剖面隐藏的马尔可夫模型（PHMM）广泛用于许多生物信息学应用中，以准确识别生物学序列（例如DNA或蛋白质序列）之间的相似性。 PHMM使用常用和高度精确的方法（称为Baum-Welch算法）来计算这些相似性。但是，Baum-Welch算法在计算上很昂贵，现有作品为固定的PHMM设计提供了软件或仅硬件解决方案。当我们分析最先进的作品时，我们发现迫切需要灵活，高性能和节能的硬件软件共同设计，以有效地有效地解决所有主要效率低下的效率PHMM的Baum-Welch算法。我们提出了APHMM，这是第一个灵活的加速框架，可以显着减少PHMM的Baum-Welch算法的计算和能量开销。 APHMM利用硬件软件共同设计来解决Baum-Welch算法中的主要效率低下，通过1）设计灵活的硬件来支持不同的PHMMS设计，2）利用可预测的数据依赖性模式，并使用chip Memory的片段记忆，使用纪念活动技术，memoigience Memoriques，Memoigience Memoriques，Memoigient， 3）通过基于硬件的过滤器快速消除可忽略的计算，4）最小化冗余计算。我们在专用硬件和2）GPU的软件优化方面实现了我们的1）硬件软件优化，以为PHMM提供首个灵活的Baum-Welch加速器。与Baum-Welch算法的CPU，GPU和FPGA实现相比，APHMM提供的显着加速度为15.55 x-260.03x，1.83x-5.34x和27.97倍，分别为27.97倍。 APHMM的表现优于三个重要的生物信息学应用程序的最新CPU实现，1）错误校正，2）蛋白质家族搜索和3）多个序列对齐，比1.29x-59.94x，1.03x-1.75x和分别为1.03x-1.95x。

过去的研究提出了许多硬件预取技术，其中大多数依赖于利用一种特定类型的程序上下文信息（例如，程序计数器，Cacheline地址）来预测未来的存储器访问。这些技术完全忽略了整个系统上的预取器的不良影响（例如，内存带宽使用），或将系统级反馈结合为返回为系统 - 不知预取算法。我们表明，由于其固有的无法在预取帐户中占用多种不同类型的程序上下文和系统级反馈信息，因此在广泛的工作负载和系统配置中往往会在广泛的工作负载和系统配置中丢失其性能效益。在本文中，我们进行了设计一个整体预取算法的案例，该算法学习使用多种不同类型的程序上下文和系统级反馈信息来预取。为此，我们提出了Pythia，它将预取器制定为钢筋学习代理。对于每种需求请求，Pythia会观察多种不同类型的程序上下文信息以进行预取决定。对于每个预取决定，Pythia接收数字奖励，该奖励评估当前内存带宽使用情况下的预取质量。 Pythia使用此奖励来加强程序上下文信息和预取决定之间的相关性，以在将来生成高度准确，及时和系统感知的预取请求。我们使用仿真和硬件综合的广泛评估表明，Pythia在各种工作负载和系统配置中优于多种最先进的预取器，同时在桌面类处理器中产生的1.03％的面积开销，并且工作负载中没有软件更改。 Pythia的源代码可以从https://github.com/cmu-safari/pythia自由下载。

Graph Neural Networks (GNNs) have been taking role in many areas, thanks to their expressive power on graph-structured data. On the other hand, Mobile Ad-Hoc Networks (MANETs) are gaining attention as network technologies have been taken to the 5G level. However, there is no study that evaluates the efficiency of GNNs on MANETs. In this study, we aim to fill this absence by implementing a MANET dataset in a popular GNN framework, i.e., PyTorch Geometric; and show how GNNs can be utilized to analyze the traffic of MANETs. We operate an edge prediction task on the dataset with GraphSAGE (SAG) model, where SAG model tries to predict whether there is a link between two nodes. We construe several evaluation metrics to measure the performance and efficiency of GNNs on MANETs. SAG model showed 82.1 accuracy on average in the experiments.

Over-approximating the reachable sets of dynamical systems is a fundamental problem in safety verification and robust control synthesis. The representation of these sets is a key factor that affects the computational complexity and the approximation error. In this paper, we develop a new approach for over-approximating the reachable sets of neural network dynamical systems using adaptive template polytopes. We use the singular value decomposition of linear layers along with the shape of the activation functions to adapt the geometry of the polytopes at each time step to the geometry of the true reachable sets. We then propose a branch-and-bound method to compute accurate over-approximations of the reachable sets by the inferred templates. We illustrate the utility of the proposed approach in the reachability analysis of linear systems driven by neural network controllers.

Recently the focus of the computer vision community has shifted from expensive supervised learning towards self-supervised learning of visual representations. While the performance gap between supervised and self-supervised has been narrowing, the time for training self-supervised deep networks remains an order of magnitude larger than its supervised counterparts, which hinders progress, imposes carbon cost, and limits societal benefits to institutions with substantial resources. Motivated by these issues, this paper investigates reducing the training time of recent self-supervised methods by various model-agnostic strategies that have not been used for this problem. In particular, we study three strategies: an extendable cyclic learning rate schedule, a matching progressive augmentation magnitude and image resolutions schedule, and a hard positive mining strategy based on augmentation difficulty. We show that all three methods combined lead up to 2.7 times speed-up in the training time of several self-supervised methods while retaining comparable performance to the standard self-supervised learning setting.

Channel charting (CC) is an unsupervised learning method allowing to locate users relative to each other without reference. From a broader perspective, it can be viewed as a way to discover a low-dimensional latent space charting the channel manifold. In this paper, this latent modeling vision is leveraged together with a recently proposed location-based beamforming (LBB) method to show that channel charting can be used for mapping channels in space or frequency. Combining CC and LBB yields a neural network resembling an autoencoder. The proposed method is empirically assessed on a channel mapping task whose objective is to predict downlink channels from uplink channels.

Adversarial training has been empirically shown to be more prone to overfitting than standard training. The exact underlying reasons still need to be fully understood. In this paper, we identify one cause of overfitting related to current practices of generating adversarial samples from misclassified samples. To address this, we propose an alternative approach that leverages the misclassified samples to mitigate the overfitting problem. We show that our approach achieves better generalization while having comparable robustness to state-of-the-art adversarial training methods on a wide range of computer vision, natural language processing, and tabular tasks.

We study the problem of profiling news media on the Web with respect to their factuality of reporting and bias. This is an important but under-studied problem related to disinformation and "fake news" detection, but it addresses the issue at a coarser granularity compared to looking at an individual article or an individual claim. This is useful as it allows to profile entire media outlets in advance. Unlike previous work, which has focused primarily on text (e.g.,~on the text of the articles published by the target website, or on the textual description in their social media profiles or in Wikipedia), here our main focus is on modeling the similarity between media outlets based on the overlap of their audience. This is motivated by homophily considerations, i.e.,~the tendency of people to have connections to people with similar interests, which we extend to media, hypothesizing that similar types of media would be read by similar kinds of users. In particular, we propose GREENER (GRaph nEural nEtwork for News mEdia pRofiling), a model that builds a graph of inter-media connections based on their audience overlap, and then uses graph neural networks to represent each medium. We find that such representations are quite useful for predicting the factuality and the bias of news media outlets, yielding improvements over state-of-the-art results reported on two datasets. When augmented with conventionally used representations obtained from news articles, Twitter, YouTube, Facebook, and Wikipedia, prediction accuracy is found to improve by 2.5-27 macro-F1 points for the two tasks.

Adversarial training is widely acknowledged as the most effective defense against adversarial attacks. However, it is also well established that achieving both robustness and generalization in adversarially trained models involves a trade-off. The goal of this work is to provide an in depth comparison of different approaches for adversarial training in language models. Specifically, we study the effect of pre-training data augmentation as well as training time input perturbations vs. embedding space perturbations on the robustness and generalization of BERT-like language models. Our findings suggest that better robustness can be achieved by pre-training data augmentation or by training with input space perturbation. However, training with embedding space perturbation significantly improves generalization. A linguistic correlation analysis of neurons of the learned models reveal that the improved generalization is due to `more specialized' neurons. To the best of our knowledge, this is the first work to carry out a deep qualitative analysis of different methods of generating adversarial examples in adversarial training of language models.

As the interest to Graph Neural Networks (GNNs) is growing, the importance of benchmarking and performance characterization studies of GNNs is increasing. So far, we have seen many studies that investigate and present the performance and computational efficiency of GNNs. However, the work done so far has been carried out using a few high-level GNN frameworks. Although these frameworks provide ease of use, they contain too many dependencies to other existing libraries. The layers of implementation details and the dependencies complicate the performance analysis of GNN models that are built on top of these frameworks, especially while using architectural simulators. Furthermore, different approaches on GNN computation are generally overlooked in prior characterization studies, and merely one of the common computational models is evaluated. Based on these shortcomings and needs that we observed, we developed a benchmark suite that is framework independent, supporting versatile computational models, easily configurable and can be used with architectural simulators without additional effort. Our benchmark suite, which we call gSuite, makes use of only hardware vendor's libraries and therefore it is independent of any other frameworks. gSuite enables performing detailed performance characterization studies on GNN Inference using both contemporary GPU profilers and architectural GPU simulators. To illustrate the benefits of our new benchmark suite, we perform a detailed characterization study with a set of well-known GNN models with various datasets; running gSuite both on a real GPU card and a timing-detailed GPU simulator. We also implicate the effect of computational models on performance. We use several evaluation metrics to rigorously measure the performance of GNN computation.