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Abstract MotivationThe increasing availability of complete genomes demands for models to study genomic variability within entire populations. Pangenome graphs capture the full genomic similarity and diversity between multiple genomes. In order to understand them, we need to see them. For visualization, we need a human-readable graph layout: a graph embedding in low (e.g. two) dimensional depictions. Due to a pangenome graph’s potential excessive size, this is a significant challenge. ResultsIn response, we introduce a novel graph layout algorithm: the Path-Guided Stochastic Gradient Descent (PG-SGD). PG-SGD uses the genomes, represented in the pangenome graph as paths, as an embedded positional system to sample genomic distances between pairs of nodes. This avoids the quadratic cost seen in previous versions of graph drawing by SGD. We show that our implementation efficiently computes the low-dimensional layouts of gigabase-scale pangenome graphs, unveiling their biological features. Availability and implementationWe integrated PG-SGD in ODGI which is released as free software under the MIT open source license. Source code is available at https://github.com/pangenome/odgi. 

Compilers for accelerator design languages (ADLs) translate high-level languages into application-specific hardware. ADL compilers rely on a hardwarecontrol interfaceto compose hardware units. There are two choices:staticcontrol, which relies on cycle-level timing; ordynamiccontrol, which uses explicit signalling to avoid depending on timing details. Static control is efficient but brittle; dynamic control incurs hardware costs to support compositional reasoning. Piezo is an ADL compiler that unifies static and dynamic control in a single intermediate language (IL). Its key insight is that the IL’s static fragment is arefinementof its dynamic fragment: static code admits a subset of the run-time behaviors of the dynamic equivalent. Piezo can optimize code by combining facts from static and dynamic submodules, and it opportunistically converts code from dynamic to static control styles. We implement Piezo as an extension to an existing dynamic ADL compiler, Calyx. We use Piezo to implement a frontend for an existing ADL, a systolic array generator, and a packet-scheduling hardware generator to demonstrate its optimizations and the static–dynamic interactions it enables. 

In this paper, we propose a new secure machine learning inference platform assisted by a small dedicated security processor, which will be easier to protect and deploy compared to today's TEEs integrated into high-performance processors. Our platform provides three main advantages over the state-of-the-art: (i) We achieve significant performance improvements compared to state-of-the-art distributed Privacy-Preserving Machine Learning (PPML) protocols, with only a small security processor that is comparable to a discrete security chip such as the Trusted Platform Module (TPM) or on-chip security subsystems in SoCs similar to the Apple enclave processor. In the semi-honest setting with WAN/GPU, our scheme is 4X-63X faster than Falcon (PoPETs'21) and AriaNN (PoPETs'22) and 3.8X-12X more communication efficient. We achieve even higher performance improvements in the malicious setting. (ii) Our platform guarantees security with abort against malicious adversaries under honest majority assumption. (iii) Our technique is not limited by the size of secure memory in a TEE and can support high-capacity modern neural networks like ResNet18 and Transformer. While previous work investigated the use of high-performance TEEs in PPML, this work represents the first to show that even tiny secure hardware with very limited performance can be leveraged to significantly speed-up distributed PPML protocols if the protocol can be carefully designed for lightweight trusted hardware. 

Special-purpose hardware accelerators are increasingly pivotal for sustaining performance improvements in emerging applications, especially as the benefits of technology scaling continue to diminish. However, designers currently lack effective tools and methodologies to construct complex, high-performance accelerator architectures in a productive manner. Existing high-level synthesis (HLS) tools often require intrusive source-level changes to attain satisfactory quality of results. Despite the introduction of several new accelerator design languages (ADLs) aiming to enhance or replace HLS, their advantages are more evident in relatively simple applications with a single kernel. Existing ADLs prove less effective for realistic hierarchical designs with multiple kernels, even if the design hierarchy is flattened. In this paper, we introduce Allo, a composable programming model for efficient spatial accelerator design. Allo decouples hardware customizations, including compute, memory, communication, and data type from algorithm specification, and encapsulates them as a set of customization primitives. Allo preserves the hierarchical structure of an input program by combining customizations from different functions in a bottom-up, type-safe manner. This approach facilitates holistic optimizations that span across function boundaries. We conduct comprehensive experiments on commonly-used HLS benchmarks and several realistic deep learning models. Our evaluation shows that Allo can outperform state-of-the-art HLS tools and ADLs on all test cases in the PolyBench. For the GPT2 model, the inference latency of the Allo generated accelerator is 1.7x faster than the NVIDIA A100 GPU with 5.4x higher energy efficiency, demonstrating the capability of Allo to handle large-scale designs. 

The ongoing trend of hardware specialization has led to a growing use of custom data formats when processing sparse workloads, which are typically memory-bound. These formats facilitate optimized software/hardware implementations by utilizing sparsity pattern- or target-aware data structures and layouts to enhance memory access latency and bandwidth utilization. However, existing sparse tensor programming models and compilers offer little or no support for productively customizing the sparse formats. Additionally, because these frameworks represent formats using a limited set of per-dimension attributes, they lack the flexibility to accommodate numerous new variations of custom sparse data structures and layouts. To overcome this deficiency, we propose UniSparse, an intermediate language that provides a unified abstraction for representing and customizing sparse formats. Unlike the existing attribute-based frameworks, UniSparse decouples the logical representation of the sparse tensor (i.e., the data structure) from its low-level memory layout, enabling the customization of both. As a result, a rich set of format customizations can be succinctly expressed in a small set of well-defined query, mutation, and layout primitives. We also develop a compiler leveraging the MLIR infrastructure, which supports adaptive customization of formats, and automatic code generation of format conversion and compute operations for heterogeneous architectures. We demonstrate the efficacy of our approach through experiments running commonly-used sparse linear algebra operations with specialized formats on multiple different hardware targets, including an Intel CPU, an NVIDIA GPU, an AMD Xilinx FPGA, and a simulated processing-in-memory (PIM) device.