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Pattern Search in Multi-structure Data: A Framework for the Next-Generation Evidence-based Medicine
With the advent of personalized and evidence-based medicine, the need for a framework to analyze/interpret quantitative measurements (blood work, toxicology, etc.) with qualitative descriptions (specialist reports after reading images, bio-medical knowledge-bases) to predict diagnostic risks is fast emerging. Addressing this need, we pose and address the following questions (i) How can we jointly analyze both qualitative and quantitative data ? (ii) Is the fusion of multi-structure data expected to provide better insights than either of them individually ? We present experiments on two bio-medical data sets - mammography and traumatic brain studies to demonstrate architectures and tools for evidence-pattern search.
Google search patterns monitoring the daily health impact of heatwaves in England: How do the findings compare to established syndromic surveillance systems from 2013 to 2017?
Highlights: • Heat health-related Google search term frequency increased during heatwave events. • Google data correlated well with validated syndromic heat health indicators. • A similar timeliness was seen between daily Google and syndromic data in England. • Google search data could be of benefit in monitoring heat-related morbidity. One of the implications of climate change is a predicted increase in frequent and severe heatwaves. The impact of heatwaves on the health of the population is captured through real-time syndromic healthcare surveillance systems monitored daily in England during the summer months. Internet search data could potentially provide improved timeliness and help to assess the wider population health impact of heat by capturing a population sub-group who are symptomatic but do not seek healthcare. A retrospective observational study was carried out from June 2013 to September 2017 in England to compare daily trends in validated syndromic surveillance heat-related morbidity indicators against symptom-based heatwave related Google search terms. The degree of correlation was determined with Spearman correlation coefficients and lag assessment was carried out to determine timeliness. Daily increases in frequency in Google search terms during heatwave events correlated well with validated syndromic indicators. Correlation coefficients between search term frequency and syndromic indicators from 2013 to 2017 were highest with the telehealth service NHS 111 (range of 0.684–0.900 by search term). Lag analysis revealed a similar timeliness between the data sources, suggesting Google data did not provide a delayed or earlier signal in the context of England's syndromic surveillance systems. This work highlights the potential benefits for countries which lack established public health surveillance systems to monitor heat-related morbidity and the use of internet search data to assess the wider population health impact of exposure to heat.
SU-E-T-295: Simultaneous Beam Sampling and Aperture Shape Optimization for Station Parameter Optimized Radiation Therapy (SPORT)
Purpose: Station Parameter Optimized Radiation Therapy (SPORT) was recently proposed to fully utilize the technical capability of emerging digital LINACs, in which the station parameters of a delivery system, (such as aperture shape and weight, couch position/angle, gantry/collimator angle) are optimized altogether. SPORT promises to deliver unprecedented radiation dose distributions efficiently, yet there does not exist any optimization algorithm to implement it. The purpose of this work is to propose an optimization algorithm to simultaneously optimize the beam sampling and aperture shapes. Methods: We build a mathematical model whose variables are beam angles (including non-coplanar and/or even nonisocentric beams) and aperture shapes. To solve the resulting large scale optimization problem, we devise an exact, convergent and fast optimization algorithm by integrating three advanced optimization techniques named column generation, gradient method, and pattern search. Column generation is used to find a good set of aperture shapes as an initial solution by adding apertures sequentially. Then we apply the gradient method to iteratively improve the current solution by reshaping the aperture shapes and updating the beam angles toward the gradient. Algorithm continues by pattern search method to explore the part of the search space that cannot be reached by the gradient method. Results: The proposed technique is applied to a series of patient cases and significantly improves the plan quality. In a head-and-neck case, for example, the left parotid gland mean-dose, brainstem max-dose, spinal cord max-dose, and mandible mean-dose are reduced by 10%, 7%, 24% and 12% respectively, compared to the conventional VMAT plan while maintaining the same PTV coverage. Conclusion: Combined use of column generation, gradient search and pattern search algorithms provide an effective way to optimize simultaneously the large collection of station parameters and significantly improves quality of resultant treatment plans as compared with conventional VMAT or IMRT treatments.
Simultaneous beam sampling and aperture shape optimization for SPORT
Purpose: Station parameter optimized radiation therapy (SPORT) was recently proposed to fully utilize the technical capability of emerging digital linear accelerators, in which the station parameters of a delivery system, such as aperture shape and weight, couch position/angle, gantry/collimator angle, can be optimized simultaneously. SPORT promises to deliver remarkable radiation dose distributions in an efficient manner, yet there exists no optimization algorithm for its implementation. The purpose of this work is to develop an algorithm to simultaneously optimize the beam sampling and aperture shapes. Methods: The authors build a mathematical model with the fundamental station point parameters as the decision variables. To solve the resulting large-scale optimization problem, the authors devise an effective algorithm by integrating three advanced optimization techniques: column generation, subgradient method, and pattern search. Column generation adds the most beneficial stations sequentially until the plan quality improvement saturates and provides a good starting point for the subsequent optimization. It also adds the new stations during the algorithm if beneficial. For each update resulted from column generation, the subgradient method improves the selected stations locally by reshaping the apertures and updating the beam angles toward a descent subgradient direction. The algorithm continues to improve the selected stations locally and globally by a pattern search algorithm to explore the part of search space not reachable by the subgradient method. By combining these three techniques together, all plausible combinations of station parameters are searched efficiently to yield the optimal solution. Results: A SPORT optimization framework with seamlessly integration of three complementary algorithms, column generation, subgradient method, and pattern search, was established. The proposed technique was applied to two previously treated clinical cases: a head and neck and a prostate case. It significantly improved the target conformality and at the same time critical structure sparing compared with conventional intensity modulated radiation therapy (IMRT). In the head and neck case, for example, the average PTV coverage D99% for two PTVs, cord and brainstem max doses, and right parotid gland mean dose were improved, respectively, by about 7%, 37%, 12%, and 16%. Conclusions: The proposed method automatically determines the number of the stations required to generate a satisfactory plan and optimizes simultaneously the involved station parameters, leading to improved quality of the resultant treatment plans as compared with the conventional IMRT plans.
Search for patterns by combining cosmic-ray energy and arrival directions at the Pierre Auger Observatory
Energy-dependent patterns in the arrival directions of cosmic rays are searched for using data of the Pierre Auger Observatory. We investigate local regions around the highest-energy cosmic rays with E ≥ 6×10 19 eV by analyzing cosmic rays with energies above E ≥ 5×10 18 eV arriving within an angular separation of approximately 15°. We characterize the energy distributions inside these regions by two independent methods, one searching for angular dependence of energy-energy correlations and one searching for collimation of energy along the local system of principal axes of the energy distribution. No significant patterns are found with this analysis. As a result, the comparison of these measurements with astrophysical scenarios can therefore be used to obtain constraints on related model parameters such as strength of cosmic-ray deflection and density of point sources.
Temporal Stability of Visual Search-Driven Biometrics
Previously, we have shown the potential of using an individual s visual search pattern as a possible biometric. That study focused on viewing images displaying dot-patterns with different spatial relationships to determine which pattern can be more effective in establishing the identity of an individual. In this follow-up study we investigated the temporal stability of this biometric. We performed an experiment with 16 individuals asked to search for a predetermined feature of a random-dot pattern as we tracked their eye movements. Each participant completed four testing sessions consisting of two dot patterns repeated twice. One dot pattern displayed concentric circles shifted to the left or right side of the screen overlaid with visual noise, and participants were asked which side the circles were centered on. The second dot-pattern displayed a number of circles (between 0 and 4) scattered on the screen overlaid with visual noise, and participants were asked how many circles they could identify. Each session contained 5 untracked tutorial questions and 50 tracked test questions (200 total tracked questions per participant). To create each participant s "fingerprint", we constructed a Hidden Markov Model (HMM) from the gaze data representing the underlying visual search and cognitive process. The accuracy of the derived HMM models was evaluated using cross-validation for various time-dependent train-test conditions. Subject identification accuracy ranged from 17.6% to 41.8% for all conditions, which is significantly higher than random guessing (1/16 = 6.25%). The results suggest that visual search pattern is a promising, fairly stable personalized fingerprint of perceptual organization.
Using Eye Tracking to Elucidate the Mechanisms Underlying Stimulation-Enhanced Visual Target Detection
Transcranial direct current stimulation (tDCS) is a noninvasive form of brain stimulation that involves passing a weak electrical current between electrodes on the scalp to modulate underlying neural tissue. TDCS has been shown to modulate cognition in a variety of domains, including memory, attention, and visual processing. Prior work from our laboratory has shown positive effects of tDCS on learning to detect target objects hidden in complex naturalistic visual scenes and learn rules for categorizing images, though the mechanism for these benefits remains unknown. One possibility is that tDCS optimizes visual search by modulating visual attention or via the reduction in search errors. One method of quantifying visual attention is to use eye tracking to record search patterns to determine if and how visual search is adjusted under verum stimulation conditions. Eye tracking data allows classification of errors into error types, including sampling errors (failing to look in the relevant region), recognition errors (looking at the critical portion of a scene, but failing to recognize it as such as evidenced by visual fixation), and decision-making errors (fixating on the relevant portion of a scene, but making the wrong determination). Our results indicate that the benefit tDCS confers on visual search for targets stems from the reduction in decision-making errors when targets are present (Cohen’s d = 0.86). Also reported is a replication of previous findings showing a tDCS-dependent improvement in learning this task, learning score (Cohen’s d = 0.88); d’ (Cohen’s d = 1.00). This provides support for moving tDCS into the application space by pairing it with analysts who are concerned with the type of search error that is corrected via stimulation.
GrammarViz 3.0: Interactive Discovery of Variable-Length Time Series Patterns
The problems of recurrent and anomalous pattern discovery in time series, e.g., motifs and discords, respectively, have received a lot of attention from researchers in the past decade. However, since the pattern search space is usually intractable, most existing detection algorithms require that the patterns have discriminative characteristics and have its length known in advance and provided as input, which is an unreasonable requirement for many real-world problems. In addition, patterns of similar structure, but of different lengths may co-exist in a time series. In order to address these issues, we have developed algorithms for variable-length time series pattern discovery that are based on symbolic discretization and grammar inference—two techniques whose combination enables the structured reduction of the search space and discovery of the candidate patterns in linear time. In this work, we present GrammarViz 3.0—a software package that provides implementations of proposed algorithms and graphical user interface for interactive variable-length time series pattern discovery. The current version of the software provides an alternative grammar inference algorithm that improves the time series motif discovery workflow, and introduces an experimental procedure for automated discretization parameter selection that builds upon the minimum cardinality maximum cover principle and aids the time series recurrent and anomalous pattern discovery.
Computing quality scores and uncertainty for approximate pattern matching in geospatial semantic graphs
Geospatial semantic graphs provide a robust foundation for representing and analyzing remote sensor data. In particular, they support a variety of pattern search operations that capture the spatial and temporal relationships among the objects and events in the data. However, in the presence of large data corpora, even a carefully constructed search query may return a large number of unintended matches. This work considers the problem of calculating a quality score for each match to the query, given that the underlying data are uncertain. As a result, we present a preliminary evaluation of three methods for determining both match quality scores and associated uncertainty bounds, illustrated in the context of an example based on overhead imagery data.
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)
In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variablelength protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw amino acids k-mer features.
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)
ABSTRACT In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variable-length protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw k-mer features. Availability Implementations of our method will be available under the Apache 2 licence at http://llp.berkeley.edu/dimotif and http://llp.berkeley.edu/protvecx .
Clustering-Based Predictive Analytics to Improve Scientific Data Discovery
Given the sheer volume of scientific data archived within the data-intensive projects at the US Department of Energy's Oak Ridge National Laboratory, finding precisely what data we are looking for may not be a trivial task; conversely, we may also miss a more prominent data product. To address such issues, we propose improving the data discovery system and using data analytics methods to comprehend what specific users might be interested in based on their physiological state, search patterns, and past data usage history. This work's primary goal is to prune the complexity, increase the visibility of popular data products, and direct users toward the data that best meet their needs. The proposed algorithm constructs a user profile based on the user's explicit or implicit interactions with the system, such as items they are currently looking at on-site and the key metadata mappings related to the data set. The pattern is then used to build a training data set, which will help find relevant data to recommend to the user.
Distributed Solution Approach for a Stackelberg Pricing Game of Aggregated Demand Response
Demand-side management is a fundamental up-to-date strategy that transforms the traditional power grid to a modern smart grid where the flexible pricing mechanisms play a critical role in its successful implementation. In this paper, the pricing-demand response between a distribution system operator (DSO) and load aggregators (LAs) is modeled as a Stackelberg game, where the DSO is the price maker that adjusts its strategy based on observed responses from LAs. With the concerns of computational cost and privacy protection, two distributed solution approaches, particle swarm optimization and pattern search algorithm, are conducted and compared with the classical centralized backward induction approach. Numerical results on a small case study demonstrate the effectiveness of the proposed distributed solution approaches in leveraging flexible demand response potential.
Modeling sequential context effects in diagnostic interpretation of screening mammograms
Prior research has shown that physicians’ medical decisions can be influenced by sequential context, particularly in cases where successive stimuli exhibit similar characteristics when analyzing medical images. This type of systematic error is known to psychophysicists as sequential context effect as it indicates that judgments are influenced by features of and decisions about the preceding case in the sequence of examined cases, rather than being based solely on the peculiarities unique to the present case. We determine if radiologists experience some form of context bias, using screening mammography as the use case. To this end, we explore correlations between previous perceptual behavior and diagnostic decisions and current decisions. We hypothesize that a radiologist’s visual search pattern and diagnostic decisions in previous cases are predictive of the radiologist’s current diagnostic decisions. To test our hypothesis, we tasked 10 radiologists of varied experience to conduct blind reviews of 100 four-view screening mammograms. Eye-tracking data and diagnostic decisions were collected from each radiologist under conditions mimicking clinical practice. Perceptual behavior was quantified using the fractal dimension of gaze scanpath, which was computed using the Minkowski–Bouligand box-counting method. To test the effect of previous behavior and decisions, we conducted a multifactor fixed-effects ANOVA. Further, to examine the predictive value of previous perceptual behavior and decisions, we trained and evaluated a predictive model for radiologists’ current diagnostic decisions. ANOVA tests showed that previous visual behavior, characterized by fractal analysis, previous diagnostic decisions, and image characteristics of previous cases are significant predictors of current diagnostic decisions. Additionally, predictive modeling of diagnostic decisions showed an overall improvement in prediction error when the model is trained on additional information about previous perceptual behavior and diagnostic decisions.
Distributed Acoustic Sensing (DAS) Data for Periodic Hydraulic Tests: Hydraulic Data
Hydraulic responses from periodic hydraulic tests conducted at the Mirror Lake Fractured Rock Research Site, during the summer of 2015. These hydraulic responses were measured also using distributed acoustic sensing (DAS) which is cataloged in a different submission under this grant number. The tests are explained in detail in Matthew Cole's MS Thesis which is cataloged here. The injection and drawdown data and the codes used to analyze the data. Sinusoidal Data is a Matlab data file containing a data table for each period-length test. Within each table is a column labeled: time (seconds since beginning of pumping), Inj_m3pm (formation injection in cubic meters per minute), and head for each observation well (meters). The three Matlab script files (*.m) were used to analyze hydraulic responses from the data file above. High-Pass Sinusoid is a routine for filtering the data, computing the FFT, and extracting phase and amplitude values. Borestore is a routine which contains the borehole storage analytic solution and compares modeled amplitude and phase from this solution to computed amplitude and phase from the data. Patsearch Borestore is a routine containing the built-in pattern search optimization method. This minimizes the total error between modeled and actual amplitude and phase in Borestore. Comments within the script files contain more specific instructions for their use.
Spread Spectrum Time Domain Reflectivity for String Monitoring in PV Power Plants (Final Technical Report)
This final report describes the methods and results of applying Spread Spectrum Time Domain Reflectivity (SSTDR) for String Monitoring in PV Power Plants for DE-EE0008169. The project created a new system for both detecting and locating electrical faults in photovoltaic systems. In this work, we address photovoltaic electric faults that are both common and costly. Based on interviews with photovoltaic power plant owners, operators, and maintainers, three types of faults are common and of significant interest: disconnects, ground faults, and arc faults. Disconnects can originate from many sources. They are often due to everyday events, such as lawnmowing (accidentally running over a cable), animals eating through the cables, or degradation that occurs over time due to corrosion or general degradation. Ground faults occur when the cables (for example, due to frayed insolation) connect to the ground, relaying current into the ground. These faults are particularly problematic since the ground faults are often intermittent. That is, ground faults commonly appear during rain storms due to a change in soil conductivity and then disappear when the rain ends. This makes the ground fault difficult to find because while current systems can detect the overall change in voltage and current associated with a ground fault, technicians are necessary to locate the fault. As a result, ground faults may disappear before the technician arrives at the power plant. Hence, locating and fixing ground faults often require multiple trips. We also study arc faults, which can result when nearby conductors create an arc of electrical current through the air. While less common, arc faults can be extremely dangerous. The energetic electrical arc can cause fires and destroy equipment, costing significant damage. Overall all three types of faults cost owners and operators money, either from the destruction of equipment or from technician time. Furthermore, while devices exist for detecting ground faults (ground fault circuit interrupters) and arc faults (arc fault circuit interrupter), these systems only search patterns of electrical current that correspond to each fault. This information cannot be used to locate the fault. In addition, these protection systems experience nuisance trips due to nearby electromagnetic interference, such as from a lawn mower or other motors that produce significant amounts of electromagnetic radiation. Hence, the overall goal of this project is to create an SSTDR tool that provides photovoltaic power plants with more reliable fault detection in addition to the localization of faults. SSTDR works by transmitting electrical signals into the photovoltaic string. Those signals reflect from impedance discontinuities (i.e., disconnects, ground faults, and arc faults). These faults are then detected by measuring the presence of a reflection at the SSTDR and can be located by identifying the location of that reflection in time. In addition, unlike current protection systems, these systems do not experience nuisance trips since their low amplitude, high frequency, and coded signal can by analyzed without interference from the regular operational voltage on the photovoltaic string.
Comparison of Fuel Loading Pattern Optimization Results using Exhaustive Search for Fresh Fuels and Local Search for Burned Fuels
Fuel loading pattern optimization is a combinatorial optimization problem from the mathematical point of view. However, exhaustive search is impractical because enormous computational cost is necessary due to huge search space. For this reason, various optimization methods have been developed so far, but no methods are able to guarantee to reach the optimum solution. In the present study, search space is divided into subspaces using key parameters that well represent characteristics of a loading pattern and then promising subspaces are extensively searched. In the present method, balance between division of a search space into subspaces and a search method used in a subspace is essential. For example, when the number of division is set to be one, it is equivalent to the exhaustive search thus is impractical. Similarly, when the division to subspaces is too coarse, an optimum (or near optimum) solution cannot be found through local search in each subspace since design space of a subspace is still too large. Contrary, if division to subspaces is too fine, number of subspaces becomes to large thus promising subspaces cannot be found. In the present study, search space is divided focusing on the location of fresh fuel assemblies with gadolinia since it has significant impact on core characteristics. Number of possible loading patterns of gadolinia bearing fresh fuel assemblies is not very large thus exhaustive search is possible. Local fine search is executed by considering location of burned fuels for each loading pattern of gadolinia bearing fresh fuel assembly. If the same solution is obtained by multiple local searches starting from different initial burnt fuel locations (but the same loading patterns for gadolinia bearing fresh fuel assemblies), the obtained solution is highly likely the optimum in the subspace. In more general, the present method is based on the 'divide and conquer' approach, which is familiar in the optimization field. Namely, after division of search space into subspaces and then promising subspace is searched. Once the promising subspace is found, the subspace is further subdivided into subspaces and repeat the above procedures. This method would be efficient when appropriate balance between search space division method and performance of local search is achieved. The previous works utilizes the similar approach. In reference [1], exhaustive search in small region in a core is carried out focusing on loading patterns of gadolinia bearing fresh fuel assemblies. In reference [2], rough exhaustive search based on the 'batch-wise' loading pattern is performed with the assist of the linear programming. By contrast, in the present study, exhaustive search is carried out for loading patterns of gadolinia bearing fresh fuel assemblies. The random Multi-start Local Search (MSLS) with the direct search or the exhaustive binary swap is used to find out optimal solutions in a subspace, which consists of loading patterns having the same arrangement of gadolinia bearing fresh fuel assemblies. (authors)