Sub-continental-scale carbon stocks of individual trees in African drylands.

The distribution of dryland trees and their density, cover, size, mass and carbon content are not well known at sub-continental to continental scales1-14. This information is important for ecological protection, carbon accounting, climate mitigation and restoration efforts of dryland ecosystems15-18. We assessed more than 9.9 billion trees derived from more than 300,000 satellite images, covering semi-arid sub-Saharan Africa north of the Equator. We attributed wood, foliage and root carbon to every tree in the 0-1,000 mm year-1 rainfall zone by coupling field data19, machine learning20-22, satellite data and high-performance computing. Average carbon stocks of individual trees ranged from 0.54 Mg C ha-1 and 63 kg C tree-1 in the arid zone to 3.7 Mg C ha-1 and 98 kg tree-1 in the sub-humid zone. Overall, we estimated the total carbon for our study area to be 0.84 (±19.8%) Pg C. Comparisons with 14 previous TRENDY numerical simulation studies23 for our area found that the density and carbon stocks of scattered trees have been underestimated by three models and overestimated by 11 models, respectively. This benchmarking can help understand the carbon cycle and address concerns about land degradation24-29. We make available a linked database of wood mass, foliage mass, root mass and carbon stock of each tree for scientists, policymakers, dryland-restoration practitioners and farmers, who can use it to estimate farmland tree carbon stocks from tablets or laptops.

An unexpectedly large count of trees in the West African Sahara and Sahel.

A large proportion of dryland trees and shrubs (hereafter referred to collectively as trees) grow in isolation, without canopy closure. These non-forest trees have a crucial role in biodiversity, and provide ecosystem services such as carbon storage, food resources and shelter for humans and animals1,2. However, most public interest relating to trees is devoted to forests, and trees outside of forests are not well-documented3. Here we map the crown size of each tree more than 3 m2 in size over a land area that spans 1.3 million km2 in the West African Sahara, Sahel and sub-humid zone, using submetre-resolution satellite imagery and deep learning4. We detected over 1.8 billion individual trees (13.4 trees per hectare), with a median crown size of 12 m2, along a rainfall gradient from 0 to 1,000 mm per year. The canopy cover increases from 0.1% (0.7 trees per hectare) in hyper-arid areas, through 1.6% (9.9 trees per hectare) in arid and 5.6% (30.1 trees per hectare) in semi-arid zones, to 13.3% (47 trees per hectare) in sub-humid areas. Although the overall canopy cover is low, the relatively high density of isolated trees challenges prevailing narratives about dryland desertification5-7, and even the desert shows a surprisingly high tree density. Our assessment suggests a way to monitor trees outside of forests globally, and to explore their role in mitigating degradation, climate change and poverty.

Towards more comprehensive nationwide familial aggregation studies in Denmark: The Danish Civil Registration System versus the lite Danish Multi-Generation Register.

AIM: Linking information on family members in the Danish Civil Registration System (CRS) with information in Danish national registers provides unique possibilities for research on familial aggregation of diseases, health patterns, social factors and demography. However, the CRS is limited in the number of generations that it can identify. To allow more complete familial linkages, we introduce the lite Danish Multi-Generation Register (lite MGR) and the future full Danish MGR that is currently being developed. METHODS: We generated the lite MGR by linking the current version of the CRS with historical versions stored by the Danish National Archives in the early 1970s, which contain familial links not saved in the current CRS. We describe and compare the completeness of familial links in the lite MGR and the current version of the CRS. We also describe planned procedures for generating the full MGR by linking the current CRS with scanned archived records from Parish Registers. RESULTS: Among people born in Denmark in 1960 or later, the current CRS contains information on both parents. However, it has limited parental information for people born earlier. Among the 732,232 people born in Denmark during 1950-1959, 444,084 (60.65%) had information on both parents in the CRS. In the lite MGR, it was 560,594 (76.56%). CONCLUSIONS: The lite MGR offers more complete information on familial relationships than the current CRS. The lite and full MGR will offer an infrastructure tying together existing research infrastructures, registers and biobanks, raising their joint research value to an unparalleled level.

High Accuracy in Classifying Endoscopic Severity in Ulcerative Colitis Using Convolutional Neural Network.

INTRODUCTION: The evaluation of endoscopic disease severity is a crucial component in managing patients with ulcerative colitis (UC). However, endoscopic assessment suffers from substantial intraobserver and interobserver variations, limiting the reliability of individual assessments. Therefore, we aimed to develop a deep learning model capable of distinguishing active from healed mucosa and differentiating between different endoscopic disease severity degrees. METHODS: One thousand four hundred eighty-four unique endoscopic images from 467 patients were extracted for classification. Two experts classified all images independently of one another according to the Mayo endoscopic subscore (MES). In cases of disagreement, a third expert classified the images. Different convolutional neural networks were considered for automatically classifying UC severity. Five-fold cross-validation was used to develop and select the final model. Afterward, unseen test data sets were used for model evaluation. RESULTS: In the most challenging task-distinguishing between all categories of MES-our final model achieved a test accuracy of 0.84. When evaluating this model on the binary tasks of distinguishing MES 0 vs 1-3 and 0-1 vs 2-3, it achieved accuracies of 0.94 and 0.93 and areas under the receiver operating characteristic curves of 0.997 and 0.998, respectively. DISCUSSION: We have developed a highly accurate, new, automated way of evaluating endoscopic images from patients with UC. We have demonstrated how our deep learning model is capable of distinguishing between all 4 MES levels of activity. This new automated approach may optimize and standardize the evaluation of disease severity measured by the MES across centers no matter the level of medical expertise.

Cross-Cohort Automatic Knee MRI Segmentation With Multi-Planar U-Nets.

BACKGROUND: Segmentation of medical image volumes is a time-consuming manual task. Automatic tools are often tailored toward specific patient cohorts, and it is unclear how they behave in other clinical settings. PURPOSE: To evaluate the performance of the open-source Multi-Planar U-Net (MPUnet), the validated Knee Imaging Quantification (KIQ) framework, and a state-of-the-art two-dimensional (2D) U-Net architecture on three clinical cohorts without extensive adaptation of the algorithms. STUDY TYPE: Retrospective cohort study. SUBJECTS: A total of 253 subjects (146 females, 107 males, ages 57 ± 12 years) from three knee osteoarthritis (OA) studies (Center for Clinical and Basic Research [CCBR], Osteoarthritis Initiative [OAI], and Prevention of OA in Overweight Females [PROOF]) with varying demographics and OA severity (64/37/24/53/2 scans of Kellgren and Lawrence [KL] grades 0-4). FIELD STRENGTH/SEQUENCE: 0.18 T, 1.0 T/1.5 T, and 3 T sagittal three-dimensional fast-spin echo T1w and dual-echo steady-state sequences. ASSESSMENT: All models were fit without tuning to knee magnetic resonance imaging (MRI) scans with manual segmentations from three clinical cohorts. All models were evaluated across KL grades. STATISTICAL TESTS: Segmentation performance differences as measured by Dice coefficients were tested with paired, two-sided Wilcoxon signed-rank statistics with significance threshold α = 0.05. RESULTS: The MPUnet performed superior or equal to KIQ and 2D U-Net on all compartments across three cohorts. Mean Dice overlap was significantly higher for MPUnet compared to KIQ and U-Net on CCBR ( 0.83±0.04 vs. 0.81±0.06 and 0.82±0.05 ), significantly higher than KIQ and U-Net OAI ( 0.86±0.03 vs. 0.84±0.04 and 0.85±0.03) , and not significantly different from KIQ while significantly higher than 2D U-Net on PROOF ( 0.78±0.07 vs. 0.77±0.07 , P=0.10 , and 0.73±0.07) . The MPUnet performed significantly better on N=22 KL grade 3 CCBR scans with 0.78±0.06 vs. 0.75±0.08 for KIQ and 0.76±0.06 for 2D U-Net. DATA CONCLUSION: The MPUnet matched or exceeded the performance of state-of-the-art knee MRI segmentation models across cohorts of variable sequences and patient demographics. The MPUnet required no manual tuning making it both accurate and easy-to-use. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY: Stage 2.

Predicting electrical storms by remote monitoring of implantable cardioverter-defibrillator patients using machine learning.

AIMS: Electrical storm (ES) is a serious arrhythmic syndrome that is characterized by recurrent episodes of ventricular arrhythmias. Electrical storm is associated with increased mortality and morbidity despite the use of implantable cardioverter-defibrillators (ICDs). Predicting ES could be essential; however, models for predicting this event have never been developed. The goal of this study was to construct and validate machine learning models to predict ES based on daily ICD remote monitoring summaries. METHODS AND RESULTS: Daily ICD summaries from 19 935 patients were used to construct and evaluate two models [logistic regression (LR) and random forest (RF)] for predicting the short-term risk of ES. The models were evaluated on the parts of the data not used for model development. Random forest performed significantly better than LR (P < 0.01), achieving a test accuracy of 0.96 and an area under the curve (AUC) of 0.80 (vs. an accuracy of 0.96 and an AUC of 0.75). The percentage of ventricular pacing and the daytime activity were the most relevant variables in the RF model. CONCLUSION: The use of large-scale machine learning showed that daily summaries of ICD measurements in the absence of clinical information can predict the short-term risk of ES.

Separating Timing, Movement Conditions and Individual Differences in the Analysis of Human Movement.

A central task in the analysis of human movement behavior is to determine systematic patterns and differences across experimental conditions, participants and repetitions. This is possible because human movement is highly regular, being constrained by invariance principles. Movement timing and movement path, in particular, are linked through scaling laws. Separating variations of movement timing from the spatial variations of movements is a well-known challenge that is addressed in current approaches only through forms of preprocessing that bias analysis. Here we propose a novel nonlinear mixed-effects model for analyzing temporally continuous signals that contain systematic effects in both timing and path. Identifiability issues of path relative to timing are overcome by using maximum likelihood estimation in which the most likely separation of space and time is chosen given the variation found in data. The model is applied to analyze experimental data of human arm movements in which participants move a hand-held object to a target location while avoiding an obstacle. The model is used to classify movement data according to participant. Comparison to alternative approaches establishes nonlinear mixed-effects models as viable alternatives to conventional analysis frameworks. The model is then combined with a novel factor-analysis model that estimates the low-dimensional subspace within which movements vary when the task demands vary. Our framework enables us to visualize different dimensions of movement variation and to test hypotheses about the effect of obstacle placement and height on the movement path. We demonstrate that the approach can be used to uncover new properties of human movement.

Early detection of Alzheimer's disease using MRI hippocampal texture.

Cognitive impairment in patients with Alzheimer's disease (AD) is associated with reduction in hippocampal volume in magnetic resonance imaging (MRI). However, it is unknown whether hippocampal texture changes in persons with mild cognitive impairment (MCI) that does not have a change in hippocampal volume. We tested the hypothesis that hippocampal texture has association to early cognitive loss beyond that of volumetric changes. The texture marker was trained and evaluated using T1-weighted MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database, and subsequently applied to score independent data sets from the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL) and the Metropolit 1953 Danish Male Birth Cohort (Metropolit). Hippocampal texture was superior to volume reduction as predictor of MCI-to-AD conversion in ADNI (area under the receiver operating characteristic curve [AUC] 0.74 vs. 0.67; DeLong test, p = 0.005), and provided even better prognostic results in AIBL (AUC 0.83). Hippocampal texture, but not volume, correlated with Addenbrooke's cognitive examination score (Pearson correlation, r = -0.25, p < 0.001) in the Metropolit cohort. The hippocampal texture marker correlated with hippocampal glucose metabolism as indicated by fluorodeoxyglucose-positron emission tomography (Pearson correlation, r = -0.57, p < 0.001). Texture statistics remained significant after adjustment for volume in all cases, and the combination of texture and volume did not improve diagnostic or prognostic AUCs significantly. Our study highlights the presence of hippocampal texture abnormalities in MCI, and the possibility that texture may serve as a prognostic neuroimaging biomarker of early cognitive impairment.

Deep learning enables image-based tree counting, crown segmentation, and height prediction at national scale.

Sustainable tree resource management is the key to mitigating climate warming, fostering a green economy, and protecting valuable habitats. Detailed knowledge about tree resources is a prerequisite for such management but is conventionally based on plot-scale data, which often neglects trees outside forests. Here, we present a deep learning-based framework that provides location, crown area, and height for individual overstory trees from aerial images at country scale. We apply the framework on data covering Denmark and show that large trees (stem diameter >10 cm) can be identified with a low bias (12.5%) and that trees outside forests contribute to 30% of the total tree cover, which is typically unrecognized in national inventories. The bias is high (46.6%) when our results are evaluated against all trees taller than 1.3 m, which involve undetectable small or understory trees. Furthermore, we demonstrate that only marginal effort is needed to transfer our framework to data from Finland, despite markedly dissimilar data sources. Our work lays the foundation for digitalized national databases, where large trees are spatially traceable and manageable.

The overlooked contribution of trees outside forests to tree cover and woody biomass across Europe.

Trees are an integral part in European landscapes, but only forest resources are systematically assessed by national inventories. The contribution of urban and agricultural trees to national-level carbon stocks remains largely unknown. Here we produced canopy cover, height and above-ground biomass maps from 3-meter resolution nanosatellite imagery across Europe. Our biomass estimates have a systematic bias of 7.6% (overestimation; R = 0.98) compared to national inventories of 30 countries, and our dataset is sufficiently highly resolved spatially to support the inclusion of tree biomass outside forests, which we quantify to 0.8 petagrams. Although this represents only 2% of the total tree biomass, large variations between countries are found (10% for UK) and trees in urban areas contribute substantially to national carbon stocks (8% for the Netherlands). The agreement with national inventory data, the scalability, and spatial details across landscapes, including trees outside forests, make our approach attractive for operational implementation to support national carbon stock inventory schemes.

Nation-wide mapping of tree-level aboveground carbon stocks in Rwanda.

Trees sustain livelihoods and mitigate climate change but a predominance of trees outside forests and limited resources make it difficult for many tropical countries to conduct automated nation-wide inventories. Here, we propose an approach to map the carbon stock of each individual overstory tree at the national scale of Rwanda using aerial imagery from 2008 and deep learning. We show that 72% of the mapped trees are located in farmlands and savannas and 17% in plantations, accounting for 48.6% of the national aboveground carbon stocks. Natural forests cover 11% of the total tree count and 51.4% of the national carbon stocks, with an overall carbon stock uncertainty of 16.9%. The mapping of all trees allows partitioning to any landscapes classification and is urgently needed for effective planning and monitoring of restoration activities as well as for optimization of carbon sequestration, biodiversity and economic benefits of trees.

More than one quarter of Africa's tree cover is found outside areas previously classified as forest.

The consistent monitoring of trees both inside and outside of forests is key to sustainable land management. Current monitoring systems either ignore trees outside forests or are too expensive to be applied consistently across countries on a repeated basis. Here we use the PlanetScope nanosatellite constellation, which delivers global very high-resolution daily imagery, to map both forest and non-forest tree cover for continental Africa using images from a single year. Our prototype map of 2019 (RMSE = 9.57%, bias = -6.9%). demonstrates that a precise assessment of all tree-based ecosystems is possible at continental scale, and reveals that 29% of tree cover is found outside areas previously classified as tree cover in state-of-the-art maps, such as in croplands and grassland. Such accurate mapping of tree cover down to the level of individual trees and consistent among countries has the potential to redefine land use impacts in non-forest landscapes, move beyond the need for forest definitions, and build the basis for natural climate solutions and tree-related studies.

Bounding the bias of contrastive divergence learning.

Optimization based on k-step contrastive divergence (CD) has become a common way to train restricted Boltzmann machines (RBMs). The k-step CD is a biased estimator of the log-likelihood gradient relying on Gibbs sampling. We derive a new upper bound for this bias. Its magnitude depends on k, the number of variables in the RBM, and the maximum change in energy that can be produced by changing a single variable. The last reflects the dependence on the absolute values of the RBM parameters. The magnitude of the bias is also affected by the distance in variation between the modeled distribution and the starting distribution of the Gibbs chain.

A dynamic neural field model of mesoscopic cortical activity captured with voltage-sensitive dye imaging.

A neural field model is presented that captures the essential non-linear characteristics of activity dynamics across several millimeters of visual cortex in response to local flashed and moving stimuli. We account for physiological data obtained by voltage-sensitive dye (VSD) imaging which reports mesoscopic population activity at high spatio-temporal resolution. Stimulation included a single flashed square, a single flashed bar, the line-motion paradigm--for which psychophysical studies showed that flashing a square briefly before a bar produces sensation of illusory motion within the bar--and moving squares controls. We consider a two-layer neural field (NF) model describing an excitatory and an inhibitory layer of neurons as a coupled system of non-linear integro-differential equations. Under the assumption that the aggregated activity of both layers is reflected by VSD imaging, our phenomenological model quantitatively accounts for the observed spatio-temporal activity patterns. Moreover, the model generalizes to novel similar stimuli as it matches activity evoked by moving squares of different speeds. Our results indicate that feedback from higher brain areas is not required to produce motion patterns in the case of the illusory line-motion paradigm. Physiological interpretation of the model suggests that a considerable fraction of the VSD signal may be due to inhibitory activity, supporting the notion that balanced intra-layer cortical interactions between inhibitory and excitatory populations play a major role in shaping dynamic stimulus representations in the early visual cortex.

U-Sleep: resilient high-frequency sleep staging.

Sleep disorders affect a large portion of the global population and are strong predictors of morbidity and all-cause mortality. Sleep staging segments a period of sleep into a sequence of phases providing the basis for most clinical decisions in sleep medicine. Manual sleep staging is difficult and time-consuming as experts must evaluate hours of polysomnography (PSG) recordings with electroencephalography (EEG) and electrooculography (EOG) data for each patient. Here, we present U-Sleep, a publicly available, ready-to-use deep-learning-based system for automated sleep staging ( sleep.ai.ku.dk ). U-Sleep is a fully convolutional neural network, which was trained and evaluated on PSG recordings from 15,660 participants of 16 clinical studies. It provides accurate segmentations across a wide range of patient cohorts and PSG protocols not considered when building the system. U-Sleep works for arbitrary combinations of typical EEG and EOG channels, and its special deep learning architecture can label sleep stages at shorter intervals than the typical 30 s periods used during training. We show that these labels can provide additional diagnostic information and lead to new ways of analyzing sleep. U-Sleep performs on par with state-of-the-art automatic sleep staging systems on multiple clinical datasets, even if the other systems were built specifically for the particular data. A comparison with consensus-scores from a previously unseen clinic shows that U-Sleep performs as accurately as the best of the human experts. U-Sleep can support the sleep staging workflow of medical experts, which decreases healthcare costs, and can provide highly accurate segmentations when human expertize is lacking.

Using machine learning for predicting intensive care unit resource use during the COVID-19 pandemic in Denmark.

The COVID-19 pandemic has put massive strains on hospitals, and tools to guide hospital planners in resource allocation during the ebbs and flows of the pandemic are urgently needed. We investigate whether machine learning (ML) can be used for predictions of intensive care requirements a fixed number of days into the future. Retrospective design where health Records from 42,526 SARS-CoV-2 positive patients in Denmark was extracted. Random Forest (RF) models were trained to predict risk of ICU admission and use of mechanical ventilation after n days (n = 1, 2, …, 15). An extended analysis was provided for n = 5 and n = 10. Models predicted n-day risk of ICU admission with an area under the receiver operator characteristic curve (ROC-AUC) between 0.981 and 0.995, and n-day risk of use of ventilation with an ROC-AUC between 0.982 and 0.997. The corresponding n-day forecasting models predicted the needed ICU capacity with a coefficient of determination (R2) between 0.334 and 0.989 and use of ventilation with an R2 between 0.446 and 0.973. The forecasting models performed worst, when forecasting many days into the future (for large n). For n = 5, ICU capacity was predicted with ROC-AUC 0.990 and R2 0.928, and use of ventilator was predicted with ROC-AUC 0.994 and R2 0.854. Random Forest-based modelling can be used for accurate n-day forecasting predictions of ICU resource requirements, when n is not too large.

The International Workshop on Osteoarthritis Imaging Knee MRI Segmentation Challenge: A Multi-Institute Evaluation and Analysis Framework on a Standardized Dataset.

PURPOSE: To organize a multi-institute knee MRI segmentation challenge for characterizing the semantic and clinical efficacy of automatic segmentation methods relevant for monitoring osteoarthritis progression. MATERIALS AND METHODS: A dataset partition consisting of three-dimensional knee MRI from 88 retrospective patients at two time points (baseline and 1-year follow-up) with ground truth articular (femoral, tibial, and patellar) cartilage and meniscus segmentations was standardized. Challenge submissions and a majority-vote ensemble were evaluated against ground truth segmentations using Dice score, average symmetric surface distance, volumetric overlap error, and coefficient of variation on a holdout test set. Similarities in automated segmentations were measured using pairwise Dice coefficient correlations. Articular cartilage thickness was computed longitudinally and with scans. Correlation between thickness error and segmentation metrics was measured using the Pearson correlation coefficient. Two empirical upper bounds for ensemble performance were computed using combinations of model outputs that consolidated true positives and true negatives. RESULTS: Six teams (T 1-T 6) submitted entries for the challenge. No differences were observed across any segmentation metrics for any tissues (P = .99) among the four top-performing networks (T 2, T 3, T 4, T 6). Dice coefficient correlations between network pairs were high (> 0.85). Per-scan thickness errors were negligible among networks T 1-T 4 (P = .99), and longitudinal changes showed minimal bias (< 0.03 mm). Low correlations (ρ < 0.41) were observed between segmentation metrics and thickness error. The majority-vote ensemble was comparable to top-performing networks (P = .99). Empirical upper-bound performances were similar for both combinations (P = .99). CONCLUSION: Diverse networks learned to segment the knee similarly, where high segmentation accuracy did not correlate with cartilage thickness accuracy and voting ensembles did not exceed individual network performance.See also the commentary by Elhalawani and Mak in this issue.Keywords: Cartilage, Knee, MR-Imaging, Segmentation © RSNA, 2020Supplemental material is available for this article.

Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients.

Patients with severe COVID-19 have overwhelmed healthcare systems worldwide. We hypothesized that machine learning (ML) models could be used to predict risks at different stages of management and thereby provide insights into drivers and prognostic markers of disease progression and death. From a cohort of approx. 2.6 million citizens in Denmark, SARS-CoV-2 PCR tests were performed on subjects suspected for COVID-19 disease; 3944 cases had at least one positive test and were subjected to further analysis. SARS-CoV-2 positive cases from the United Kingdom Biobank was used for external validation. The ML models predicted the risk of death (Receiver Operation Characteristics-Area Under the Curve, ROC-AUC) of 0.906 at diagnosis, 0.818, at hospital admission and 0.721 at Intensive Care Unit (ICU) admission. Similar metrics were achieved for predicted risks of hospital and ICU admission and use of mechanical ventilation. Common risk factors, included age, body mass index and hypertension, although the top risk features shifted towards markers of shock and organ dysfunction in ICU patients. The external validation indicated fair predictive performance for mortality prediction, but suboptimal performance for predicting ICU admission. ML may be used to identify drivers of progression to more severe disease and for prognostication patients in patients with COVID-19. We provide access to an online risk calculator based on these findings.

Impact of device programming on the success of the first anti-tachycardia pacing therapy: An anonymized large-scale study.

BACKGROUND: Antitachycardia pacing (ATP) is an effective treatment for ventricular tachycardia (VT). We evaluated the efficacy of different ATP programs based on a large remote monitoring data set from patients with implantable cardioverter-defibrillators (ICDs). METHODS: A dataset from 18,679 ICD patients was used to evaluate the first delivered ATP treatment. We considered all device programs that were used for at least 50 patients, leaving us with 7 different programs and a total of 32,045 episodes. We used the two-proportions z-test (α = 0.01) to compare the probability of success and the probability for acceleration in each group with the corresponding values of the default setting. RESULTS: Overall, the first ATP treatment terminated in 78.4%-97.5% of episodes with slow VT and 81.5%-91.1% of episodes with fast VT. The default setting of the ATP programs with the number of sequences S = 3 was applied to treat 30.1% of the slow and 36.6% of the fast episodes. Reducing the maximum number of sequences to S = 2 decreased the success rate for slow VT (P < 0.0001, h = 0.38), while the setting S = 4 resulted in the highest success rate of 97.5% (P < 0.0001, h = 0.27). CONCLUSION: While the default programs performed well, we found that increasing the number of sequences from 3 to 4 was a promising option to improve the overall ATP performance.

Gradient-based optimization of kernel-target alignment for sequence kernels applied to bacterial gene start detection.

Biological data mining using kernel methods can be improved by a task-specific choice of the kernel function. Oligo kernels for genomic sequence analysis have proven to have a high discriminative power and to provide interpretable results. Oligo kernels that consider subsequences of different lengths can be combined and parameterized to increase their flexibility. For adapting these parameters efficiently, gradient-based optimization of the kernel-target alignment is proposed. The power of this new, general model selection procedure and the benefits of fitting kernels to problem classes are demonstrated by adapting oligo kernels for bacterial gene start detection.