The process of screening molecules for desirable properties is a key step in several applications, ranging from drug discovery to material design. During the process of drug discovery specifically, protein-ligand docking, or chemical docking, is a standard in-silico scoring technique that estimates the binding affinity of molecules with a specific protein target. Recently, however, as the number of virtual molecules available to test has rapidly grown, these classical docking algorithms have created a significant computational bottleneck. We address this problem by introducing Deep Surrogate Docking (DSD), a framework that applies deep learning-based surrogate modeling to accelerate the docking process substantially. DSD can be interpreted as a formalism of several earlier surrogate prefiltering techniques, adding novel metrics and practical training practices. Specifically, we show that graph neural networks (GNNs) can serve as fast and accurate estimators of classical docking algorithms. Additionally, we introduce FiLMv2, a novel GNN architecture which we show outperforms existing state-of-the-art GNN architectures, attaining more accurate and stable performance by allowing the model to filter out irrelevant information from data more efficiently. Through extensive experimentation and analysis, we show that the DSD workflow combined with the FiLMv2 architecture provides a 9.496x speedup in molecule screening with a <3% recall error rate on an example docking task. Our open-source code is available at https://github.com/ryienh/graph-dock.

基于机器学习（ML）的转向可以通过在线选择更科学意义的计算来提高基于合奏的模拟的性能。我们提出了DeepDrivemd，这是ML驱动的科学模拟转向的框架，我们用来通过在大型平行计算机上的有效耦合ML和HPC来实现分子动力学（MD）性能的稳定性提高。我们讨论了DeepDrivemd的设计，并描述了其性能。我们证明，与其他方法相对于其他方法，DeepDrivemd可以在100-1000倍加速度之间达到100-1000倍的加速度，这是通过执行的模拟时间量来衡量的，同时覆盖了模拟过程中采样的状态所量化的相同构象景观。实验是在最多1020个节点的领导级平台上进行的。该结果将DeepDrivemd作为ML驱动的HPC模拟方案的高性能框架建立，该场景支持不同的MD仿真和ML后端，并通过改善当前计算能力来改善长度和时间尺度来实现新的科学见解。

Code generation models have achieved impressive performance. However, they tend to be brittle as slight edits to a prompt could lead to very different generations; these robustness properties, critical for user experience when deployed in real-life applications, are not well understood. Most existing works on robustness in text or code tasks have focused on classification, while robustness in generation tasks is an uncharted area and to date there is no comprehensive benchmark for robustness in code generation. In this paper, we propose ReCode, a comprehensive robustness evaluation benchmark for code generation models. We customize over 30 transformations specifically for code on docstrings, function and variable names, code syntax, and code format. They are carefully designed to be natural in real-life coding practice, preserve the original semantic meaning, and thus provide multifaceted assessments of a model's robustness performance. With human annotators, we verified that over 90% of the perturbed prompts do not alter the semantic meaning of the original prompt. In addition, we define robustness metrics for code generation models considering the worst-case behavior under each type of perturbation, taking advantage of the fact that executing the generated code can serve as objective evaluation. We demonstrate ReCode on SOTA models using HumanEval, MBPP, as well as function completion tasks derived from them. Interesting observations include: better robustness for CodeGen over InCoder and GPT-J; models are most sensitive to syntax perturbations; more challenging robustness evaluation on MBPP over HumanEval.

While pre-trained language models (LM) for code have achieved great success in code completion, they generate code conditioned only on the contents within the file, i.e., in-file context, but ignore the rich semantics in other files within the same project, i.e., cross-file context, a critical source of information that is especially useful in modern modular software development. Such overlooking constrains code language models' capacity in code completion, leading to unexpected behaviors such as generating hallucinated class member functions or function calls with unexpected arguments. In this work, we develop a cross-file context finder tool, CCFINDER, that effectively locates and retrieves the most relevant cross-file context. We propose CoCoMIC, a framework that incorporates cross-file context to learn the in-file and cross-file context jointly on top of pretrained code LMs. CoCoMIC successfully improves the existing code LM with a 19.30% relative increase in exact match and a 15.41% relative increase in identifier matching for code completion when the cross-file context is provided.

Advancement in large pretrained language models has significantly improved their performance for conditional language generation tasks including summarization albeit with hallucinations. To reduce hallucinations, conventional methods proposed improving beam search or using a fact checker as a postprocessing step. In this paper, we investigate the use of the Natural Language Inference (NLI) entailment metric to detect and prevent hallucinations in summary generation. We propose an NLI-assisted beam re-ranking mechanism by computing entailment probability scores between the input context and summarization model-generated beams during saliency-enhanced greedy decoding. Moreover, a diversity metric is introduced to compare its effectiveness against vanilla beam search. Our proposed algorithm significantly outperforms vanilla beam decoding on XSum and CNN/DM datasets.

Generative Adversarial Networks (GANs) have received wide acclaim among the machine learning (ML) community for their ability to generate realistic 2D images. ML is being applied more often to complex problems beyond those of computer vision. However, current frameworks often serve as black boxes and lack physics embeddings, leading to poor ability in enforcing constraints and unreliable models. In this work, we develop physics embeddings that can be stringently imposed, referred to as hard constraints, in the neural network architecture. We demonstrate their capability for 3D turbulence by embedding them in GANs, particularly to enforce the mass conservation constraint in incompressible fluid turbulence. In doing so, we also explore and contrast the effects of other methods of imposing physics constraints within the GANs framework, especially penalty-based physics constraints popular in literature. By using physics-informed diagnostics and statistics, we evaluate the strengths and weaknesses of our approach and demonstrate its feasibility.

Dynamic movement primitives are widely used for learning skills which can be demonstrated to a robot by a skilled human or controller. While their generalization capabilities and simple formulation make them very appealing to use, they possess no strong guarantees to satisfy operational safety constraints for a task. In this paper, we present constrained dynamic movement primitives (CDMP) which can allow for constraint satisfaction in the robot workspace. We present a formulation of a non-linear optimization to perturb the DMP forcing weights regressed by locally-weighted regression to admit a Zeroing Barrier Function (ZBF), which certifies workspace constraint satisfaction. We demonstrate the proposed CDMP under different constraints on the end-effector movement such as obstacle avoidance and workspace constraints on a physical robot. A video showing the implementation of the proposed algorithm using different manipulators in different environments could be found here https://youtu.be/hJegJJkJfys.

Duckiebots是低成本的移动机器人，在研究和教育领域广泛使用。尽管Duckietown平台有现有的自动驾驶算法，但它们要么太复杂，要么表现太差，无法导航多车道轨道。此外，必须将内存和计算资源提供给Duckiebot，以便它可以执行其他任务，例如分布式输入检测。为了满足这些约束，我们构建了一种低成本的自主驾驶算法，能够在两车道轨道上驾驶。该算法使用传统的计算机视觉技术来识别轨道上的中央车道并获得相关的转向角度。然后，转向由PID控制器控制，该PID控制器使Duckiebot的运动平滑。将算法的性能与Neurips 2018 AI驾驶奥运会（AIDO）决赛入围者进行了比较，并且除了一名决赛选手以外，它的表现优于所有球员。我们算法的两个主要贡献是其低计算要求和非常快速的设置，并持续努力使其更加可靠。

仇恨言论以贬义的评论以多种形式针对社区，并使人类退后一步。 Hatexplain是最近出版的第一个数据集，用于以理由的形式使用带注释的跨度，以及语音分类类别和有针对性的社区，以使分类更具人性化，可解释，准确和偏见。我们调整BERT以理由和阶级预测的形式执行此任务，并比较我们对跨精度，解释性和偏见的不同指标的性能。我们的新颖性是三倍。首先，我们尝试具有不同重要性值的合并理由类损失。其次，我们对理由的地面真相注意值进行了广泛的实验。随着保守和宽大的关注，我们比较了hatexplain模型的性能并检验我们的假设。第三，为了改善模型中的意外偏见，我们使用目标社区单词的掩盖，并注意偏见和解释性指标的改善。总体而言，我们成功地实现了模型的解释性，偏差删除和对原始BERT实施的几个增量改进。

深度神经网络的过度参数性质导致在低端设备上的部署过程中有很大的障碍，并具有时间和空间限制。使用迭代修剪培训方案稀疏DNN的网络修剪策略通常在计算上很昂贵。结果，在训练之前，在初始化时修剪修剪的技术变得越来越流行。在这项工作中，我们提出了神经元到神经元的跳过连接，这些连接是稀疏的加权跳过连接，以增强修剪的DNN的整体连通性。遵循初步修剪步骤，在修剪网络的单个神经元/通道之间随机添加N2NSKIP连接，同时保持网络的整体稀疏性。我们证明，与没有N2NSKIP连接的修剪的网络相比，在修剪网络中引入N2NSKIP连接可以显着卓越的性能，尤其是在高稀疏度水平上。此外，我们提出了基于热扩散的连接分析，以定量确定修剪网络相对于参考网络的连通性。我们评估方法对两种不同初步修剪方法的疗效，这些方法在初始化时修剪，并通过利用N2NSKIP连接引起的增强连接性来始终获得卓越的性能。