Simultaneous Measurement Imputation and Outcome Prediction for Achilles Tendon Rupture Rehabilitation

Achilles Tendon Rupture (ATR) is one of the typical soft tissue injuries. Rehabilitation after such a musculoskeletal injury remains a prolonged process with a very variable outcome. Accurately predicting rehabilitation outcome is crucial for treatment decision support. However, it is challenging to train an automatic method for predicting the ATR rehabilitation outcome from treatment data, due to a massive amount of missing entries in the data recorded from ATR patients, as well as complex nonlinear relations between measurements and outcomes. In this work, we design an end-to-end probabilistic framework to impute missing data entries and predict rehabilitation outcomes simultaneously. We evaluate our model on a real-life ATR clinical cohort, comparing with various baselines. The proposed method demonstrates its clear superiority over traditional methods which typically perform imputation and prediction in two separate stages

Neuropathic Pain Diagnosis Simulator for Causal Discovery Algorithm Evaluation

Discovery of causal relations from observational data is essential for many disciplines of science and real-world applications. However, unlike other machine learning algorithms, whose development has been greatly fostered by a large amount of available benchmark datasets, causal discovery algorithms are notoriously difficult to be systematically evaluated because few datasets with known ground-truth causal relations are available. In this work, we handle the problem of evaluating causal discovery algorithms by building a flexible simulator in the medical setting. We develop a neuropathic pain diagnosis simulator, inspired by the fact that the biological processes of neuropathic pathophysiology are well studied with well-understood causal influences. Our simulator exploits the causal graph of the neuropathic pain pathology and its parameters in the generator are estimated from real-life patient cases. We show that the data generated from our simulator have similar statistics as real-world data. As a clear advantage, the simulator can produce infinite samples without jeopardizing the privacy of real-world patients. Our simulator provides a natural tool for evaluating various types of causal discovery algorithms, including those to deal with practical issues in causal discovery, such as unknown confounders, selection bias, and missing data. Using our simulator, we have evaluated extensively causal discovery algorithms under various settings.Comment: Accepted by NeurIPS 2019, 6 figures, 10 table

Improved Transient Modeling and Stability Analysis for Grid-Following Wind Turbine: Third-Order Sequence Mapping EAC

The increasing penetration of wind power leads to diverse stability issues, which present more extreme fluctuation and nonlinearity, especially under a weak grid. For the nonlinear transient process, it is particularly complex to estimate since no analytical solution can be found in math. To determine the transient stability of the grid-following (GFL) wind turbine, this article develops a third-order transient model of the GFL-doubly fed induction generator, which consists of a second-order phase-locked loop model and a first-order active power control model. Then, a motion discretization equal area criterion (MD-EAC) method is proposed to estimate the damping effect in the second-order system, which could enhance transient trajectory accuracy and improve stable region reliability. Based on MD-EAC, a power angle to time sequence mapping EAC (SM-EAC) method is proposed to perform the stability analysis in third-order systems with active power control. Finally, numerical simulation results are given to validate the effectiveness of the proposed MD-EAC and SM-EAC under various scenarios. And the mechanism of multi-swing stability is analyzed by numerical simulation and SM-EAC

Physics of arctic landfast sea ice and implications on the cryosphere : An overview

Landfast sea ice (LFSI) is a critical component of the Arctic sea ice cover, and is changing as a result of Arctic amplification of climate change. Located in coastal areas, LFSI is of great significance to the physical and ecological systems of the Arctic shelf and in local indigenous communities. We present an overview of the physics of Arctic LFSI and the associated implications on the cryosphere. LFSI is kept in place by four fasten mechanisms. The evolution of LFSI is mostly determined by thermodynamic processes, and can therefore be used as an indicator of local climate change. We also present the dynamic processes that are active prior to the formation of LFSI, and those that are involved in LFSI freeze-up and breakup. Season length, thickness and extent of Arctic LFSI are decreasing and showing different trends in different seas, and therefore, causing environmental and climatic impacts. An improved coordination of Arctic LFSI observation is needed with a unified and systematic observation network supported by cooperation between scientists and indigenous communities, as well as a better application of remote sensing data to acquire detailed LFSI cryosphere physical parameters, hence revolving both its annual cycle and long-term changes. Integrated investigations combining in situ measurements, satellite remote sensing and numerical modeling are needed to improve our understanding of the physical mechanisms of LFSI seasonal changes and their impacts on the environment and climate.Peer reviewe

Topological regression as an interpretable and efficient tool for quantitative structureactivity relationship modeling

Quantitative structure-activity relationship (QSAR)modeling is a powerful tool for drug discovery, yet the lack of interpretability of commonly used QSAR models hinders their application inmolecular design.We propose a similaritybased regression framework, topological regression (TR), that offers a statistically grounded, computationally fast, and interpretable technique to predict drug responses. We compare the predictive performance of TR on 530 ChEMBL human target activity datasets against the predictive performance of deep-learning-based QSAR models. Our results suggest that our sparse TR model can achieve equal, if not better, performance than the deep learningbased QSAR models and provide better intuitive interpretation by extracting an approximate isometry between the chemical space of the drugs and their activity space

Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR

<p>Abstract</p> <p>Background</p> <p>Real-time quantitative reverse transcription PCR (RT-qPCR) data needs to be normalized for its proper interpretation. Housekeeping genes are routinely employed for this purpose, but their expression level cannot be assumed to remain constant under all possible experimental conditions. Thus, a systematic validation of reference genes is required to ensure proper normalization. For soybean, only a small number of validated reference genes are available to date.</p> <p>Results</p> <p>A systematic comparison of 14 potential reference genes for soybean is presented. These included seven commonly used (<it>ACT2, ACT11, TUB4, TUA5, CYP, UBQ10, EF1b</it>) and seven new candidates (<it>SKIP16, MTP, PEPKR1, HDC, TIP41, UKN1, UKN2</it>). Expression stability was examined by RT-qPCR across 116 biological samples, representing tissues at various developmental stages, varied photoperiodic treatments, and a range of soybean cultivars. Expression of all 14 genes was variable to some extent, but that of <it>SKIP16, UKN1 </it>and <it>UKN2 </it>was overall the most stable. A combination of <it>ACT11, UKN1 </it>and <it>UKN2 </it>would be appropriate as a reference panel for normalizing gene expression data among different tissues, whereas the combination SKIP16, UKN1 and MTP was most suitable for developmental stages. <it>ACT11, TUA5 </it>and <it>TIP41 </it>were the most stably expressed when the photoperiod was altered, and <it>TIP41, UKN1 </it>and <it>UKN2 </it>when the light quality was changed. For six different cultivars in long day (LD) and short day (SD), their expression stability did not vary significantly with <it>ACT11, UKN2 </it>and <it>TUB4 </it>being the most stable genes. The relative gene expression level of <it>GmFTL3</it>, an ortholog of Arabidopsis <it>FT </it>(<it>FLOWERING LOCUS T</it>) was detected to validate the reference genes selected in this study.</p> <p>Conclusion</p> <p>None of the candidate reference genes was uniformly expressed across all experimental conditions, and the most suitable reference genes are conditional-, tissue-specific-, developmental-, and cultivar-dependent. Most of the new reference genes performed better than the conventional housekeeping genes. These results should guide the selection of reference genes for gene expression studies in soybean.</p