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Author(s):  
Narelle Jones ◽  
Sally Sherwen ◽  
Rachel Robbins ◽  
David McLelland ◽  
Alexandra Whittaker

Zoos are increasingly putting in place formalized animal welfare assessment programs to allow monitoring of welfare over time, as well as to aid in resource prioritization. These programs tend to rely on assessment tools that incorporate resource-based and observational animal- focused measures since it is rarely feasible to obtain measures of physiology in zoo-housed animals. A range of assessment tools are available which commonly have a basis in the Five Domains framework. A comprehensive review of the literature was conducted to bring together recent studies examining welfare assessment methods in zoo animals. A summary of these methods is provided with advantages and limitations of the approach es presented. We then highlight practical considerations with respect to implementation of these tools into practice, for example scoring schemes, weighting of criteria, and innate animal factors for consideration. It is concluded that would be value in standardizing guidelines for development of welfare assessment tools since zoo accreditation bodies rarely prescribe these. There is also a need to develop taxon or species- specific assessment tools to inform welfare management.


Author(s):  
narelle jones ◽  
Sally Sherwen ◽  
Rachel Robbins ◽  
David McLelland ◽  
Alexandra Whittaker

Zoos are increasingly putting in place formalized animal welfare assessment programs to allow monitoring of welfare over time, as well as to aid in resource prioritization. These programs tend to rely on assessment tools that incorporate resource-based and observational animal- focused measures since it is rarely feasible to obtain measures of physiology in zoo-housed animals. A range of assessment tools are available which commonly have a basis in the Five Domains framework. A comprehensive review of the literature was conducted to bring together recent studies examining welfare assessment methods in zoo animals. A summary of these methods is provided with advantages and limitations of the approach es presented. We then highlight practical considerations with respect to implementation of these tools into practice, for example scoring schemes, weighting of criteria, and innate animal factors for consideration. It is concluded that would be value in standardizing guidelines for development of welfare assessment tools since zoo accreditation bodies rarely prescribe these. There is also a need to develop taxon or species- specific assessment tools to inform welfare management.


2021 ◽  
Author(s):  
Daniel Liu ◽  
Martin Steinegger

Background: The Smith-Waterman-Gotoh alignment algorithm is the most popular method for comparing biological sequences. Recently, Single Instruction Multiple Data methods have been used to speed up alignment. However, these algorithms have limitations like being optimized for specific scoring schemes, cannot handle large gaps, or require quadratic time computation. Results: We propose a new algorithm called block aligner for aligning nucleotide and protein sequences. It greedily shifts and grows a block of computed scores to span large gaps within the aligned sequences. This greedy approach is able to only compute a fraction of the DP matrix. In exchange for these features, there is no guarantee that the computed scores are accurate compared to full DP. However, in our experiments, we show that block aligner performs accurately on various realistic datasets, and it is up to 9 times faster than the popular Farrar's algorithm for protein global alignments. Conclusions: Our algorithm has applications in computing global alignments and X-drop alignments on proteins and long reads. It is available as a Rust library at https://github.com/Daniel-Liu-c0deb0t/block-aligner.


2021 ◽  
Author(s):  
Bhasker Sri Harsha Suri ◽  
Manish Srivastava ◽  
Kalidas Yeturu

Neural networks suffer from catastrophic forgetting problem when deployed in a continual learning scenario where new batches of data arrive over time; however they are of different distributions from the previous data used for training the neural network. For assessing the performance of a model in a continual learning scenario, two aspects are important (i) to compute the difference in data distribution between a new and old batch of data and (ii) to understand the retention and learning behavior of deployed neural networks. Current techniques indicate the novelty of a new data batch by comparing its statistical properties with that of the old batch in the input space. However, it is still an open area of research to consider the perspective of a deployed neural network’s ability to generalize on the unseen data samples. In this work, we report a dataset distance measuring technique that indicates the novelty of a new batch of data while considering the deployed neural network’s perspective. We propose the construction of perspective histograms which are a vector representation of the data batches based on the correctness and confidence in the prediction of the deployed model. We have successfully tested the hypothesis empirically on image data coming MNIST Digits, MNIST Fashion, CIFAR10, for its ability to detect data perturbations of type rotation, Gaussian blur, and translation. Upon new data, given a model and its training data, we have proposed and evaluated four new scoring schemes, retention score (R), learning score (L), Oscore and SP-score for studying how much the model can retain its performance on past data, how much it can learn new data, the combined expression for the magnitude of retention and learning and stability-plasticity characteristics respectively. The scoring schemes have been evaluated MNIST Digits and MNIST Fashion data sets on different types of neural network architectures based on the number of parameters, activation functions, and learning loss functions, and an instance of a typical analysis report is presented. Machine learning model maintenance is a reality in production systems in the industry, and we hope our proposed methodology offers a solution to the need of the day in this aspect.


2021 ◽  
Author(s):  
Bhasker Sri Harsha Suri ◽  
Manish Srivastava ◽  
Kalidas Yeturu

Neural networks suffer from catastrophic forgetting problem when deployed in a continual learning scenario where new batches of data arrive over time; however they are of different distributions from the previous data used for training the neural network. For assessing the performance of a model in a continual learning scenario, two aspects are important (i) to compute the difference in data distribution between a new and old batch of data and (ii) to understand the retention and learning behavior of deployed neural networks. Current techniques indicate the novelty of a new data batch by comparing its statistical properties with that of the old batch in the input space. However, it is still an open area of research to consider the perspective of a deployed neural network’s ability to generalize on the unseen data samples. In this work, we report a dataset distance measuring technique that indicates the novelty of a new batch of data while considering the deployed neural network’s perspective. We propose the construction of perspective histograms which are a vector representation of the data batches based on the correctness and confidence in the prediction of the deployed model. We have successfully tested the hypothesis empirically on image data coming MNIST Digits, MNIST Fashion, CIFAR10, for its ability to detect data perturbations of type rotation, Gaussian blur, and translation. Upon new data, given a model and its training data, we have proposed and evaluated four new scoring schemes, retention score (R), learning score (L), Oscore and SP-score for studying how much the model can retain its performance on past data, how much it can learn new data, the combined expression for the magnitude of retention and learning and stability-plasticity characteristics respectively. The scoring schemes have been evaluated MNIST Digits and MNIST Fashion data sets on different types of neural network architectures based on the number of parameters, activation functions, and learning loss functions, and an instance of a typical analysis report is presented. Machine learning model maintenance is a reality in production systems in the industry, and we hope our proposed methodology offers a solution to the need of the day in this aspect.


2020 ◽  
Vol 21 (S13) ◽  
Author(s):  
Nauman Ahmed ◽  
Tong Dong Qiu ◽  
Koen Bertels ◽  
Zaid Al-Ars

Abstract Background In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a fast and accurate read overlapper that can be used for de novo assembly of state-of-the-art third generation long DNA reads. Darwin is designed to be hardware-friendly and can be accelerated on specialized computer system hardware to achieve higher performance. Results This work accelerates Darwin on GPUs. Using real Pacbio data, our GPU implementation on Tesla K40 has shown a speedup of 109x vs 8 CPU threads of an Intel Xeon machine and 24x vs 64 threads of IBM Power8 machine. The GPU implementation supports both linear and affine gap, scoring model. The results show that the GPU implementation can achieve the same high speedup for different scoring schemes. Conclusions The GPU implementation proposed in this work shows significant improvement in performance compared to the CPU version, thereby making it accessible for utilization as a practical read overlapper in a DNA assembly pipeline. Furthermore, our GPU acceleration can also be used for performing fast Smith-Waterman alignment between long DNA reads. GPU hardware has become commonly available in the field today, making the proposed acceleration accessible to a larger public. The implementation is available at https://github.com/Tongdongq/darwin-gpu.


2020 ◽  
Vol 13 (1) ◽  
pp. 84-107
Author(s):  
Farah Shooraki ◽  
Hossein Barati ◽  
Ahmad Moinzadeh

Abstract This study aims to determine the linguistic and discoursal differences in essays produced by Iranian test-takers of TOEFL-iBT in response to integrated and independent writing tasks. A sample of 40 essays, written by 20 Iranian test-takers of scored integrated and independent writing tasks, was compared and analyzed in terms of the four latent constructs of text easability (fourteen variables), cohesion (nine variables), lexical sophistication (nineteen variables), and syntactic complexity (six variables), using the Coh-Metrix 3.0 program. Results indicate differences in the linguistic and discoursal features of integrated and independent writing tasks. The findings reveal that the scores on writing tasks of EFL test-takers can be anchored empirically through the analysis of some discourse qualities like cohesion. Independent tasks contain more connectives and particles so they can result in better discourse structure organization and the generation of more cohesive devices. Stakeholders of the test should verify test constructs in terms of particular contexts like EFL and communicative views of language proficiency. Consequently, the findings contribute to the ongoing validity argument on TOEFL-iBT writing tasks for designing and interpreting scoring schemes for the writing component of the test.


2020 ◽  
Vol 48 (10) ◽  
pp. e55-e55 ◽  
Author(s):  
Simon Cabello-Aguilar ◽  
Mélissa Alame ◽  
Fabien Kon-Sun-Tack ◽  
Caroline Fau ◽  
Matthieu Lacroix ◽  
...  

Abstract Single-cell transcriptomics offers unprecedented opportunities to infer the ligand–receptor (LR) interactions underlying cellular networks. We introduce a new, curated LR database and a novel regularized score to perform such inferences. For the first time, we try to assess the confidence in predicted LR interactions and show that our regularized score outperforms other scoring schemes while controlling false positives. SingleCellSignalR is implemented as an open-access R package accessible to entry-level users and available from https://github.com/SCA-IRCM. Analysis results come in a variety of tabular and graphical formats. For instance, we provide a unique network view integrating all the intercellular interactions, and a function relating receptors to expressed intracellular pathways. A detailed comparison of related tools is conducted. Among various examples, we demonstrate SingleCellSignalR on mouse epidermis data and discover an oriented communication structure from external to basal layers.


Author(s):  
Simon Cabello-Aguilar ◽  
Fabien Kon Sun Tack ◽  
Mélissa Alame ◽  
Caroline Fau ◽  
Matthieu Lacroix ◽  
...  

ABSTRACTSingle-cell transcriptomics offers unprecedented opportunities to infer the ligand-receptor interactions underlying cellular networks. We introduce a new, curated ligand-receptor database and a novel regularized score to perform such inferences. For the first time, we try to assess the confidence in predicted ligand-receptor interactions and show that our regularized score outperforms other scoring schemes while controlling false positives. SingleCellSignalR is implemented as an open-access R package accessible to entry-level users and available from https://github.com/SCA-IRCM. Analysis results come in a variety of tabular and graphical formats. For instance, we provide a unique network view integrating all the intercellular interactions, and a function relating receptors to expressed intracellular pathways. A detailed comparison with related tools is conducted. Among various examples, we demonstrate SingleCellSignalR on mouse epidermis data and discover an oriented communication structure from external to basal layers.


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