshop: Combinatorial Optimization, Statistics, and Applications, March 2011 (talk)

Abstract
Combinatorial problems with submodular cost functions have recently drawn interest. In a standard combinatorial problem, the sum-of-weights cost is replaced by a submodular set function. The result is a powerful model that is though very hard. In this talk, I will introduce cooperative cuts, minimum cuts with submodular edge weights. I will outline methods to approximately solve this problem, and show an application in computer vision. If time permits, the talk will also sketch regret-minimizing online algorithms for submodular-cost combinatorial problems. This is joint work with Jeff Bilmes (University of Washington).

Web [BibTex]

Web [BibTex]


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Support Vector Machines for finding deletions and short insertions using paired-end short reads

Grimm, D., Hagmann, J., König, D., Weigel, D., Borgwardt, KM.

International Conference on Intelligent Systems for Molecular Biology (ISMB), 2011 (poster)

Web [BibTex]

Web [BibTex]


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Statistical estimation for optimization problems on graphs

Langovoy, M., Sra, S.

Empirical Inference Symposium, 2011 (poster)

[BibTex]


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Transfer Learning with Copulas

Lopez-Paz, D., Hernandez-Lobato, J.

Neural Information Processing Systems (NIPS), 2011 (poster)

PDF [BibTex]

PDF [BibTex]


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Discrete vs. Continuous: Two Sides of Machine Learning

Zhou, D.

October 2004 (talk)

Abstract
We consider the problem of transductive inference. In many real-world problems, unlabeled data is far easier to obtain than labeled data. Hence transductive inference is very significant in many practical problems. According to Vapnik's point of view, one should predict the function value only on the given points directly rather than a function defined on the whole space, the latter being a more complicated problem. Inspired by this idea, we develop discrete calculus on finite discrete spaces, and then build discrete regularization. A family of transductive algorithms is naturally derived from this regularization framework. We validate the algorithms on both synthetic and real-world data from text/web categorization to bioinformatics problems. A significant by-product of this work is a powerful way of ranking data based on examples including images, documents, proteins and many other kinds of data. This talk is mainly based on the followiing contribution: (1) D. Zhou and B. Sch{\"o}lkopf: Transductive Inference with Graphs, MPI Technical report, August, 2004; (2) D. Zhou, B. Sch{\"o}lkopf and T. Hofmann. Semi-supervised Learning on Directed Graphs. NIPS 2004; (3) D. Zhou, O. Bousquet, T.N. Lal, J. Weston and B. Sch{\"o}lkopf. Learning with Local and Global Consistency. NIPS 2003.

PDF [BibTex]


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S-cones contribute to flicker brightness in human vision

Wehrhahn, C., Hill, NJ., Dillenburger, B.

34(174.12), 34th Annual Meeting of the Society for Neuroscience (Neuroscience), October 2004 (poster)

Abstract
In the retina of primates three cone types sensitive to short, middle and long wavelengths of light convert photons into electrical signals. Many investigators have presented evidence that, in color normal observers, the signals of cones sensitive to short wavelengths of light (S-cones) do not contribute to the perception of brightness of a colored surface when this is alternated with an achromatic reference (flicker brightness). Other studies indicate that humans do use S-cone signals when performing this task. Common to all these studies is the small number of observers, whose performance data are reported. Considerable variability in the occurrence of cone types across observers has been found, but, to our knowledge, no cone counts exist from larger populations of humans. We reinvestigated how much the S-cones contribute to flicker brightness. 76 color normal observers were tested in a simple psychophysical procedure neutral to the cone type occurence (Teufel & Wehrhahn (2000), JOSA A 17: 994 - 1006). The data show that, in the majority of our observers, S-cones provide input with a negative sign - relative to L- and M-cone contribution - in the task in question. There is indeed considerable between-subject variability such that for 20 out of 76 observers the magnitude of this input does not differ significantly from 0. Finally, we argue that the sign of S-cone contribution to flicker brightness perception by an observer cannot be used to infer the relative sign their contributions to the neuronal signals carrying the information leading to the perception of flicker brightness. We conclude that studies which use only a small number of observers may easily fail to find significant evidence for the small but significant population tendency for the S-cones to contribute to flicker brightness. Our results confirm all earlier results and reconcile their contradictory interpretations.

Web [BibTex]

Web [BibTex]


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Grundlagen von Support Vector Maschinen und Anwendungen in der Bildverarbeitung

Eichhorn, J.

September 2004 (talk)

Abstract
Invited talk at the workshop "Numerical, Statistical and Discrete Methods in Image Processing" at the TU M{\"u}nchen (in GERMAN)

PDF [BibTex]


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Riemannian Geometry on Graphs and its Application to Ranking and Classification

Zhou, D.

June 2004 (talk)

Abstract
We consider the problem of transductive inference. In many real-world problems, unlabeled data is far easier to obtain than labeled data. Hence transductive inference is very significant in many practical problems. According to Vapnik's point of view, one should predict the function value only on the given points directly rather than a function defined on the whole space, the latter being a more complicated problem. Inspired by this idea, we develop discrete calculus on finite discrete spaces, and then build discrete regularization. A family of transductive algorithms is naturally derived from this regularization framework. We validate the algorithms on both synthetic and real-world data from text/web categorization to bioinformatics problems. A significant by-product of this work is a powerful way of ranking data based on examples including images, documents, proteins and many other kinds of data.

PDF [BibTex]


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Human Classification Behaviour Revisited by Machine Learning

Graf, A., Wichmann, F., Bülthoff, H., Schölkopf, B.

7, pages: 134, (Editors: Bülthoff, H.H., H.A. Mallot, R. Ulrich and F.A. Wichmann), 7th T{\"u}bingen Perception Conference (TWK), Febuary 2004 (poster)

Abstract
We attempt to understand visual classication in humans using both psychophysical and machine learning techniques. Frontal views of human faces were used for a gender classication task. Human subjects classied the faces and their gender judgment, reaction time (RT) and condence rating (CR) were recorded for each face. RTs are longer for incorrect answers than for correct ones, high CRs are correlated with low classication errors and RTs decrease as the CRs increase. This results suggest that patterns difcult to classify need more computation by the brain than patterns easy to classify. Hyperplane learning algorithms such as Support Vector Machines (SVM), Relevance Vector Machines (RVM), Prototype learners (Prot) and K-means learners (Kmean) were used on the same classication task using the Principal Components of the texture and oweld representation of the faces. The classication performance of the learning algorithms was estimated using the face database with the true gender of the faces as labels, and also with the gender estimated by the subjects. Kmean yield a classication performance close to humans while SVM and RVM are much better. This surprising behaviour may be due to the fact that humans are trained on real faces during their lifetime while they were here tested on articial ones, while the algorithms were trained and tested on the same set of stimuli. We then correlated the human responses to the distance of the stimuli to the separating hyperplane (SH) of the learning algorithms. On the whole stimuli far from the SH are classied more accurately, faster and with higher condence than those near to the SH if we pool data across all our subjects and stimuli. We also nd three noteworthy results. First, SVMs and RVMs can learn to classify faces using the subjects' labels but perform much better when using the true labels. Second, correlating the average response of humans (classication error, RT or CR) with the distance to the SH on a face-by-face basis using Spearman's rank correlation coefcients shows that RVMs recreate human performance most closely in every respect. Third, the mean-of-class prototype, its popularity in neuroscience notwithstanding, is the least human-like classier in all cases examined.

Web [BibTex]

Web [BibTex]


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m-Alternative-Forced-Choice: Improving the Efficiency of the Method of Constant Stimuli

Jäkel, F., Hill, J., Wichmann, F.

7, pages: 118, 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
We explored several ways to improve the efficiency of measuring psychometric functions without resorting to adaptive procedures. a) The number m of alternatives in an m-alternative-forced-choice (m-AFC) task improves the efficiency of the method of constant stimuli. b) When alternatives are presented simultaneously on different positions on a screen rather than sequentially time can be saved and memory load for the subject can be reduced. c) A touch-screen can further help to make the experimental procedure more intuitive. We tested these ideas in the measurement of contrast sensitivity and compared them to results obtained by sequential presentation in two-interval-forced-choice (2-IFC). Qualitatively all methods (m-AFC and 2-IFC) recovered the characterictic shape of the contrast sensitivity function in three subjects. The m-AFC paradigm only took about 60% of the time of the 2-IFC task. We tried m=2,4,8 and found 4-AFC to give the best model fits and 2-AFC to have the least bias.

Web [BibTex]

Web [BibTex]


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Efficient Approximations for Support Vector Classifiers

Kienzle, W., Franz, M.

7, pages: 68, 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
In face detection, support vector machines (SVM) and neural networks (NN) have been shown to outperform most other classication methods. While both approaches are learning-based, there are distinct advantages and drawbacks to each method: NNs are difcult to design and train but can lead to very small and efcient classiers. In comparison, SVM model selection and training is rather straightforward, and, more importantly, guaranteed to converge to a globally optimal (in the sense of training errors) solution. Unfortunately, SVM classiers tend to have large representations which are inappropriate for time-critical image processing applications. In this work, we examine various existing and new methods for simplifying support vector decision rules. Our goal is to obtain efcient classiers (as with NNs) while keeping the numerical and statistical advantages of SVMs. For a given SVM solution, we compute a cascade of approximations with increasing complexities. Each classier is tuned so that the detection rate is near 100%. At run-time, the rst (simplest) detector is evaluated on the whole image. Then, any subsequent classier is applied only to those positions that have been classied as positive throughout all previous stages. The false positive rate at the end equals that of the last (i.e. most complex) detector. In contrast, since many image positions are discarded by lower-complexity classiers, the average computation time per patch decreases signicantly compared to the time needed for evaluating the highest-complexity classier alone.

Web [BibTex]

Web [BibTex]


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Selective Attention to Auditory Stimuli: A Brain-Computer Interface Paradigm

Hill, N., Lal, T., Schröder, M., Hinterberger, T., Birbaumer, N., Schölkopf, B.

7, pages: 102, (Editors: Bülthoff, H.H., H.A. Mallot, R. Ulrich and F.A. Wichmann), 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
During the last 20 years several paradigms for Brain Computer Interfaces have been proposed— see [1] for a recent review. They can be divided into (a) stimulus-driven paradigms, using e.g. event-related potentials or visual evoked potentials from an EEG signal, and (b) patient-driven paradigms such as those that use premotor potentials correlated with imagined action, or slow cortical potentials (e.g. [2]). Our aim is to develop a stimulus-driven paradigm that is applicable in practice to patients. Due to the unreliability of visual perception in “locked-in” patients in the later stages of disorders such as Amyotrophic Lateral Sclerosis, we concentrate on the auditory modality. Speci- cally, we look for the effects, in the EEG signal, of selective attention to one of two concurrent auditory stimulus streams, exploiting the increased activation to attended stimuli that is seen under some circumstances [3]. We present the results of our preliminary experiments on normal subjects. On each of 400 trials, two repetitive stimuli (sequences of drum-beats or other pulsed stimuli) could be heard simultaneously. The two stimuli were distinguishable from one another by their acoustic properties, by their source location (one from a speaker to the left of the subject, the other from the right), and by their differing periodicities. A visual cue preceded the stimulus by 500 msec, indicating which of the two stimuli to attend to, and the subject was instructed to count the beats in the attended stimulus stream. There were up to 6 beats of each stimulus: with equal probability on each trial, all 6 were played, or the fourth was omitted, or the fth was omitted. The 40-channel EEG signals were analyzed ofine to reconstruct which of the streams was attended on each trial. A linear Support Vector Machine [4] was trained on a random subset of the data and tested on the remainder. Results are compared from two types of pre-processing of the signal: for each stimulus stream, (a) EEG signals at the stream's beat periodicity are emphasized, or (b) EEG signals following beats are contrasted with those following missing beats. Both forms of pre-processing show promising results, i.e. that selective attention to one or the other auditory stream yields signals that are classiable signicantly above chance performance. In particular, the second pre-processing was found to be robust to reduction in the number of features used for classication (cf. [5]), helping us to eliminate noise.

PDF Web [BibTex]

PDF Web [BibTex]


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Texture and Haptic Cues in Slant Discrimination: Measuring the Effect of Texture Type

Rosas, P., Wichmann, F., Ernst, M., Wagemans, J.

7, pages: 165, (Editors: Bülthoff, H. H., H. A. Mallot, R. Ulrich, F. A. Wichmann), 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
In a number of models of depth cue combination the depth percept is constructed via a weighted average combination of independent depth estimations. The inuence of each cue in such average depends on the reliability of the source of information [1,5]. In particular, Ernst and Banks (2002) formulate such combination as that of the minimum variance unbiased estimator that can be constructed from the available cues. We have observed systematic differences in slant discrimination performance of human observers when different types of textures were used as cue to slant [4]. If the depth percept behaves as described above, our measurements of the slopes of the psychometric functions provide the predicted weights for the texture cue for the ranked texture types. However, the results for slant discrimination obtained when combining these texture types with object motion results are difcult to reconcile with the minimum variance unbiased estimator model [3]. This apparent failure of such model might be explained by the existence of a coupling of texture and motion, violating the assumption of independence of cues. Hillis, Ernst, Banks, and Landy (2002) [2] have shown that while for between-modality combination the human visual system has access to the single-cue information, for withinmodality combination (visual cues) the single-cue information is lost. This suggests a coupling between visual cues and independence between visual and haptic cues. Then, in the present study we combined the different texture types with haptic information in a slant discrimination task, to test whether in the between-modality condition these cues are combined as predicted by an unbiased, minimum variance estimator model. The measured weights for the cues were consistent with a combination rule sensitive to the reliability of the sources of information, but did not match the predictions of a statistically optimal combination.

PDF Web [BibTex]

PDF Web [BibTex]


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Efficient Approximations for Support Vector Classiers

Kienzle, W., Franz, M.

7, pages: 68, 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
In face detection, support vector machines (SVM) and neural networks (NN) have been shown to outperform most other classication methods. While both approaches are learning-based, there are distinct advantages and drawbacks to each method: NNs are difcult to design and train but can lead to very small and efcient classiers. In comparison, SVM model selection and training is rather straightforward, and, more importantly, guaranteed to converge to a globally optimal (in the sense of training errors) solution. Unfortunately, SVM classiers tend to have large representations which are inappropriate for time-critical image processing applications. In this work, we examine various existing and new methods for simplifying support vector decision rules. Our goal is to obtain efcient classiers (as with NNs) while keeping the numerical and statistical advantages of SVMs. For a given SVM solution, we compute a cascade of approximations with increasing complexities. Each classier is tuned so that the detection rate is near 100%. At run-time, the rst (simplest) detector is evaluated on the whole image. Then, any subsequent classier is applied only to those positions that have been classied as positive throughout all previous stages. The false positive rate at the end equals that of the last (i.e. most complex) detector. In contrast, since many image positions are discarded by lower-complexity classiers, the average computation time per patch decreases signicantly compared to the time needed for evaluating the highest-complexity classier alone.

Web [BibTex]

Web [BibTex]


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EEG Channel Selection for Brain Computer Interface Systems Based on Support Vector Methods

Schröder, M., Lal, T., Bogdan, M., Schölkopf, B.

7, pages: 50, (Editors: Bülthoff, H.H., H.A. Mallot, R. Ulrich and F.A. Wichmann), 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
A Brain Computer Interface (BCI) system allows the direct interpretation of brain activity patterns (e.g. EEG signals) by a computer. Typical BCI applications comprise spelling aids or environmental control systems supporting paralyzed patients that have lost motor control completely. The design of an EEG based BCI system requires good answers for the problem of selecting useful features during the performance of a mental task as well as for the problem of classifying these features. For the special case of choosing appropriate EEG channels from several available channels, we propose the application of variants of the Support Vector Machine (SVM) for both problems. Although these algorithms do not rely on prior knowledge they can provide more accurate solutions than standard lter methods [1] for feature selection which usually incorporate prior knowledge about neural activity patterns during the performed mental tasks. For judging the importance of features we introduce a new relevance measure and apply it to EEG channels. Although we base the relevance measure for this purpose on the previously introduced algorithms, it does in general not depend on specic algorithms but can be derived using arbitrary combinations of feature selectors and classifiers.

Web [BibTex]

Web [BibTex]


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Learning Depth

Sinz, F., Franz, MO.

pages: 69, (Editors: H.H.Bülthoff, H.A.Mallot, R.Ulrich,F.A.Wichmann), 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
The depth of a point in space can be estimated by observing its image position from two different viewpoints. The classical approach to stereo vision calculates depth from the two projection equations which together form a stereocamera model. An unavoidable preparatory work for this solution is a calibration procedure, i.e., estimating the external (position and orientation) and internal (focal length, lens distortions etc.) parameters of each camera from a set of points with known spatial position and their corresponding image positions. This is normally done by iteratively linearizing the single camera models and reestimating their parameters according to the error on the known datapoints. The advantage of the classical method is the maximal usage of prior knowledge about the underlying physical processes and the explicit estimation of meaningful model parameters such as focal length or camera position in space. However, the approach neglects the nonlinear nature of the problem such that the results critically depend on the choice of the initial values for the parameters. In this study, we approach the depth estimation problem from a different point of view by applying generic machine learning algorithms to learn the mapping from image coordinates to spatial position. These algorithms do not require any domain knowledge and are able to learn nonlinear functions by mapping the inputs into a higher-dimensional space. Compared to classical calibration, machine learning methods give a direct solution to the depth estimation problem which means that the values of the stereocamera parameters cannot be extracted from the learned mapping. On the poster, we compare the performance of classical camera calibration to that of different machine learning algorithms such as kernel ridge regression, gaussian processes and support vector regression. Our results indicate that generic learning approaches can lead to higher depth accuracies than classical calibration although no domain knowledge is used.

PDF Web [BibTex]

PDF Web [BibTex]


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Learning from Labeled and Unlabeled Data: Semi-supervised Learning and Ranking

Zhou, D.

January 2004 (talk)

Abstract
We consider the general problem of learning from labeled and unlabeled data, which is often called semi-supervised learning or transductive inference. A principled approach to semi-supervised learning is to design a classifying function which is sufficiently smooth with respect to the intrinsic structure collectively revealed by known labeled and unlabeled points. We present a simple algorithm to obtain such a smooth solution. Our method yields encouraging experimental results on a number of classification problems and demonstrates effective use of unlabeled data.

PDF [BibTex]


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Introduction to Category Theory

Bousquet, O.

Internal Seminar, January 2004 (talk)

Abstract
A brief introduction to the general idea behind category theory with some basic definitions and examples. A perspective on higher dimensional categories is given.

PDF [BibTex]

PDF [BibTex]


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Neural mechanisms underlying control of a Brain-Computer-Interface (BCI): Simultaneous recording of bold-response and EEG

Hinterberger, T., Wilhelm, B., Veit, R., Weiskopf, N., Lal, TN., Birbaumer, N.

2004 (poster)

Abstract
Brain computer interfaces (BCI) enable humans or animals to communicate or activate external devices without muscle activity using electric brain signals. The BCI Thought Translation Device (TTD) uses learned regulation of slow cortical potentials (SCPs), a skill most people and paralyzed patients can acquire with training periods of several hours up to months. The neurophysiological mechanisms and anatomical sources of SCPs and other event-related brain macro-potentials are well understood, but the neural mechanisms underlying learning of the self-regulation skill for BCI-use are unknown. To uncover the relevant areas of brain activation during regulation of SCPs, the TTD was combined with functional MRI and EEG was recorded inside the MRI scanner in twelve healthy participants who have learned to regulate their SCP with feedback and reinforcement. The results demonstrate activation of specific brain areas during execution of the brain regulation skill: successf! ul control of cortical positivity allowing a person to activate an external device was closely related to an increase of BOLD (blood oxygen level dependent) response in the basal ganglia and frontal premotor deactivation indicating learned regulation of a cortical-striatal loop responsible for local excitation thresholds of cortical assemblies. The data suggest that human users of a BCI learn the regulation of cortical excitation thresholds of large neuronal assemblies as a prerequisite of direct brain communication: the learning of this skill depends critically on an intact and flexible interaction between these cortico-basal ganglia-circuits. Supported by the Deutsche Forschungsgemeinschaft (DFG) and the National Institute of Health (NIH).

[BibTex]

[BibTex]


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Masking by plaid patterns revisited

Wichmann, F.

Experimentelle Psychologie. Beitr{\"a}ge zur 46. Tagung experimentell arbeitender Psychologen, 46, pages: 285, 2004 (poster)

[BibTex]

[BibTex]