数据驱动的预测方法可以有效,准确地将蛋白质序列转化为生物活性结构,对于科学研究和治疗发展非常有价值。使用共同进化信息确定准确的折叠格局是现代蛋白质结构预测方法的成功基础。作为最新的状态,AlphaFold2显着提高了准确性,而无需进行明确的共同进化分析。然而,其性能仍然显示出对可用序列同源物的强烈依赖。我们研究了这种依赖性的原因,并提出了一种元生成模型Evogen,以弥补较差的MSA靶标的Alphafold2的表现不佳。 Evogen使我们能够通过降低搜索的MSA或生成虚拟MSA来操纵折叠景观,并帮助Alphafold2在低数据表方面准确地折叠,甚至通过单序预测来实现令人鼓舞的性能。能够用很少的MSA做出准确的预测,不仅可以更好地概括为孤儿序列的Alphafold2,而且使其在高通量应用程序中的使用民主化。此外,Evogen与AlphaFold2结合产生了一种概率结构生成方法,该方法可以探索蛋白质序列的替代构象,并且序列生成的任务意识可区分算法将使包括蛋白质设计在内的其他相关任务受益。
translated by 谷歌翻译
蛋白质是人类生命的重要组成部分,其结构对于功能和机制分析很重要。最近的工作表明了AI驱动方法对蛋白质结构预测的潜力。但是,新模型的开发受到数据集和基准测试培训程序的限制。据我们所知,现有的开源数据集远不足以满足现代蛋白质序列相关研究的需求。为了解决这个问题,我们介绍了具有高覆盖率和多样性的第一个百万级蛋白质结构预测数据集,称为PSP。该数据集由570K真实结构序列(10TB)和745K互补蒸馏序列(15TB)组成。此外,我们还提供了该数据集上SOTA蛋白结构预测模型的基准测试训练程序。我们通过参与客串比赛验证该数据集的实用程序进行培训,我们的模特赢得了第一名。我们希望我们的PSP数据集以及培训基准能够为AI驱动的蛋白质相关研究提供更广泛的AI/生物学研究人员社区。
translated by 谷歌翻译
部分微分方程(PDES)在科学和工程的许多学科中都是普遍的,难以解决。通常,PDE的闭合形式溶液不可用,数值近似方法是计算昂贵的。 PDE的参数在许多应用中是可变的,例如逆问题,控制和优化,风险评估和不确定性量化。在这些应用程序中,我们的目标是解决参数PDE而不是其中一个实例。我们所提出的方法,称为元 - 自动解码器(MAD),将参数PDES作为元学习问题求解,并利用\ Cite {Park2019DeepsDF}中的自动解码器结构来处理不同的任务/ PDE。从PDE管理方程和边界条件诱导的物理知识损失被用作不同任务的培训损失。疯狂的目标是学习一个良好的模型初始化,可以概括不同的任务,最终使未能学习的任务能够更快地学习。疯狂的灵感来自于(猜想)参数PDE解决方案的低维结构,并从流形学习的角度解释了我们的方法。最后,我们展示了疯狂的力量,虽然广泛的数值研究,包括汉堡等式,拉普尔斯方程和时域麦克斯韦方程。与其他深度学习方法相比,MAD表现出更快的收敛速度而不会失去准确性。
translated by 谷歌翻译
近年来,深入学习技术已被用来解决部分微分方程(PDE),其中物理信息的神经网络(PINNS)出现是解决前向和反向PDE问题的有希望的方法。具有点源的PDE,其表示为管理方程中的DIRAC DELTA函数是许多物理过程的数学模型。然而,由于DIRAC DELTA功能所带来的奇点,它们不能直接通过传统的PINNS方法来解决。我们提出了一种普遍的解决方案,以用三种新颖的技术解决这个问题。首先,DIRAC DELTA功能被建模为连续概率密度函数以消除奇点;其次,提出了下限约束的不确定性加权算法,以平衡点源区和其他区域之间的Pinns损失;第三,使用具有周期性激活功能的多尺度深度神经网络来提高PinnS方法的准确性和收敛速度。我们评估了三种代表性PDE的提出方法,实验结果表明,我们的方法优于基于深度学习的方法,涉及准确性,效率和多功能性。
translated by 谷歌翻译
A further understanding of cause and effect within observational data is critical across many domains, such as economics, health care, public policy, web mining, online advertising, and marketing campaigns. Although significant advances have been made to overcome the challenges in causal effect estimation with observational data, such as missing counterfactual outcomes and selection bias between treatment and control groups, the existing methods mainly focus on source-specific and stationary observational data. Such learning strategies assume that all observational data are already available during the training phase and from only one source. This practical concern of accessibility is ubiquitous in various academic and industrial applications. That's what it boiled down to: in the era of big data, we face new challenges in causal inference with observational data, i.e., the extensibility for incrementally available observational data, the adaptability for extra domain adaptation problem except for the imbalance between treatment and control groups, and the accessibility for an enormous amount of data. In this position paper, we formally define the problem of continual treatment effect estimation, describe its research challenges, and then present possible solutions to this problem. Moreover, we will discuss future research directions on this topic.
translated by 谷歌翻译
In contrast to the control-theoretic methods, the lack of stability guarantee remains a significant problem for model-free reinforcement learning (RL) methods. Jointly learning a policy and a Lyapunov function has recently become a promising approach to ensuring the whole system with a stability guarantee. However, the classical Lyapunov constraints researchers introduced cannot stabilize the system during the sampling-based optimization. Therefore, we propose the Adaptive Stability Certification (ASC), making the system reach sampling-based stability. Because the ASC condition can search for the optimal policy heuristically, we design the Adaptive Lyapunov-based Actor-Critic (ALAC) algorithm based on the ASC condition. Meanwhile, our algorithm avoids the optimization problem that a variety of constraints are coupled into the objective in current approaches. When evaluated on ten robotic tasks, our method achieves lower accumulated cost and fewer stability constraint violations than previous studies.
translated by 谷歌翻译
Text-based speech editing allows users to edit speech by intuitively cutting, copying, and pasting text to speed up the process of editing speech. In the previous work, CampNet (context-aware mask prediction network) is proposed to realize text-based speech editing, significantly improving the quality of edited speech. This paper aims at a new task: adding emotional effect to the editing speech during the text-based speech editing to make the generated speech more expressive. To achieve this task, we propose Emo-CampNet (emotion CampNet), which can provide the option of emotional attributes for the generated speech in text-based speech editing and has the one-shot ability to edit unseen speakers' speech. Firstly, we propose an end-to-end emotion-selectable text-based speech editing model. The key idea of the model is to control the emotion of generated speech by introducing additional emotion attributes based on the context-aware mask prediction network. Secondly, to prevent the emotion of the generated speech from being interfered by the emotional components in the original speech, a neutral content generator is proposed to remove the emotion from the original speech, which is optimized by the generative adversarial framework. Thirdly, two data augmentation methods are proposed to enrich the emotional and pronunciation information in the training set, which can enable the model to edit the unseen speaker's speech. The experimental results that 1) Emo-CampNet can effectively control the emotion of the generated speech in the process of text-based speech editing; And can edit unseen speakers' speech. 2) Detailed ablation experiments further prove the effectiveness of emotional selectivity and data augmentation methods. The demo page is available at https://hairuo55.github.io/Emo-CampNet/
translated by 谷歌翻译
In this work, we study the black-box targeted attack problem from the model discrepancy perspective. On the theoretical side, we present a generalization error bound for black-box targeted attacks, which gives a rigorous theoretical analysis for guaranteeing the success of the attack. We reveal that the attack error on a target model mainly depends on empirical attack error on the substitute model and the maximum model discrepancy among substitute models. On the algorithmic side, we derive a new algorithm for black-box targeted attacks based on our theoretical analysis, in which we additionally minimize the maximum model discrepancy(M3D) of the substitute models when training the generator to generate adversarial examples. In this way, our model is capable of crafting highly transferable adversarial examples that are robust to the model variation, thus improving the success rate for attacking the black-box model. We conduct extensive experiments on the ImageNet dataset with different classification models, and our proposed approach outperforms existing state-of-the-art methods by a significant margin. Our codes will be released.
translated by 谷歌翻译
Event-based simulations of Spiking Neural Networks (SNNs) are fast and accurate. However, they are rarely used in the context of event-based gradient descent because their implementations on GPUs are difficult. Discretization with the forward Euler method is instead often used with gradient descent techniques but has the disadvantage of being computationally expensive. Moreover, the lack of precision of discretized simulations can create mismatches between the simulated models and analog neuromorphic hardware. In this work, we propose a new exact error-backpropagation through spikes method for SNNs, extending Fast \& Deep to multiple spikes per neuron. We show that our method can be efficiently implemented on GPUs in a fully event-based manner, making it fast to compute and precise enough for analog neuromorphic hardware. Compared to the original Fast \& Deep and the current state-of-the-art event-based gradient-descent algorithms, we demonstrate increased performance on several benchmark datasets with both feedforward and convolutional SNNs. In particular, we show that multi-spike SNNs can have advantages over single-spike networks in terms of convergence, sparsity, classification latency and sensitivity to the dead neuron problem.
translated by 谷歌翻译
The error Backpropagation algorithm (BP) is a key method for training deep neural networks. While performant, it is also resource-demanding in terms of computation, memory usage and energy. This makes it unsuitable for online learning on edge devices that require a high processing rate and low energy consumption. More importantly, BP does not take advantage of the parallelism and local characteristics offered by dedicated neural processors. There is therefore a demand for alternative algorithms to BP that could improve the latency, memory requirements, and energy footprint of neural networks on hardware. In this work, we propose a novel method based on Direct Feedback Alignment (DFA) which uses Forward-Mode Automatic Differentiation to estimate backpropagation paths and learn feedback connections in an online manner. We experimentally show that Directional DFA achieves performances that are closer to BP than other feedback methods on several benchmark datasets and architectures while benefiting from the locality and parallelization characteristics of DFA. Moreover, we show that, unlike other feedback learning algorithms, our method provides stable learning for convolution layers.
translated by 谷歌翻译