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The ability to handle a large volume of data generated by scientific applications is crucial. We have seen an increase in the heterogeneity of storage technologies available to scientific applications, such as burst buffers, local temporary block storage, managed cloud parallel file systems (PFS), and non-POSIX object stores. However, scientific applications designed for traditional HPC systems can not easily exploit those storage systems due to cost, throughput, and programming model challenges. We present iFast, a new library-level approach to transparently accelerating scientific applications based on MPI-IO. It decouples application I/O, data caching, and data storage to support heterogeneous storage models. Design decisions of iFast are based on a strong emphasis on deployability. It is highly general with only MPI as a core dependency, allowing users to run unmodified MPI-based applications with unmodified MPI implementations - even proprietary ones like IntelMPI and Cray MPICH. Our approach supports a wide range of networked storage, including traditional PFS, ordinary NFS, and S3-based cloud storage. Unlike previous approaches, iFast ensures crash consistency even across compute nodes. We demonstrate iFast in cloud HPC platform, small local cluster, and hybrid of both to show its generality. Our results show that iFast reduces end-to-end execution time by 13-26% for three popular scientific applications on the cloud. It also outperforms the state-of-the-art system, SymphonyFS, a filesystem-based approach for similar goals but without crash consistency, by 12-23%.

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Thresholded hybrid systems are restricted dynamical systems, where the current mode, and hence the ODE system describing its behavior, is solely determined by externally supplied digital input signals and where the only output signals are digital ones generated by comparing an internal state variable to a threshold value. An attractive feature of such systems is easy composition, which is facilitated by their purely digital interface. A particularly promising application domain of thresholded hybrid systems is digital integrated circuits: Modern digital circuit design considers them as a composition of Millions and even Billions of elementary logic gates, like inverters, GOR and Gand. Since every such logic gate is eventually implemented as an electronic circuit, however, which exhibits a behavior that is governed by some ODE system, thresholded hybrid systems are ideally suited for making the transition from the analog to the digital world rigorous. In this paper, we prove that the mapping from digital input signals to digital output signals is continuous for a large class of thresholded hybrid systems. Moreover, we show that, under some mild conditions regarding causality, this continuity also continues to hold for arbitrary compositions, which in turn guarantees that the composition faithfully captures the analog reality. By applying our generic results to some recently developed thresholded hybrid gate models, both for single-input single-output gates like inverters and for a two-input CMOS NOR gate, we show that they are continuous. Moreover, we provide a novel thresholded hybrid model for the two-input NOR gate, which is not only continuous but also, unlike the existing one, faithfully models all multi-input switching effects.

Diffusion models, which convert noise into new data instances by learning to reverse a Markov diffusion process, have become a cornerstone in contemporary generative modeling. While their practical power has now been widely recognized, the theoretical underpinnings remain far from mature. In this work, we develop a suite of non-asymptotic theory towards understanding the data generation process of diffusion models in discrete time, assuming access to $\ell_2$-accurate estimates of the (Stein) score functions. For a popular deterministic sampler (based on the probability flow ODE), we establish a convergence rate proportional to $1/T$ (with $T$ the total number of steps), improving upon past results; for another mainstream stochastic sampler (i.e., a type of the denoising diffusion probabilistic model), we derive a convergence rate proportional to $1/\sqrt{T}$, matching the state-of-the-art theory. Imposing only minimal assumptions on the target data distribution (e.g., no smoothness assumption is imposed), our results characterize how $\ell_2$ score estimation errors affect the quality of the data generation processes. In contrast to prior works, our theory is developed based on an elementary yet versatile non-asymptotic approach without resorting to toolboxes for SDEs and ODEs. Further, we design two accelerated variants, improving the convergence to $1/T^2$ for the ODE-based sampler and $1/T$ for the DDPM-type sampler, which might be of independent theoretical and empirical interest.

One common way to speed up the find operation within a set of text files involves a trigram index. This structure is merely a map from a trigram (sequence consisting of three characters) to a set of files which contain it. When searching for a pattern, potential file locations are identified by intersecting the sets related to the trigrams in the pattern. Then, the search proceeds only in these files. However, in a code repository, the trigram index evolves across different versions. Upon checking out a new version, this index is typically built from scratch, which is a time-consuming task, while we want our index to have almost zero-time startup. Thus, we explore the persistent version of a trigram index for full-text and key word patterns search. Our approach just uses the current version of the trigram index and applies only the changes between versions during checkout, significantly enhancing performance. Furthermore, we extend our data structure to accommodate CamelHump search for class and function names.

Genetic programming (GP) has the potential to generate explainable results, especially when used for dimensionality reduction. In this research, we investigate the potential of leveraging eXplainable AI (XAI) and large language models (LLMs) like ChatGPT to improve the interpretability of GP-based non-linear dimensionality reduction. Our study introduces a novel XAI dashboard named GP4NLDR, the first approach to combine state-of-the-art GP with an LLM-powered chatbot to provide comprehensive, user-centred explanations. We showcase the system's ability to provide intuitive and insightful narratives on high-dimensional data reduction processes through case studies. Our study highlights the importance of prompt engineering in eliciting accurate and pertinent responses from LLMs. We also address important considerations around data privacy, hallucinatory outputs, and the rapid advancements in generative AI. Our findings demonstrate its potential in advancing the explainability of GP algorithms. This opens the door for future research into explaining GP models with LLMs.

As a primary means of information acquisition, information retrieval (IR) systems, such as search engines, have integrated themselves into our daily lives. These systems also serve as components of dialogue, question-answering, and recommender systems. The trajectory of IR has evolved dynamically from its origins in term-based methods to its integration with advanced neural models. While the neural models excel at capturing complex contextual signals and semantic nuances, thereby reshaping the IR landscape, they still face challenges such as data scarcity, interpretability, and the generation of contextually plausible yet potentially inaccurate responses. This evolution requires a combination of both traditional methods (such as term-based sparse retrieval methods with rapid response) and modern neural architectures (such as language models with powerful language understanding capacity). Meanwhile, the emergence of large language models (LLMs), typified by ChatGPT and GPT-4, has revolutionized natural language processing due to their remarkable language understanding, generation, generalization, and reasoning abilities. Consequently, recent research has sought to leverage LLMs to improve IR systems. Given the rapid evolution of this research trajectory, it is necessary to consolidate existing methodologies and provide nuanced insights through a comprehensive overview. In this survey, we delve into the confluence of LLMs and IR systems, including crucial aspects such as query rewriters, retrievers, rerankers, and readers. Additionally, we explore promising directions within this expanding field.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

Causality can be described in terms of a structural causal model (SCM) that carries information on the variables of interest and their mechanistic relations. For most processes of interest the underlying SCM will only be partially observable, thus causal inference tries to leverage any exposed information. Graph neural networks (GNN) as universal approximators on structured input pose a viable candidate for causal learning, suggesting a tighter integration with SCM. To this effect we present a theoretical analysis from first principles that establishes a novel connection between GNN and SCM while providing an extended view on general neural-causal models. We then establish a new model class for GNN-based causal inference that is necessary and sufficient for causal effect identification. Our empirical illustration on simulations and standard benchmarks validate our theoretical proofs.

Graph Neural Networks (GNNs) are widely used for analyzing graph-structured data. Most GNN methods are highly sensitive to the quality of graph structures and usually require a perfect graph structure for learning informative embeddings. However, the pervasiveness of noise in graphs necessitates learning robust representations for real-world problems. To improve the robustness of GNN models, many studies have been proposed around the central concept of Graph Structure Learning (GSL), which aims to jointly learn an optimized graph structure and corresponding representations. Towards this end, in the presented survey, we broadly review recent progress of GSL methods for learning robust representations. Specifically, we first formulate a general paradigm of GSL, and then review state-of-the-art methods classified by how they model graph structures, followed by applications that incorporate the idea of GSL in other graph tasks. Finally, we point out some issues in current studies and discuss future directions.

Spectral clustering is a leading and popular technique in unsupervised data analysis. Two of its major limitations are scalability and generalization of the spectral embedding (i.e., out-of-sample-extension). In this paper we introduce a deep learning approach to spectral clustering that overcomes the above shortcomings. Our network, which we call SpectralNet, learns a map that embeds input data points into the eigenspace of their associated graph Laplacian matrix and subsequently clusters them. We train SpectralNet using a procedure that involves constrained stochastic optimization. Stochastic optimization allows it to scale to large datasets, while the constraints, which are implemented using a special-purpose output layer, allow us to keep the network output orthogonal. Moreover, the map learned by SpectralNet naturally generalizes the spectral embedding to unseen data points. To further improve the quality of the clustering, we replace the standard pairwise Gaussian affinities with affinities leaned from unlabeled data using a Siamese network. Additional improvement can be achieved by applying the network to code representations produced, e.g., by standard autoencoders. Our end-to-end learning procedure is fully unsupervised. In addition, we apply VC dimension theory to derive a lower bound on the size of SpectralNet. State-of-the-art clustering results are reported on the Reuters dataset. Our implementation is publicly available at //github.com/kstant0725/SpectralNet .

Convolutional Neural Networks (CNNs) have gained significant traction in the field of machine learning, particularly due to their high accuracy in visual recognition. Recent works have pushed the performance of GPU implementations of CNNs to significantly improve their classification and training times. With these improvements, many frameworks have become available for implementing CNNs on both CPUs and GPUs, with no support for FPGA implementations. In this work we present a modified version of the popular CNN framework Caffe, with FPGA support. This allows for classification using CNN models and specialized FPGA implementations with the flexibility of reprogramming the device when necessary, seamless memory transactions between host and device, simple-to-use test benches, and the ability to create pipelined layer implementations. To validate the framework, we use the Xilinx SDAccel environment to implement an FPGA-based Winograd convolution engine and show that the FPGA layer can be used alongside other layers running on a host processor to run several popular CNNs (AlexNet, GoogleNet, VGG A, Overfeat). The results show that our framework achieves 50 GFLOPS across 3x3 convolutions in the benchmarks. This is achieved within a practical framework, which will aid in future development of FPGA-based CNNs.

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