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Reproductive behavior affects spatial population structure and our ability to manage for sustainability in marine and diadromous fishes. In this study, we used fishery independent capture-based sampling to evaluate where Common Snook occurred in Tampa Bay and if it changed with spawning season, and passive acoustic telemetry to assess fine scale behavior at an inlet spawning site (2007-2009). Snook concentrated in three areas during the spawning season only one of which fell within the expected spawning habitat. Although in lower numbers, they remained in these areas throughout the winter months. Acoustically-tagged snook (n = 31) showed two seasonal patterns at the spawning site: Most fish occurred during the spawning season but several fish displayed more extended residency, supporting the capture-based findings that Common Snook exhibit facultative catadromy. Spawning site selection for iteroparous, multiple-batch spawning fishes occurs at the lifetime, annual, or intra-annual temporal scales. In this study we show colonization of a new spawning site, indicating that lifetime spawning site fidelity of Common Snook is not fixed at this fine spatial scale. However, individuals did exhibit annual and intra-seasonal spawning site fidelity to this new site over the three years studied. The number of fish at the spawning site increased in June and July (peak spawning months) and on new and full lunar phases indicating within population variability in spawning and movement patterns. Intra-seasonal patterns of detection also differed significantly with sex. Common Snook exhibited divergent migration tactics and habitat use at the annual and estuarine scales, with contingents using different overwintering habitat. Migration tactics also varied at the spawning site at the intra-seasonal scale and with sex. These results have important implications for understanding how reproductive behavior affects spatio-temporal patterns of fish abundance and their resilience to disturbance events and fishing pressure.

There is an increasing number of medical use cases where classification algorithms based on deep neural networks reach performance levels that are competitive with human medical experts. To alleviate the challenges of small dataset sizes, these systems often rely on pretraining. In this work, we aim to assess the broader implications of these approaches in order to better understand what type of pretraining works reliably (with respect to performance, robustness, learned representation etc.) in practice and what type of pretraining dataset is best suited to achieve good performance in small target dataset size scenarios. Considering diabetic retinopathy grading as an exemplary use case, we compare the impact of different training procedures including recently established self-supervised pretraining methods based on contrastive learning. To this end, we investigate different aspects such as quantitative performance, statistics of the learned feature representations, interpretability and robustness to image distortions. Our results indicate that models initialized from ImageNet pretraining report a significant increase in performance, generalization and robustness to image distortions. In particular, self-supervised models show further benefits to supervised models. Self-supervised models with initialization from ImageNet pretraining not only report higher performance, they also reduce overfitting to large lesions along with improvements in taking into account minute lesions indicative of the progression of the disease. Understanding the effects of pretraining in a broader sense that goes beyond simple performance comparisons is of crucial importance for the broader medical imaging community beyond the use case considered in this work.

More than ever, technical inventions are the symbol of our society's advance. Patents guarantee their creators protection against infringement. For an invention being patentable, its novelty and inventiveness have to be assessed. Therefore, a search for published work that describes similar inventions to a given patent application needs to be performed. Currently, this so-called search for prior art is executed with semi-automatically composed keyword queries, which is not only time consuming, but also prone to errors. In particular, errors may systematically arise by the fact that different keywords for the same technical concepts may exist across disciplines. In this paper, a novel approach is proposed, where the full text of a given patent application is compared to existing patents using machine learning and natural language processing techniques to automatically detect inventions that are similar to the one described in the submitted document. Various state-of-the-art approaches for feature extraction and document comparison are evaluated. In addition to that, the quality of the current search process is assessed based on ratings of a domain expert. The evaluation results show that our automated approach, besides accelerating the search process, also improves the search results for prior art with respect to their quality.

Brain-Computer Interfaces (BCIs) are inefficient for a non-negligible part of the population, estimated around 25%. To understand this phenomenon in Sensorimotor Rhythm (SMR) based BCIs, data from a large-scale screening study conducted on 80 novice participants with the Berlin BCI system and its standard machine-learning approach were investigated. Each participant performed one BCI session with resting state Encephalography, Motor Observation, Motor Execution and Motor Imagery recordings and 128 electrodes. A significant portion of the participants (40%) could not achieve BCI control (feedback performance > 70%). Based on the performance of the calibration and feedback runs, BCI users were stratified in three groups. Analyses directed to detect and elucidate the differences in the SMR activity of these groups were performed. Statistics on reactive frequencies, task prevalence and classification results are reported. Based on their SMR activity, also a systematic list of potential reasons leading to performance drops and thus hints for possible improvements of BCI experimental design are given. The categorization of BCI users has several advantages, allowing researchers 1) to select subjects for further analyses as well as for testing new BCI paradigms or algorithms, 2) to adopt a better subject-dependent training strategy and 3) easier comparisons between different studies.

High prediction accuracies are not the only objective to consider when solving problems using machine learning. Instead, particular scientific applications require some explanation of the learned prediction function. For computational biology, positional oligomer importance matrices (POIMs) have been successfully applied to explain the decision of support vector machines (SVMs) using weighted-degree (WD) kernels. To extract relevant biological motifs from POIMs, the motifPOIM method has been devised and showed promising results on real-world data. Our contribution in this paper is twofold: as an extension to POIMs, we propose gPOIM, a general measure of feature importance for arbitrary learning machines and feature sets (including, but not limited to, SVMs and CNNs) and devise a sampling strategy for efficient computation. As a second contribution, we derive a convex formulation of motifPOIMs that leads to more reliable motif extraction from gPOIMs. Empirical evaluations confirm the usefulness of our approach on artificially generated data as well as on real-world datasets.

The robust analysis of neural signals is a challenging problem. Here, we contribute a convolutional neural network (CNN) for the robust classification of a steady-state visual evoked potentials (SSVEPs) paradigm. We measure electroencephalogram (EEG)-based SSVEPs for a brain-controlled exoskeleton under ambulatory conditions in which numerous artifacts may deteriorate decoding. The proposed CNN is shown to achieve reliable performance under these challenging conditions. To validate the proposed method, we have acquired an SSVEP dataset under two conditions: 1) a static environment, in a standing position while fixated into a lower-limb exoskeleton and 2) an ambulatory environment, walking along a test course wearing the exoskeleton (here, artifacts are most challenging). The proposed CNN is compared to a standard neural network and other state-of-the-art methods for SSVEP decoding (i.e., a canonical correlation analysis (CCA)-based classifier, a multivariate synchronization index (MSI), a CCA combined with k-nearest neighbors (CCA-KNN) classifier) in an offline analysis. We found highly encouraging SSVEP decoding results for the CNN architecture, surpassing those of other methods with classification rates of 99.28% and 94.03% in the static and ambulatory conditions, respectively. A subsequent analysis inspects the representation found by the CNN at each layer and can thus contribute to a better understanding of the CNN's robust, accurate decoding abilities.

Text documents can be described by a number of abstract concepts such as semantic category, writing style, or sentiment. Machine learning (ML) models have been trained to automatically map documents to these abstract concepts, allowing to annotate very large text collections, more than could be processed by a human in a lifetime. Besides predicting the text's category very accurately, it is also highly desirable to understand how and why the categorization process takes place. In this paper, we demonstrate that such understanding can be achieved by tracing the classification decision back to individual words using layer-wise relevance propagation (LRP), a recently developed technique for explaining predictions of complex non-linear classifiers. We train two word-based ML models, a convolutional neural network (CNN) and a bag-of-words SVM classifier, on a topic categorization task and adapt the LRP method to decompose the predictions of these models onto words. Resulting scores indicate how much individual words contribute to the overall classification decision. This enables one to distill relevant information from text documents without an explicit semantic information extraction step. We further use the word-wise relevance scores for generating novel vector-based document representations which capture semantic information. Based on these document vectors, we introduce a measure of model explanatory power and show that, although the SVM and CNN models perform similarly in terms of classification accuracy, the latter exhibits a higher level of explainability which makes it more comprehensible for humans and potentially more useful for other applications.

There are some practical factors, such as arm position change and donning/doffing, which prevent robust myoelectric control. The objective of this study is to precisely characterize the impacts of the two representative factors on myoelectric controllability in practical control situations, thereby providing useful references that can be potentially used to find better solutions for clinically reliable myoelectric control. To this end, a real-time target acquisition task was performed by fourteen subjects including one individual with congenital upper-limb deficiency, where the impacts of arm position change, donning/doffing and a combination of both factors on control performance was systematically evaluated. The changes in online performance were examined with seven different performance metrics to comprehensively evaluate various aspects of myoelectric controllability. As a result, arm position change significantly affects offline prediction accuracy, but not online control performance due to real-time feedback, thereby showing no significant correlation between offline and online performance. Donning/doffing was still problematic in online control conditions. It was further observed that no benefit was attained when using a control model trained with multiple position data in terms of arm position change, and the degree of electrode shift caused by donning/doffing was not severely associated with the degree of performance loss under practical conditions (around 1 cm electrode shift). Since this study is the first to concurrently investigate the impacts of arm position change and donning/doffing in practical myoelectric control situations, all findings of this study provide new insights into robust myoelectric control with respect to arm position change and donning/doffing.

OBJECTIVE:Using traditional approaches, a brain-computer interface (BCI) requires the collection of calibration data for new subjects prior to online use. Calibration time can be reduced or eliminated e.g., by subject-to-subject transfer of a pre-trained classifier or unsupervised adaptive classification methods which learn from scratch and adapt over time. While such heuristics work well in practice, none of them can provide theoretical guarantees. Our objective is to modify an event-related potential (ERP) paradigm to work in unison with the machine learning decoder, and thus to achieve a reliable unsupervised calibrationless decoding with a guarantee to recover the true class means. METHOD:We introduce learning from label proportions (LLP) to the BCI community as a new unsupervised, and easy-to-implement classification approach for ERP-based BCIs. The LLP estimates the mean target and non-target responses based on known proportions of these two classes in different groups of the data. We present a visual ERP speller to meet the requirements of LLP. For evaluation, we ran simulations on artificially created data sets and conducted an online BCI study with 13 subjects performing a copy-spelling task. RESULTS:Theoretical considerations show that LLP is guaranteed to minimize the loss function similar to a corresponding supervised classifier. LLP performed well in simulations and in the online application, where 84.5% of characters were spelled correctly on average without prior calibration. SIGNIFICANCE:The continuously adapting LLP classifier is the first unsupervised decoder for ERP BCIs guaranteed to find the optimal decoder. This makes it an ideal solution to avoid tedious calibration sessions. Additionally, LLP works on complementary principles compared to existing unsupervised methods, opening the door for their further enhancement when combined with LLP.

On sedation motivated by the clinical needs for safety and reliability, recent studies have attempted to identify brain-specific signatures for tracking patient transition into and out of consciousness, but the differences in neurophysiological effects between 1) the sedative types and 2) the presence/absence of surgical stimulations still remain unclear. Here we used multimodal electroencephalography-functional near-infrared spectroscopy (EEG-fNIRS) measurements to observe electrical and hemodynamic responses during sedation simultaneously. Forty healthy volunteers were instructed to push the button to administer sedatives in response to auditory stimuli every 9-11 s. To generally illustrate brain activity at repetitive transition points at the loss of consciousness (LOC) and the recovery of consciousness (ROC), patient-controlled sedation was performed using two different sedatives (midazolam (MDZ) and propofol (PPF)) under two surgical conditions. Once consciousness was lost via sedatives, we observed gradually increasing EEG power at lower frequencies (15 Hz), as well as spatially increased EEG powers in the delta and lower alpha bands, and particularly also in the upper alpha rhythm, at the frontal and parieto-occipital areas over time. During ROC from unconsciousness, these spatio-temporal changes were reversed. Interestingly, the level of consciousness was switched on/off at significantly higher effect-site concentrations of sedatives in the brain according to the use of surgical stimuli, but the spatio-temporal EEG patterns were similar, regardless of the sedative used. We also observed sudden phase shifts in fronto-parietal connectivity at the LOC and the ROC as critical points. fNIRS measurement also revealed mild hemodynamic fluctuations. Compared with general anesthesia, our results provide insights into critical hallmarks of sedative-induced (un)consciousness, which have similar spatio-temporal EEG-fNIRS patterns regardless of the stage and the sedative used.

Understanding and interpreting classification decisions of automated image classification systems is of high value in many applications, as it allows to verify the reasoning of the system and provides additional information to the human expert. Although machine learning methods are solving very successfully a plethora of tasks, they have in most cases the disadvantage of acting as a black box, not providing any information about what made them arrive at a particular decision. This work proposes a general solution to the problem of understanding classification decisions by pixel-wise decomposition of nonlinear classifiers. We introduce a methodology that allows to visualize the contributions of single pixels to predictions for kernel-based classifiers over Bag of Words features and for multilayered neural networks. These pixel contributions can be visualized as heatmaps and are provided to a human expert who can intuitively not only verify the validity of the classification decision, but also focus further analysis on regions of potential interest. We evaluate our method for classifiers trained on PASCAL VOC 2009 images, synthetic image data containing geometric shapes, the MNIST handwritten digits data set and for the pre-trained ImageNet model available as part of the Caffe open source package.

Identifying discriminative motifs underlying the functionality and evolution of organisms is a major challenge in computational biology. Machine learning approaches such as support vector machines (SVMs) achieve state-of-the-art performances in genomic discrimination tasks, but--due to its black-box character--motifs underlying its decision function are largely unknown. As a remedy, positional oligomer importance matrices (POIMs) allow us to visualize the significance of position-specific subsequences. Although being a major step towards the explanation of trained SVM models, they suffer from the fact that their size grows exponentially in the length of the motif, which renders their manual inspection feasible only for comparably small motif sizes, typically k ≤ 5. In this work, we extend the work on positional oligomer importance matrices, by presenting a new machine-learning methodology, entitled motifPOIM, to extract the truly relevant motifs--regardless of their length and complexity--underlying the predictions of a trained SVM model. Our framework thereby considers the motifs as free parameters in a probabilistic model, a task which can be phrased as a non-convex optimization problem. The exponential dependence of the POIM size on the oligomer length poses a major numerical challenge, which we address by an efficient optimization framework that allows us to find possibly overlapping motifs consisting of up to hundreds of nucleotides. We demonstrate the efficacy of our approach on a synthetic data set as well as a real-world human splice site data set.

Brain-Computer Interfaces (BCIs) strive to decode brain signals into control commands for severely handicapped people with no means of muscular control. These potential users of noninvasive BCIs display a large range of physical and mental conditions. Prior studies have shown the general applicability of BCI with patients, with the conflict of either using many training sessions or studying only moderately restricted patients. We present a BCI system designed to establish external control for severely motor-impaired patients within a very short time. Within only six experimental sessions, three out of four patients were able to gain significant control over the BCI, which was based on motor imagery or attempted execution. For the most affected patient, we found evidence that the BCI could outperform the best assistive technology (AT) of the patient in terms of control accuracy, reaction time and information transfer rate. We credit this success to the applied user-centered design approach and to a highly flexible technical setup. State-of-the art machine learning methods allowed the exploitation and combination of multiple relevant features contained in the EEG, which rapidly enabled the patients to gain substantial BCI control. Thus, we could show the feasibility of a flexible and tailorable BCI application in severely disabled users. This can be considered a significant success for two reasons: Firstly, the results were obtained within a short period of time, matching the tight clinical requirements. Secondly, the participating patients showed, compared to most other studies, very severe communication deficits. They were dependent on everyday use of AT and two patients were in a locked-in state. For the most affected patient a reliable communication was rarely possible with existing AT.

Despite several approaches to realize subject-to-subject transfer of pre-trained classifiers, the full performance of a Brain-Computer Interface (BCI) for a novel user can only be reached by presenting the BCI system with data from the novel user. In typical state-of-the-art BCI systems with a supervised classifier, the labeled data is collected during a calibration recording, in which the user is asked to perform a specific task. Based on the known labels of this recording, the BCI's classifier can learn to decode the individual's brain signals. Unfortunately, this calibration recording consumes valuable time. Furthermore, it is unproductive with respect to the final BCI application, e.g. text entry. Therefore, the calibration period must be reduced to a minimum, which is especially important for patients with a limited concentration ability. The main contribution of this manuscript is an online study on unsupervised learning in an auditory event-related potential (ERP) paradigm. Our results demonstrate that the calibration recording can be bypassed by utilizing an unsupervised trained classifier, that is initialized randomly and updated during usage. Initially, the unsupervised classifier tends to make decoding mistakes, as the classifier might not have seen enough data to build a reliable model. Using a constant re-analysis of the previously spelled symbols, these initially misspelled symbols can be rectified posthoc when the classifier has learned to decode the signals. We compare the spelling performance of our unsupervised approach and of the unsupervised posthoc approach to the standard supervised calibration-based dogma for n = 10 healthy users. To assess the learning behavior of our approach, it is unsupervised trained from scratch three times per user. Even with the relatively low SNR of an auditory ERP paradigm, the results show that after a limited number of trials (30 trials), the unsupervised approach performs comparably to a classic supervised model.

Recently, spatio-temporal filtering to enhance decoding for Brain-Computer-Interfacing (BCI) has become increasingly popular. In this work, we discuss a novel, fully Bayesian-and thereby probabilistic-framework, called Bayesian Spatio-Spectral Filter Optimization (BSSFO) and apply it to a large data set of 80 non-invasive EEG-based BCI experiments. Across the full frequency range, the BSSFO framework allows to analyze which spatio-spectral parameters are common and which ones differ across the subject population. As expected, large variability of brain rhythms is observed between subjects. We have clustered subjects according to similarities in their corresponding spectral characteristics from the BSSFO model, which is found to reflect their BCI performances well. In BCI, a considerable percentage of subjects is unable to use a BCI for communication, due to their missing ability to modulate their brain rhythms-a phenomenon sometimes denoted as BCI-illiteracy or inability. Predicting individual subjects' performance preceding the actual, time-consuming BCI-experiment enhances the usage of BCIs, e.g., by detecting users with BCI inability. This work additionally contributes by using the novel BSSFO method to predict the BCI-performance using only 2 minutes and 3 channels of resting-state EEG data recorded before the actual BCI-experiment. Specifically, by grouping the individual frequency characteristics we have nicely classified them into the subject 'prototypes' (like μ - or β -rhythm type subjects) or users without ability to communicate with a BCI, and then by further building a linear regression model based on the grouping we could predict subjects' performance with the maximum correlation coefficient of 0.581 with the performance later seen in the actual BCI session.

Event-related potential (ERP)-based P300 spellers are commonly used in the field of brain-computer interfaces as an alternative channel of communication for people with severe neuro-muscular diseases. This study introduces a novel P300 based brain-computer interface (BCI) stimulus paradigm using a random set presentation pattern and exploiting the effects of face familiarity. The effect of face familiarity is widely studied in the cognitive neurosciences and has recently been addressed for the purpose of BCI. In this study we compare P300-based BCI performances of a conventional row-column (RC)-based paradigm with our approach that combines a random set presentation paradigm with (non-) self-face stimuli. Our experimental results indicate stronger deflections of the ERPs in response to face stimuli, which are further enhanced when using the self-face images, and thereby improving P300-based spelling performance. This lead to a significant reduction of stimulus sequences required for correct character classification. These findings demonstrate a promising new approach for improving the speed and thus fluency of BCI-enhanced communication with the widely used P300-based BCI setup.

Robust and reliable covariance estimates play a decisive role in financial and many other applications. An important class of estimators is based on factor models. Here, we show by extensive Monte Carlo simulations that covariance matrices derived from the statistical Factor Analysis model exhibit a systematic error, which is similar to the well-known systematic error of the spectrum of the sample covariance matrix. Moreover, we introduce the Directional Variance Adjustment (DVA) algorithm, which diminishes the systematic error. In a thorough empirical study for the US, European, and Hong Kong stock market we show that our proposed method leads to improved portfolio allocation.

Combining information from various image features has become a standard technique in concept recognition tasks. However, the optimal way of fusing the resulting kernel functions is usually unknown in practical applications. Multiple kernel learning (MKL) techniques allow to determine an optimal linear combination of such similarity matrices. Classical approaches to MKL promote sparse mixtures. Unfortunately, 1-norm regularized MKL variants are often observed to be outperformed by an unweighted sum kernel. The main contributions of this paper are the following: we apply a recently developed non-sparse MKL variant to state-of-the-art concept recognition tasks from the application domain of computer vision. We provide insights on benefits and limits of non-sparse MKL and compare it against its direct competitors, the sum-kernel SVM and sparse MKL. We report empirical results for the PASCAL VOC 2009 Classification and ImageCLEF2010 Photo Annotation challenge data sets. Data sets (kernel matrices) as well as further information are available at http://doc.ml.tu-berlin.de/image_mkl/(Accessed 2012 Jun 25).

Electroencephalogram (EEG) signals are highly subject-specific and vary considerably even between recording sessions of the same user within the same experimental paradigm. This challenges a stable operation of Brain-Computer Interface (BCI) systems. The classical approach is to train users by neurofeedback to produce fixed stereotypical patterns of brain activity. In the machine learning approach, a widely adapted method for dealing with those variances is to record a so called calibration measurement on the beginning of each session in order to optimize spatial filters and classifiers specifically for each subject and each day. This adaptation of the system to the individual brain signature of each user relieves from the need of extensive user training. In this paper we suggest a new method that overcomes the requirement of these time-consuming calibration recordings for long-term BCI users. The method takes advantage of knowledge collected in previous sessions: By a novel technique, prototypical spatial filters are determined which have better generalization properties compared to single-session filters. In particular, they can be used in follow-up sessions without the need to recalibrate the system. This way the calibration periods can be dramatically shortened or even completely omitted for these 'experienced' BCI users. The feasibility of our novel approach is demonstrated with a series of online BCI experiments. Although performed without any calibration measurement at all, no loss of classification performance was observed.