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Machine learning to predict developmental neurotoxicity with high-throughput data from 2D bio-engineered tissues. 利用2D生物工程组织的高通量数据预测发育神经毒性的机器学习。
Finn Kuusisto, Vitor Santos Costa, Zhonggang Hou, James Thomson, David Page, Ron Stewart

There is a growing need for fast and accurate methods for testing developmental neurotoxicity across several chemical exposure sources. Current approaches, such as in vivo animal studies, and assays of animal and human primary cell cultures, suffer from challenges related to time, cost, and applicability to human physiology. Prior work has demonstrated success employing machine learning to predict developmental neurotoxicity using gene expression data collected from human 3D tissue models exposed to various compounds. The 3D model is biologically similar to developing neural structures, but its complexity necessitates extensive expertise and effort to employ. By instead focusing solely on constructing an assay of developmental neurotoxicity, we propose that a simpler 2D tissue model may prove sufficient. We thus compare the accuracy of predictive models trained on data from a 2D tissue model with those trained on data from a 3D tissue model, and find the 2D model to be substantially more accurate. Furthermore, we find the 2D model to be more robust under stringent gene set selection, whereas the 3D model suffers substantial accuracy degradation. While both approaches have advantages and disadvantages, we propose that our described 2D approach could be a valuable tool for decision makers when prioritizing neurotoxicity screening.

越来越需要快速和准确的方法来测试几种化学暴露源的发育神经毒性。目前的方法,如动物体内研究,以及动物和人类原代细胞培养的测定,受到时间、成本和对人类生理学适用性的挑战。先前的工作已经证明,利用机器学习来预测发育性神经毒性是成功的,使用的是暴露于各种化合物的人体3D组织模型收集的基因表达数据。3D模型在生物学上类似于开发神经结构,但其复杂性需要广泛的专业知识和努力。而不是专注于构建发育神经毒性的分析,我们提出一个更简单的二维组织模型可能证明是足够的。因此,我们比较了基于二维组织模型和基于三维组织模型的预测模型的准确性,发现二维模型的准确性要高得多。此外,我们发现2D模型在严格的基因集选择下更具鲁棒性,而3D模型则遭受严重的精度下降。虽然这两种方法都有优点和缺点,但我们认为,我们所描述的2D方法可能是决策者在优先考虑神经毒性筛查时的有价值的工具。
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引用次数: 4
Evaluating the Performance of the Deep Active Imitation Learning Algorithm in the Dynamic Environment of FIFA Player Agents 深度主动模仿学习算法在FIFA球员代理动态环境中的性能评价
Matheus Prado Prandini Faria, Rita Maria Silva Julia, Lidia Bononi Paiva Tomaz
Deep Learning is a state-of-the-art approach for machine learning using real-world or realist data. FIFA is a soccer simulation game that provides a very realistic environment, but which has been relatively poorly explored in the context of learned game-playing agents. This paper explores the Deep Active Imitation (DAI) learning strategy applied to a dynamic environment in FIFA game. DAI is a segment of Imitation Learning, which consists of a supervised Deep Learning training strategy where the agents learn by observing and replicating human experts' behavior. Noteworthy here is that such learning strategy has only been validated in static navigation scenarios in the sense that the environment is changed only through the actions of the agent. In this way, the main objective of the present work is to investigate the efficacy of DAI to cope with a dynamic FIFA scenario named confrontation mode. The agents were evaluated in terms of in-game score through tournaments against FIFA's engine. The results show that DAI performs well in the confrontation mode. Thus, this work indicates that such learning strategy can be used to solve complex problems.
深度学习是使用真实世界或现实数据进行机器学习的最先进方法。《FIFA》是一款足球模拟游戏,它提供了一个非常逼真的环境,但在学习游戏代理的背景下,这方面的探索相对较少。本文探讨了深度主动模仿(DAI)学习策略在FIFA游戏动态环境中的应用。人工智能是模仿学习的一个部分,它包括一个有监督的深度学习训练策略,其中智能体通过观察和复制人类专家的行为来学习。值得注意的是,这种学习策略只在静态导航场景中得到验证,因为环境只通过智能体的动作来改变。通过这种方式,本工作的主要目的是研究DAI在应对名为对抗模式的动态FIFA场景中的功效。通过与FIFA引擎的比赛来评估代理的游戏内得分。结果表明,DAI在对抗模式下表现良好。因此,这项工作表明,这种学习策略可以用于解决复杂的问题。
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引用次数: 1
Two-Stage Machine Learning Framework for Simultaneous Forecasting of Price-Load in the Smart Grid 智能电网价格负荷同步预测的两阶段机器学习框架
T. Victoire, B. Gobu, S. Jaikumar, Arulmozhi Nagarajan, P. Kanimozhi, T. AmalrajVictoire
In this paper, the electricity load and price patterns of consumers are forecasted using a two-stage forecasting framework. The electricity usage statistics of the consumers are recorded through smart meters and based on the historical load and price patterns the proposed model forecasts the future loads and prices used for further bidding purposes. A hybrid two stage forecasting framework combining the variational mode decomposition (VMD) method, echo state neural network (ESNN) and differential evolution (DE) algorithm is proposed. The training of the hybrid forecasting framework is done by decomposing the load and price time-series data using the VMD. The decomposed data are then used for training the ESNN. Differential evolution algorithm is used to tune the ESNN. Initially, the price and load data are used separately to train the ESNN, and in the second stage, both the data are used along with the forecasted output of the previous stage are used to train the ESNN. The proposed forecasting framework is experimented on 3 smart gird data derived from Smart Meter Energy Consumption Data in London Households of UK Power Networks (UKPN), for demonstration purpose.
本文采用两阶段预测框架对消费者的电力负荷和电价模式进行了预测。智能电表记录了用户的用电量统计数据,并根据历史负荷和价格模式预测未来的负荷和价格,以供进一步投标。提出了一种结合变分模态分解(VMD)方法、回声状态神经网络(ESNN)和差分进化(DE)算法的混合两阶段预测框架。混合预测框架的训练是通过使用VMD分解负荷和价格时间序列数据来完成的。然后将分解后的数据用于训练ESNN。采用差分进化算法对ESNN进行优化。最初,价格和负荷数据分别用于训练ESNN,在第二阶段,这两个数据与前一阶段的预测输出一起用于训练ESNN。该预测框架在英国电网(UKPN)伦敦家庭智能电表能耗数据的3个智能电网数据上进行了实验,以进行演示。
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引用次数: 1
Elastic Time Series Motifs and Discords 弹性时间序列的主题和不和谐
Diego Furtado Silva, Gustavo E. A. P. A. Batista
The recent proposal of the Matrix Profile (MP) has brought the attention of the time series community to the usefulness and versatility of the similarity joins. This primitive has numerous applications including the discovery of time series motifs and discords. However, the original MP algorithm has two prominent limitations: the algorithm only works for Euclidean distance (ED) and it is sensitive to the subsequences length. Is this work, we extend the MP algorithm to overcome both limitations. We use a recently proposed variant of Dynamic Time Warping (DTW), the Prefix and Suffix Invariant DTW (PSI-DTW) distance. The PSI-DTW allows invariance to warp and spurious endpoints caused by segmenting subsequences and has a side-effect of supporting the match of subsequences with different lengths. Besides, we propose a suite of simple methods to speed up the MP calculation, making it more than one order of magnitude faster than a straightforward implementation and providing an anytime feature. We show that using PSI-DTW avoids false positives and false dismissals commonly observed by applying ED, improving the time series motifs and discords discovery in several application domains.
最近提出的矩阵轮廓(Matrix Profile, MP)引起了时间序列界对相似性连接的实用性和通用性的关注。这个原语有许多应用,包括发现时间序列的图案和不和谐。然而,原始的MP算法有两个突出的局限性:该算法只适用于欧几里得距离(ED)和对子序列长度敏感。在这项工作中,我们扩展了MP算法来克服这两个限制。我们使用了最近提出的动态时间扭曲(DTW)的一种变体,前缀和后缀不变量DTW (PSI-DTW)距离。PSI-DTW允许不变性扭曲和由分段子序列引起的伪端点,并且具有支持不同长度子序列匹配的副作用。此外,我们提出了一套简单的方法来加速MP计算,使其比直接实现快一个数量级以上,并提供随时可用的功能。我们表明,使用PSI-DTW可以避免误报和误解雇,从而在多个应用领域改善时间序列基序和不一致发现。
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引用次数: 6
Application of a Graphical Model to Investigate the Utility of Cross-channel Information for Mitigating Reverberation in Cochlear Implants. 应用图形模型研究人工耳蜗中跨通道信息对减轻混响的效用。
Lidea K Shahidi, Leslie M Collins, Boyla O Mainsah

Individuals with cochlear implants (CIs) experience more difficulty understanding speech in reverberant environ-ments than normal hearing listeners. As a result, recent research has targeted mitigating the effects of late reverberant signal reflections in CIs by using a machine learning approach to detect and delete affected segments in the CI stimulus pattern. Previous work has trained electrode-specific classification models to mitigate late reverberant signal reflections based on features extracted from only the acoustic activity within the electrode of interest. Since adjacent CI electrodes tend to be activated concurrently during speech, we hypothesized that incorporating additional information from the other electrode channels, termed cross-channel information, as features could improve classification performance. Cross-channel information extracted in real-world conditions will likely contain errors that will impact classification performance. To simulate extracting cross-channel information in realistic conditions, we developed a graphical model based on the Ising model to systematically introduce errors to specific types of cross-channel information. The Ising-like model allows us to add errors while maintaining the important geometric information contained in cross-channel information, which is due to the spectro-temporal structure of speech. Results suggest the potential utility of leveraging cross-channel information to improve the performance of the reverberation mitigation algorithm from the baseline channel-based features, even when the cross-channel information contains errors.

植入人工耳蜗的个体在混响环境中比正常听力的听者更难以理解言语。因此,最近的研究旨在通过使用机器学习方法来检测和删除CI刺激模式中受影响的片段,从而减轻CI中晚期混响信号反射的影响。以前的工作已经训练了特定于电极的分类模型,以减轻基于仅从感兴趣的电极内的声学活动提取的特征的晚期混响信号反射。由于相邻的CI电极在讲话时往往同时被激活,我们假设将来自其他电极通道的附加信息(称为跨通道信息)作为特征可以提高分类性能。在实际条件下提取的跨通道信息可能包含影响分类性能的错误。为了模拟在现实条件下提取跨通道信息,我们开发了一个基于Ising模型的图形模型,系统地引入特定类型跨通道信息的误差。类ising模型允许我们在保留跨信道信息中包含的重要几何信息的同时添加误差,这是由于语音的光谱-时间结构。结果表明,即使在跨通道信息包含错误的情况下,利用跨通道信息来改善基于基线通道特征的混响缓解算法的性能也具有潜在的效用。
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引用次数: 0
Document Retrieval for Biomedical Question Answering with Neural Sentence Matching. 基于神经语句匹配的生物医学问答文档检索。
Jiho Noh, Ramakanth Kavuluru

Document retrieval (DR) forms an important component in end-to-end question-answering (QA) systems where particular answers are sought for well-formed questions. DR in the QA scenario is also useful by itself even without a more involved natural language processing component to extract exact answers from the retrieved documents. This latter step may simply be done by humans like in traditional search engines granted the retrieved documents contain the answer. In this paper, we take advantage of datasets made available through the BioASQ end-to-end QA shared task series and build an effective biomedical DR system that relies on relevant answer snippets in the BioASQ training datasets. At the core of our approach is a question-answer sentence matching neural network that learns a measure of relevance of a sentence to an input question in the form of a matching score. In addition to this matching score feature, we also exploit two auxiliary features for scoring document relevance: the name of the journal in which a document is published and the presence/absence of semantic relations (subject-predicate-object triples) in a candidate answer sentence connecting entities mentioned in the question. We rerank our baseline sequential dependence model scores using these three additional features weighted via adaptive random research and other learning-to-rank methods. Our full system placed 2nd in the final batch of Phase A (DR) of task B (QA) in BioASQ 2018. Our ablation experiments highlight the significance of the neural matching network component in the full system.

文档检索(DR)是端到端问答(QA)系统中的一个重要组成部分,在该系统中,为格式良好的问题寻求特定的答案。即使没有更复杂的自然语言处理组件来从检索到的文档中提取准确的答案,QA场景中的DR本身也很有用。后一步可以像在传统搜索引擎中一样由人类简单地完成,只要检索到的文档包含答案。在本文中,我们利用通过BioASQ端到端QA共享任务系列提供的数据集,构建了一个有效的生物医学DR系统,该系统依赖于BioASQ训练数据集中的相关答案片段。我们方法的核心是问答句匹配神经网络,该网络以匹配分数的形式学习句子与输入问题的相关性。除了这种匹配分数特征外,我们还利用了两个辅助特征来对文档相关性进行评分:文档发表的期刊名称,以及连接问题中提到的实体的候选答案句子中是否存在语义关系(主谓宾语三元组)。我们使用这三个额外的特征,通过自适应随机研究和其他学习排序方法进行加权,对基线序列依赖性模型得分进行重新排序。我们的全系统在2018年BioASQ任务B(QA)的最后一批A阶段(DR)中排名第二。我们的消融实验强调了神经匹配网络组件在整个系统中的重要性。
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引用次数: 3
Distributed Primal-Dual Proximal Method for Regularized Empirical Risk Minimization 正则化经验风险最小化的分布原-对偶近端方法
M. B. Khuzani
Most high-dimensional estimation and classification methods propose to minimize a loss function (empirical risk) that is the sum of losses associated with each observed data point. We consider the special case of binary classification problems, where the loss is a function of the inner product of the feature vectors and a weight vector. For this special class of classification tasks, the empirical risk minimization problem can be recast as a minimax optimization which has a unique saddle point when the losses are smooth functions. We propose a distributed proximal primal-dual method to solve the minimax problem. We also analyze the convergence of the proposed primal-dual method and show its convergence to the unique saddle point. To prove the convergence results, we present a novel analysis of the consensus terms that takes into account the non-Euclidean geometry of the parameter space. We also numerically verify the convergence of the proposed algorithm for the logistic regression on the Erdos-Reyni random graphs and lattices.
大多数高维估计和分类方法建议最小化损失函数(经验风险),即与每个观测数据点相关的损失总和。我们考虑二元分类问题的特殊情况,其中损失是特征向量和权向量的内积的函数。对于这类特殊的分类任务,当损失为光滑函数时,经验风险最小化问题可以转化为具有唯一鞍点的极大极小优化问题。提出了一种求解极大极小问题的分布式近端原始对偶方法。我们还分析了所提出的原对偶方法的收敛性,并证明了其收敛到唯一鞍点。为了证明收敛性结果,我们提出了一种考虑参数空间的非欧几里德几何的一致项的新分析。在Erdos-Reyni随机图和格上验证了该算法的收敛性。
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引用次数: 0
Fuzzy Echo State Neural Network with Differential Evolution Framework for Time Series Forecasting 基于差分演化框架的模糊回声状态神经网络时间序列预测
D. Nachimuthu, S. Govindaraj, Anand Tirupur Shanmuganathan
In this paper, differential evolution (DE) is used to find optimal weights for echo state neural network model and also to optimize the number of rules of the modeled fuzzy system that presents the input to the echo state neural network (ESNN) model. ESNN designed in this work possess a recurrent neuronal infra-structure called as reservoir. This work aims to develop a good reservoir for the ESNN model employing the coherent features and the ability of the differential evolution algorithm and fuzzy rule base system. DE aims to pre-train the fixed weight values of the network with its effective exploration and exploitation capability and fuzzy rule base system (FRBS) formulates a set of rules, which provides inferences for the inputs presented to the echo state network model. The performance of the developed optimized network is evaluated based on the error metrics and the computational time incurred for the training of the model. The test results of ESNN model using DE and FRBS are compared with that of ESNN without optimization and fuzzy rule to prove its validity and also with the related existing techniques. The perceived DE based fuzzy ESNN model is verified for its effectiveness with a set of time series forecasting benchmark problems. The empirical results prove the superiority and the effectiveness of the DE based fuzzy ESNN learning outcomes.
本文采用差分进化方法对回声状态神经网络模型求最优权值,并对作为回声状态神经网络(ESNN)模型输入的模糊系统规则数进行优化。在这项工作中设计的ESNN具有称为水库的循环神经元基础结构。本工作旨在利用差分进化算法和模糊规则库系统的相干特征和能力,为ESNN模型开发一个良好的库。模糊规则库系统(FRBS)利用其有效的探索和开发能力对网络的固定权值进行预训练,并制定一套规则,为回波状态网络模型的输入提供推理。基于误差度量和模型训练所需的计算时间,对所开发的优化网络的性能进行了评估。将基于DE和FRBS的ESNN模型的测试结果与未优化和模糊规则的ESNN模型的测试结果进行了比较,以证明其有效性,并与现有相关技术进行了比较。通过一组时间序列预测基准问题验证了基于感知DE的模糊ESNN模型的有效性。实验结果证明了基于DE的模糊ESNN学习结果的优越性和有效性。
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引用次数: 1
Evaluation of a New Kernel-Based Classifier in Eye Pupil Detection 一种新的基于核的瞳孔检测分类器的评价
P. Monforte, G. Araujo, A. Lima
Accurate pupil location is paramount to applications such as gaze estimation, assistive technologies and several man-machine interfaces as the ones found in smartphones and VR applications. We introduce a new classifier stemmed from the Inner Product Detector and investigate its features on the challenging task of pupil localization. IPD (Inner Product Detector) is a classifier with high potential in facial landmarks detection. It is robust to variations in the desired pattern while maintaining good generalization and computational efficiency. However, one possible limitation is its linear behavior, which could be overcome by aggregating non-linear techniques, such as kernel methods. Although kernel classifiers have been exhaustively studied in the past two decades, it was not analyzed or applied with IPD, yet. The proposed KIPD achieves in the worst case an accuracy of 97.41% on the BioID dataset and 93.71% in LFPW dataset both at 10% of the interocular distance. In this paper the KIPD is compared to the state of the art methods, including the ones using deep learning, being competitive in terms of accuracy as well as computational complexity.
准确的瞳孔定位对于诸如凝视估计、辅助技术和智能手机和虚拟现实应用中的一些人机界面等应用至关重要。我们引入了一种源于内积检测器的分类器,并研究了它在瞳孔定位这一具有挑战性的任务上的特点。内积检测器(Inner Product Detector, IPD)是一种很有潜力的人脸识别分类器。它对期望模式的变化具有鲁棒性,同时保持良好的泛化和计算效率。然而,一个可能的限制是它的线性行为,这可以通过聚合非线性技术(如核方法)来克服。尽管在过去的二十年里,核分类器已经得到了详尽的研究,但它还没有被分析或应用于IPD。在眼间距离为10%的情况下,所提出的KIPD在BioID数据集上的准确率为97.41%,在LFPW数据集上的准确率为93.71%。在本文中,KIPD与最先进的方法进行了比较,包括使用深度学习的方法,在准确性和计算复杂性方面具有竞争力。
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引用次数: 2
An Approximative Bayes-Optimal Kernel Classifier Based on Version Space Reduction 基于版本空间约简的近似贝叶斯最优核分类器
Karen Braga Enes, Saulo Moraes Villela, G. Pappa, R. F. Neto
The Bayes-optimal classifier is defined as a classifier that induces an hypothesis able to minimize the prediction error for any given sample in binary classification problems. Finding the Bayes-optimal classifier is an intractable problem. It is known that it is approximately equivalent to the center of mass of the version space, which is given by the set of all classifiers consistent with the training set. Previously solutions to find the center of mass are not feasible, as they present a high computational cost, and do not work properly in non-linear separable problems. Aiming to solve these problems, this paper presents the Dual Version Space Reduction Machine (Dual VSRM), an effective kernel method to approximate the center of mass of the version space. The Dual VSRM algorithm employs successive reductions of the version space based on an oracle's decision. As an oracle, we propose the Ensemble of Dissimilar Balanced Kernel Perceptrons (EBPK). EBPK enhances the accuracy of each individual classifier by balancing the final hyperplane solution while maximizing the diversity of its components by applying a dissimilarity measure. In order to evaluate the proposed methods, we conduct an experimental evaluation on 7 datasets. We compare the performance of our proposed methods against several baselines. Our results for EBKP indicate the strategies for improving individual accuracy and diversity of the ensemble components work properly. Also, the Dual VSRM consistently outperforms the baselines, indicating that the proposed method generates a better approximation to the center of mass.
贝叶斯最优分类器被定义为一种分类器,它可以诱导一个假设,使任何给定样本在二值分类问题中的预测误差最小化。寻找贝叶斯最优分类器是一个棘手的问题。已知它近似等价于版本空间的质心,由与训练集一致的所有分类器的集合给出。以前的求解质心的方法是不可行的,因为它们的计算成本很高,而且在非线性可分离问题中不能正常工作。针对这些问题,本文提出了一种有效的逼近版本空间质心的核方法——双版本空间约简机(Dual VSRM)。Dual VSRM算法基于oracle的决策对版本空间进行连续缩减。作为一种预测,我们提出了不相似平衡核感知器集成(EBPK)。EBPK通过平衡最终的超平面解决方案来提高每个分类器的准确性,同时通过应用不相似性度量来最大化其组件的多样性。为了评估所提出的方法,我们在7个数据集上进行了实验评估。我们将我们提出的方法的性能与几个基线进行比较。我们对EBKP的结果表明,提高集成组件的个体精度和多样性的策略是有效的。此外,Dual VSRM始终优于基线,表明所提出的方法可以更好地逼近质心。
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引用次数: 0
期刊
Proceedings of the ... International Conference on Machine Learning and Applications. International Conference on Machine Learning and Applications
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