Motivation: Enhancers are important cis-regulatory elements that regulate a wide range of biological functions and enhance the transcription of target genes. Although many state-of-the-art computational methods have been proposed in order to efficiently identify enhancers, learning globally contextual features is still one of the challenges for computational methods. Regarding the similarities between biological sequences and natural language sentences, the novel BERT-based language techniques have been applied to extracting complex contextual features in various computational biology tasks such as protein function/structure prediction. To speed up the research on enhancer identification, it is urgent to construct a BERT-based enhancer language model. Results: In this paper, we propose a multi-scale enhancer identification method (iEnhancer-ELM) based on enhancer language models, which treat enhancer sequences as natural language sentences that are composed of k-mer nucleotides. iEnhancer-ELM can extract contextual information of multi-scale k-mers with positions from raw enhancer sequences. Benefiting from the complementary information of k-mers in multi-scale, we ensemble four iEnhancer-ELM models for improving enhancer identification. The benchmark comparisons show that our model outperforms state-of-the-art methods. By the interpretable attention mechanism, we finds 30 biological patterns, where 40% (12/30) are verified by a widely used motif tool (STREME) and a popular dataset (JASPAR), demonstrating our model has a potential ability to reveal the biological mechanism of enhancer. Availability: The source code are available at https://github.com/chen-bioinfo/iEnhancer-ELM Contact: junjiechen@hit.edu.cn and junjie.chen.hit@gmail.com; Supplementary information: Supplementary data are available at Bioinformatics online.
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In deep neural networks (DNNs), there are a huge number of weights and multiply-and-accumulate (MAC) operations. Accordingly, it is challenging to apply DNNs on resource-constrained platforms, e.g., mobile phones. Quantization is a method to reduce the size and the computational complexity of DNNs. Existing quantization methods either require hardware overhead to achieve a non-uniform quantization or focus on model-wise and layer-wise uniform quantization, which are not as fine-grained as filter-wise quantization. In this paper, we propose a class-based quantization method to determine the minimum number of quantization bits for each filter or neuron in DNNs individually. In the proposed method, the importance score of each filter or neuron with respect to the number of classes in the dataset is first evaluated. The larger the score is, the more important the filter or neuron is and thus the larger the number of quantization bits should be. Afterwards, a search algorithm is adopted to exploit the different importance of filters and neurons to determine the number of quantization bits of each filter or neuron. Experimental results demonstrate that the proposed method can maintain the inference accuracy with low bit-width quantization. Given the same number of quantization bits, the proposed method can also achieve a better inference accuracy than the existing methods.
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Deep neural networks (DNNs) have successfully been applied in many fields in the past decades. However, the increasing number of multiply-and-accumulate (MAC) operations in DNNs prevents their application in resource-constrained and resource-varying platforms, e.g., mobile phones and autonomous vehicles. In such platforms, neural networks need to provide acceptable results quickly and the accuracy of the results should be able to be enhanced dynamically according to the computational resources available in the computing system. To address these challenges, we propose a design framework called SteppingNet. SteppingNet constructs a series of subnets whose accuracy is incrementally enhanced as more MAC operations become available. Therefore, this design allows a trade-off between accuracy and latency. In addition, the larger subnets in SteppingNet are built upon smaller subnets, so that the results of the latter can directly be reused in the former without recomputation. This property allows SteppingNet to decide on-the-fly whether to enhance the inference accuracy by executing further MAC operations. Experimental results demonstrate that SteppingNet provides an effective incremental accuracy improvement and its inference accuracy consistently outperforms the state-of-the-art work under the same limit of computational resources.
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Entities, as important carriers of real-world knowledge, play a key role in many NLP tasks. We focus on incorporating entity knowledge into an encoder-decoder framework for informative text generation. Existing approaches tried to index, retrieve, and read external documents as evidence, but they suffered from a large computational overhead. In this work, we propose an encoder-decoder framework with an entity memory, namely EDMem. The entity knowledge is stored in the memory as latent representations, and the memory is pre-trained on Wikipedia along with encoder-decoder parameters. To precisely generate entity names, we design three decoding methods to constrain entity generation by linking entities in the memory. EDMem is a unified framework that can be used on various entity-intensive question answering and generation tasks. Extensive experimental results show that EDMem outperforms both memory-based auto-encoder models and non-memory encoder-decoder models.
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通常,通过解决轨迹优化问题并使用跟踪控制器来执行轨迹,通常在四足机器人上实现了专业运动。这种方法与通常通过在线重新计划控制常规步态的模型预测控制(MPC)策略平行。在这项工作中,我们提出了一种非线性MPC(NMPC)技术,该技术可以在统一框架内自然地重新计划专门运动技能和常规运动。 NMPC有关混合动力学模型的原因,并使用约束差分动态编程(DDP)求解器的变体来解决。拟议的NMPC使机器人能够发挥各种敏捷技能,例如跳跃,边界和小跑,以及这些技能之间的快速过渡。我们通过三个具有挑战性的运动序列评估了提出的算法,这些算法将多个敏捷技能结合在两个四倍的平台,即Unitree A1和MIT Mini Cheetah上,显示了其有效性和通用性。
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强化学习(RL)见证了四足动物的大步进展,在可靠的SIM转移到现实的政策转移方面持续进展。但是,重用另一个机器人的政策仍然是一个挑战,这可以节省重新培训的时间。在这项工作中,我们提出了一个用于零射击政策重新定位的框架,其中可以在不同形状和尺寸的机器人之间转移多种运动技能。新框架以系统整合RL和模型预测控制(MPC)的计划和控制管道为中心。计划阶段采用RL来生成动态合理的轨迹以及联系时间表,避免了接触序列优化的组合复杂性。然后,将这些信息用于播种MPC,以通过新的混合运动动力学(HKD)模型稳定和鲁棒性地推出策略,该模型隐含地优化了立足点位置。硬件结果表明能够将政策从A1和Laikago机器人转移到MIT MIT MINI CHEETAH机器人,而无需重新调整政策。
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本文提出了一种新方法,该方法融合了混响场中的声学测量和低临界性惯性测量单元(IMU)运动报告,以同时定位和映射(SLAM)。与仅使用声学数据进行到达方向(DOA)估计的现有研究不同,源与传感器的距离是通过直接到依次的能量比(DRR)计算的,并用作新约束以消除非线性噪声从运动报告。应用粒子过滤器估计临界距离,这是将源距离与DRR关联的关键。使用密钥帧方法来消除源位置估计向机器人的偏差。拟议的DOA-DRR声学大满贯(D-D大满贯)设计用于三维运动,适合大多数机器人。该方法是第一个在现实世界中仅包含声学数据和IMU测量值的现实世界室内场景数据集上验证的声学大满贯算法。与以前的方法相比,D-D SLAM在定位机器人和从现实世界室内数据集中构建源地图方面具有可接受的性能。平均位置精度为0.48 m,而源位置误差在2.8 s内收敛到小于0.25 m。这些结果证明了D-D SLAM在现实世界室内场景中的有效性,这可能在环境有雾(即不适合光或激光辐照的环境)之后特别有用。
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自动路面遇险分类有助于提高路面维护的效率并降低劳动力和资源的成本。该任务的最近有影响力的分支将路面图像划分为贴片,并从多实体学习的角度解决了这些问题。但是,这些方法忽略了斑块之间的相关性,并且在模型优化和推理中遇到了低效率。同时,Swin Transformer能够以其独特的优势来解决这两个问题。我们构建了Swin Transformer,我们提供了一个名为\ TextBf {p} avement \ textbf {i} mage \ textbf {c} lassification \ textbf {t} ransformer(\ textbf {pict})的视觉变压器。为了更好地利用贴片级别的路面图像的判别信息,提出了\ textit {patch labeling conterg},以利用教师模型在每次迭代期间从图像标签中动态生成贴片的伪标签,并将模型引导到模型上了解补丁的判别特征。 Swin Transformer的广泛分类头可能会稀释特征聚合步骤中遇险斑块的判别特征,这是由于路面图像的遇险面积较小。为了克服这个缺点,我们提出了一个\ textit {Patch Refiner}将补丁聚集到不同的组中,并且仅选择最高的遇险风险组来产生最终图像分类的纤细头部。我们在CQU-BPDD上评估了我们的方法。广泛的结果表明,\ textbf {pict}在检测任务中,p@r中的$+2.4 \%$的大幅度优于第二好的模型,$+3.9 \%\%\%$ f1 $ f1 $ in识别任务和识别任务和1.8倍吞吐量,同时使用相同的计算资源享受7倍的训练速度。我们的代码和模型已在\ href {https://github.com/dearcaat/pict} {https://github.com/dearcaat/pict}上发布。
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在马尔可夫决策过程(MDP)中,可能存在不可观察的混杂因素并对数据生成过程产生影响,因此经典的非政策评估(OPE)估计器可能无法识别目标策略的真实价值函数。在本文中,我们研究了与可观察的仪器变量混杂的MDP中OPE的统计特性。具体而言,我们根据仪器变量提出了一个两阶段估计器,并在具有线性结构的混杂MDP中建立了其统计属性。对于非反应分析,我们证明了一个$ \ Mathcal {o}(n^{ - 1/2})$ - 错误绑定了$ n $是样本的数量。对于渐近分析,我们证明了两阶段估计量在渐近正常上,典型速率为$ n^{1/2} $。据我们所知,我们是第一个通过仪器变量显示混合线性MDP的两阶段估计量的统计结果。
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进化策略(ES)算法由于其巨大的并行能力,简单的实现,有效的参数空间探索和快速训练时间,在训练复杂的机器人控制策略中显示出令人鼓舞的结果。但是,ES的关键限制是其对大容量模型(包括现代神经网络体系结构)的可扩展性。在这项工作中,我们开发了预测信息增强随机搜索(PI-ARS),以通过利用表示表示学习来减少ES的参数搜索空间来减轻这种限制。即,PI-ARS将基于梯度的表示技术,预测信息(PI)与无梯度ES算法,增强随机搜索(ARS)结合在一起,以训练可以处理复杂机器人感觉输入并处理高度非线性机器人的策略动力学。我们在一系列具有挑战性的视觉范围任务上评估了PI-ARS,四倍的机器人需要在不平坦的踏脚石,Quincuncial Pile和移动平台上行走,并完成室内导航任务。在所有任务中,与ARS基线相比,PI-ARS表现出明显更好的学习效率和表现。我们通过证明学识渊博的政策可以成功地转移到真正的四倍机器人的情况下,进一步验证我们的算法,例如,在现实世界中的垫脚石环境上取得了100%的成功率,从而显着提高了先前的结果,从而实现了40%的成功。
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