Radiomics feature stability of open-source software evaluated on apparent diffusion coefficient maps in head and neck cancer

Radiomics is a promising technique for discovering image based biomarkers of therapy response in cancer. Reproducibility of radiomics features is a known issue that is addressed by the image biomarker standardisation initiative (IBSI), but it remains challenging to interpret previously published radiomics signatures. This study investigates the reproducibility of radiomics features calculated with two widely used radiomics software packages (IBEX, MaZda) in comparison to an IBSI compliant software package (PyRadiomics). Intensity histogram, shape and textural features were extracted from 334 diffusion weighted magnetic resonance images of 59 head and neck cancer (HNC) patients from the PREDICT-HN observational radiotherapy study. Based on name and linear correlation, PyRadiomics shares 83 features with IBEX and 49 features with MaZda, a sub-set of well correlated features are considered reproducible (IBEX: 15 features, MaZda: 18 features). We explore the impact of including non-reproducible radiomics features in a HNC radiotherapy response model. It is possible to classify equivalent patient groups using radiomic features from either software, but only when restricting the model to reliable features using a correlation threshold method. This is relevant for clinical biomarker validation trials as it provides a framework to assess the reproducibility of reported radiomic signatures from existing trials.

Fin whale acoustic populations present in New Zealand waters: Description of song types, occurrence and seasonality using passive acoustic monitoring

Southern fin whales (Balaenoptera physalus) are known to migrate from the Antarctic to mid-latitudes during winter for breeding, but the occurrence and distribution of this species is not well known in the waters around New Zealand. The ‘doublet’ calls are one of the main calls emitted specifically by fin whales and repeated in a regular pattern, which make the acoustic detection of these calls relevant to detect the presence of fin whales. Using a signal processing algorithm to detect ‘doublet’ calls emitted by fin whales, we studied the occurrence, characteristics and seasonality of these ‘doublet’ calls in two regions around New Zealand; Cook Strait in 2016/2017 and offshore Gisborne in 2014/2015. The call detection procedure consisted of binarization of the spectrogram and a cross-correlation between the binarized spectrogram and a template of binarized ‘doublet’ calls spectrogram. A binarization threshold for the data spectrograms and a cross correlation threshold were then determined through multiple trials on a training dataset and a Receiver Operating Characteristics (ROC) curve. Fin whale ‘doublet’ calls occurred on the east side of New Zealand’s Cook Strait during austral winter, specifically in June 2017 and offshore Gisborne in June-August 2014. No ‘doublet’ calls were detected on the west side of Cook Strait. The ‘doublet’ calls’ Inter-Note Interval (INI) was similar in both datasets. However, there was a difference in alternation of the mean frequency for both HF components of ‘doublet’ calls in Cook Strait and Gisborne. As the song types were compared with those previously described in the literature, our findings suggest that some fin whales wintering in New Zealand waters may be part of a broader ‘acoustic population’ whose range extends west to southern Australia and south to Antarctica.

Correlation and Calibration of 4D Seismic Vintages for Effective Postproduction Intervention

Poor or low data quality usually has an adverse effect on the quantitative usage of (4D) seismic data for accurate analysis. Repeatability of 4D Seismic or time-lapse survey is considered as a vital tool for effective, potent, and impressive monitoring of productivity of reservoirs. Inconsistencies and disagreement of ‘time-lapse’ data will greatly affect the accuracy and outcome of research when comparing two or more seismic surveys having low repeatability. Correlation is a statistic procedure that measures the linear relation between all points of two variables. Error due to acquisition and processing must be checked for before interpretation in order to minimize exploration failure and the number of dry holes drilled. The seismic data available for this study comprises of 779 crosslines and 494 inlines. The 4D seismic data consisting of the base Seismic shot in 1998 before production and the monitor Seismic shot in 2010 at different stages of hydrocarbon production were cross correlated to ascertain repeatability between the two vintages. A global average matching process was applied while phase and time shift were estimated using the Russell-Liang technique. Two pass full shaping filters were applied for the phase matching. Maximum and minimum ‘cross-correlation’ are 0.85 (85%) and 0.60 (60%) respectively. Statistics of the ‘cross-correlation’ shift show standard deviation (0.3), variance (0.12), and root mean square (0.78). For high percentage repeatability and maximum correlations, the requested correlation threshold is 0.7 but 1 and 0.99 were obtained for the first and the second matching respectively. Conclusively, the overall results show that there is high repeatability between the 4D seismic data used and the data can be employed conveniently for accurate ‘time-lapse’ (future) production monitoring and investigation on the field.

Robust Frame Duplication Detection for Degraded Videos

To detect frame duplication in degraded videos, we proposed a coarse-to-fine approach based on locality-sensitive hashing and image registration. The proposed method consists of a coarse matching stage and a duplication verification step. In the coarse matching stage, visually similar frame sequences are preclustered by locality-sensitive hashing and considered as potential duplication candidates. These candidates are further checked by a duplication verification step. Being different from the existing methods, our duplication verification does not rely on a fixed distance (or correlation) threshold to judge whether two frames are identical. We resorted to image registration, which is intrinsically a global optimal matching process, to determine whether two frames coincide with each other. We integrated the stability information into the registration objective function to make the registration process more robust for degraded videos. To test the performance of the proposed method, we created a dataset, which consists of 3 subsets of different kinds of degradation and 117 forged videos in total. The experimental results show that our method outperforms state-of-the-art methods for most cases in our dataset and exhibits outstanding robustness under different conditions. Thanks to the coarse-to-fine strategy, the running time of the proposed method is also quite competitive.

Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel

Background Correlation network analysis has become an integral tool to study metabolite datasets. Networks are constructed by omitting correlations between metabolites based on two thresholds—namely the r and the associated p-values. While p-value threshold settings follow the rules of multiple hypotheses testing correction, guidelines for r-value threshold settings have not been defined. Results Here, we introduce a method that allows determining the r-value threshold based on an iterative approach, where different networks are constructed and their network topology is monitored. Once the network topology changes significantly, the threshold is set to the corresponding correlation coefficient value. The approach was exemplified on: (i) a metabolite and morphological trait dataset from a potato association panel, which was grown under normal irrigation and water recovery conditions; and validated (ii) on a metabolite dataset of hearts of fed and fasted mice. For the potato normal irrigation correlation network a threshold of Pearson’s |r|≥ 0.23 was suggested, while for the water recovery correlation network a threshold of Pearson’s |r|≥ 0.41 was estimated. For both mice networks the threshold was calculated with Pearson’s |r|≥ 0.84. Conclusions Our analysis corrected the previously stated Pearson’s correlation coefficient threshold from 0.4 to 0.41 in the water recovery network and from 0.4 to 0.23 for the normal irrigation network. Furthermore, the proposed method suggested a correlation threshold of 0.84 for both mice networks rather than a threshold of 0.7 as applied earlier. We demonstrate that the proposed approach is a valuable tool for constructing biological meaningful networks.

Optimization of In-Core Detector Locations in AHWR Using Bond Energy Algorithm

A solution to optimization of in-core detectors placement for Advanced Heavy Water Reactor (AHWR) has been attempted. AHWR houses in-core detector units with Self-Powered Neutron Detectors (SPND) distributed axially and their measurement serves as an input to Online Flux Mapping System (OFMS) to monitor the three-dimensional neutron flux distribution. There is a requirement of placing these in-core detectors at optimum locations to retrieve maximum information about the reactor while keeping their number to the minimum. This paper attempts to optimize SPND placement through the application of Bond Energy Algorithm (BEA), a clustering technique which groups the SPNDs based on correlation. This works on the concept of grouping strongly correlated SPNDs into blocks and choosing one SPND from each block as the optimal location. The higher the uncorrelation among optimal SPNDs, the higher the independent information retrieved about the actual configuration of the reactor. It can be inferred from this work that the number and location of SPNDs are highly dependent on the initial set of SPND locations and the correlation threshold. It can be seen that as the correlation threshold increases, the number of optimal locations increases. The obtained optimal locations have been validated for various operational reactor configurations using different Flux Mapping Algorithms (FMA).

Silent VLPs At Stromboli: Implications For Slug Vs. Plug

<p>Very long period (VLP) seismic signals observed in volcanic environments are thought to be produced by magma and gas flow through conduits. Stromboli Volcano, Italy, typically produces hundreds of VLPs per day. These have been generally attributed to the flow of gas slugs through the shallow plumbing system and thus linked to the mechanism thought to drive Strombolian explosions. During a 6-day-long seismo-acoustic campaign in May 2018 (a period characterized by relatively low activity) we recorded 1900+ seismic events, the majority of which have significant energy in the VLP (2-100 s) band. We used a coincident STA/LTA trigger to identify seismic events in continuous waveform data and then used the PeakMatch algorithm (Rodgers et al., 2015) to identify seismic multiplets, with a focus on VLPs. To identify explosions, we applied the same coincident trigger to infrasound data, and manually identified gas jetting events using spectrograms and high-pass-filtered (20 Hz) waveforms. </p><p> </p><p>We identified ~250 explosions and ~600 jetting events. Seismic multiplet analysis identified two main families of repeating events. Family 1 (F1) has over 500 events and Family 2 (F2) has over 150 events based on a 0.7 correlation threshold. We find that F1 VLPs coincide in time with ~6% of explosions and ~0.8% of jetting events and F2 VLPs coincide in time with ~28% of explosions and ~2.7% of jetting events (we term these “silent VLPs”). These VLPs do not correspond with lava effusion (Marchetti and Ripepe, 2005; Ripepe et al., 2015). F2 have a higher dominant period (8-10 s) compared to F1 (3-4 s). The repeating VLPs are part of a broadband signal and the higher frequencies start after the VLP. VLP peak amplitudes are generally larger for F1 events. The dip of the VLP particle motion roughly locates the F1 and F2 VLP source centroids beneath the active crater and are stable throughout the dataset. Both VLP displacements show a small outward, large inward, and subsequent large outward motion from the crater. The lack of explosions relative to repeating VLPs does not support the slug model, where a slug rises through a conduit, generates a VLP through interactions with changes in conduit geometry, and then bursts at the lava free surface. Our observations support the plug model (Suckale et al., 2016). We suggest the “silent” VLPs are generated when the gas bubbles interact with and move into the semipermeable plug. Then the plug behaves as a mechanical filter for gas escape and allows for passive and explosive escape mechanisms.</p>

Is the world small enough? — A view from currencies

Exchange rates are important indicators of the economic power of countries, directly affected by the international trading patterns and relations. Since almost every pair of countries in the globalized world are economically and financially related, exchange rates can be evaluated as nodes of a global financial network to make meaningful inferences. In this study, a financial network approach is conducted by evaluating the movements of the most traded 35 currencies against gold between years 2005 and 2017. Using graph theory and statistical methods, the analysis of economic relations between currencies is carried out, supported with geographical and cultural inferences. A risk map of currencies is generated through the portfolio optimization. Another approach of applying various threshold levels for correlations to determine connections between currencies is also employed. Results indicate that there exists a saddle point for correlation threshold as 0.9 which results in a robust network topology that is highly modular and clustered, also dominantly displaying small-world and scale-free properties.

A Correlation–Scale–Threshold Method for Spatial Variability of Rainfall

Rainfall data at fine spatial resolutions are often required for various studies in hydrology and water resources. However, such data are not widely available, as their collection is normally expensive and time-consuming. A common practice to obtain fine-spatial-resolution rainfall data is to employ interpolation schemes to derive them based on data available at nearby locations. Such interpolation schemes are generally based on rainfall correlation or distance between stations. The present study proposes a combined rainfall correlation-spatial scale-correlation threshold method for representing spatial rainfall variability. The method is applied to monthly rainfall data at a resolution of 0.25 × 0.25 latitude/longitude across Australia, available from the Tropical Rainfall Measuring Mission (TRMM 3B43 version). The results indicate that rainfall dynamics in northern and northeastern Australia have far greater spatial correlations when compared to the other regions, especially in southern and southeastern Australia, suggesting that tropical climates generally have greater spatial rainfall correlations when compared to temperate, oceanic, and continental climates, subject to other influencing factors. The implications of the outcomes for rainfall data interpolation and the rain gauge monitoring network are also discussed, especially based on results obtained for ten major cities in Australia.

Passive Detection of Low-Altitude Signal Sources Using an Improved Cross-Correlation Algorithm

The passive detection of low-altitude signal sources is studied using an improved cross-correlation method in the time–frequency domain. A matching template is designed for signal cross-correlation, and a cross-correlation threshold is used to determine whether a signal source is present or not. An improved cross-correlation method is also proposed to estimate the direction of arrival and communication frequency of a signal source. Furthermore, the distance and signal-to-noise ratio are estimated using an energy detector. Outdoor data from a bridge in the Jimo District, Qingdao, and indoor data from a research laboratory are used for performance evaluation. The results obtained show that the proposed method can provide better passive detection of low-altitude signal sources compared to several well-known algorithms in the literature. In addition, this method is more suitable for long-distance detection.