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The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a key component in DNA variant calling tools such as the GATK HaplotypeCaller but can be highly time consuming due to its quadratic time complexity and the large number of pairs to be aligned. Unfortunately, previous approaches to accelerate this task using the massively parallel processing capabilities of modern GPUs are limited by inefficient memory access schemes. This established the need for significantly faster solutions. We address this need by presenting gpuPairHMM -- a novel GPU-based parallelization scheme for the dynamic-programming based Pair-HMM forward algorithm based on wavefronts and warp-shuffles. It gains efficiency by minimizing both memory accesses and instructions. We show that our approach achieves close-to-peak performance on several generations of modern CUDA-enabled GPUs (Volta, Ampere, Ada, Hopper). It also outperforms prior implementations on GPUs, CPUs, and FPGAs by a factor of at least 8.6, 10.4, and 14.5, respectively. gpuPairHMM is publicly available at https://github.com/asbschmidt/gpuPairHMM.

Members of the Human-Robot Interaction (HRI) and Artificial Intelligence (AI) communities have proposed Large Language Models (LLMs) as a promising resource for robotics tasks such as natural language interactions, doing household and workplace tasks, approximating `common sense reasoning', and modeling humans. However, recent research has raised concerns about the potential for LLMs to produce discriminatory outcomes and unsafe behaviors in real-world robot experiments and applications. To address these concerns, we conduct an HRI-based evaluation of discrimination and safety criteria on several highly-rated LLMs. Our evaluation reveals that LLMs currently lack robustness when encountering people across a diverse range of protected identity characteristics (e.g., race, gender, disability status, nationality, religion, and their intersections), producing biased outputs consistent with directly discriminatory outcomes -- e.g. `gypsy' and `mute' people are labeled untrustworthy, but not `european' or `able-bodied' people. Furthermore, we test models in settings with unconstrained natural language (open vocabulary) inputs, and find they fail to act safely, generating responses that accept dangerous, violent, or unlawful instructions -- such as incident-causing misstatements, taking people's mobility aids, and sexual predation. Our results underscore the urgent need for systematic, routine, and comprehensive risk assessments and assurances to improve outcomes and ensure LLMs only operate on robots when it is safe, effective, and just to do so. Data and code will be made available., Comment: 40 pages (52 with references), 21 Figures, 6 Tables

Previous work has observed how Neurodivergence is often harmfully pathologized in Human-Computer Interaction (HCI) and Human-Robot interaction (HRI) research. We conduct a review of autism robot reviews and find the dominant research direction is Autistic people's second to lowest (24 of 25) research priority: interventions and treatments purporting to 'help' neurodivergent individuals to conform to neurotypical social norms, become better behaved, improve social and emotional skills, and otherwise 'fix' us -- rarely prioritizing the internal experiences that might lead to such differences. Furthermore, a growing body of evidence indicates many of the most popular current approaches risk inflicting lasting trauma and damage on Autistic people. We draw on the principles and findings of the latest Autism research, Feminist HRI, and Robotics to imagine a role reversal, analyze the implications, then conclude with actionable guidance on Autistic-led scientific methods and research directions., Comment: 3 pages; In Assistive Applications, Accessibility, and Disability Ethics (A3DE) workshop at the Human Robot Interaction (HRI) Conference 2024; https://sites.google.com/view/love-joy-and-autism-robots/home

Imagine activating new robots meant to aid staff in an elder care facility, only to discover the robots are counterproductive. They undermine the most meaningful moments of the jobs and increase staff workloads, because robots demand care too. Eventually, they're returned. This vignette captures key elements of James Adrian Wright's ethnography, "Robots Won't Save Japan", an essential resource for understanding the state of elder care robotics. Wright's rich ethnographic interviews and observations challenge the prevailing funding, research, and development paradigms for robotics. Elder care residents tend to be Disabled, so this review article augments Wrights' insights with overlooked perspectives from Disability and Robotics research. This article highlights how care recipients' portrayal suggests that Paro, a plush robot seal, might perform better than the care team and author indicated -- leading to insights that support urgent paradigm shifts in elder care, ethnographic studies, and robotics. It presents some of the stronger technical status quo counter-arguments to the book's core narratives, then confronts their own assumptions. Furthermore, it explores exceptional cases where Japanese and international roboticists attend to care workers and recipients, justifying key arguments in Wright's compelling book. Finally, it addresses how "Robots won't save Japan" will save Robotics., Comment: 8 pages

Machine Learning (ML) and 'Artificial Intelligence' ('AI') methods tend to replicate and amplify existing biases and prejudices, as do Robots with AI. For example, robots with facial recognition have failed to identify Black Women as human, while others have categorized people, such as Black Men, as criminals based on appearance alone. A 'culture of modularity' means harms are perceived as 'out of scope', or someone else's responsibility, throughout employment positions in the 'AI supply chain'. Incidents are routine enough (incidentdatabase.ai lists over 2000 examples) to indicate that few organizations are capable of completely respecting peoples' rights; meeting claimed equity, diversity, and inclusion (EDI or DEI) goals; or recognizing and then addressing such failures in their organizations and artifacts. We propose a framework for adapting widely practiced Research and Development (R&D) project management methodologies to build organizational equity capabilities and better integrate known evidence-based best practices. We describe how project teams can organize and operationalize the most promising practices, skill sets, organizational cultures, and methods to detect and address rights-based fairness, equity, accountability, and ethical problems as early as possible when they are often less harmful and easier to mitigate; then monitor for unforeseen incidents to adaptively and constructively address them. Our primary example adapts an Agile development process based on Scrum, one of the most widely adopted approaches to organizing R&D teams. We also discuss limitations of our proposed framework and future research directions., Comment: 15 pages (32 with refs + appendix), 2 figures, 1 table (7 with appendix), incorporates changes based on WeRobot 2023 Draft feedback

We propose the geometry-informed neural operator (GINO), a highly efficient approach to learning the solution operator of large-scale partial differential equations with varying geometries. GINO uses a signed distance function and point-cloud representations of the input shape and neural operators based on graph and Fourier architectures to learn the solution operator. The graph neural operator handles irregular grids and transforms them into and from regular latent grids on which Fourier neural operator can be efficiently applied. GINO is discretization-convergent, meaning the trained model can be applied to arbitrary discretization of the continuous domain and it converges to the continuum operator as the discretization is refined. To empirically validate the performance of our method on large-scale simulation, we generate the industry-standard aerodynamics dataset of 3D vehicle geometries with Reynolds numbers as high as five million. For this large-scale 3D fluid simulation, numerical methods are expensive to compute surface pressure. We successfully trained GINO to predict the pressure on car surfaces using only five hundred data points. The cost-accuracy experiments show a $26,000 \times$ speed-up compared to optimized GPU-based computational fluid dynamics (CFD) simulators on computing the drag coefficient. When tested on new combinations of geometries and boundary conditions (inlet velocities), GINO obtains a one-fourth reduction in error rate compared to deep neural network approaches.

Fourier Neural Operators (FNOs) have proven to be an efficient and effective method for resolution-independent operator learning in a broad variety of application areas across scientific machine learning. A key reason for their success is their ability to accurately model long-range dependencies in spatio-temporal data by learning global convolutions in a computationally efficient manner. To this end, FNOs rely on the discrete Fourier transform (DFT), however, DFTs cause visual and spectral artifacts as well as pronounced dissipation when learning operators in spherical coordinates since they incorrectly assume a flat geometry. To overcome this limitation, we generalize FNOs on the sphere, introducing Spherical FNOs (SFNOs) for learning operators on spherical geometries. We apply SFNOs to forecasting atmospheric dynamics, and demonstrate stable auto\-regressive rollouts for a year of simulated time (1,460 steps), while retaining physically plausible dynamics. The SFNO has important implications for machine learning-based simulation of climate dynamics that could eventually help accelerate our response to climate change.

Stereotypes, bias, and discrimination have been extensively documented in Machine Learning (ML) methods such as Computer Vision (CV) [18, 80], Natural Language Processing (NLP) [6], or both, in the case of large image and caption models such as OpenAI CLIP [14]. In this paper, we evaluate how ML bias manifests in robots that physically and autonomously act within the world. We audit one of several recently published CLIP-powered robotic manipulation methods, presenting it with objects that have pictures of human faces on the surface which vary across race and gender, alongside task descriptions that contain terms associated with common stereotypes. Our experiments definitively show robots acting out toxic stereotypes with respect to gender, race, and scientifically-discredited physiognomy, at scale. Furthermore, the audited methods are less likely to recognize Women and People of Color. Our interdisciplinary sociotechnical analysis synthesizes across fields and applications such as Science Technology and Society (STS), Critical Studies, History, Safety, Robotics, and AI. We find that robots powered by large datasets and Dissolution Models (sometimes called "foundation models", e.g. CLIP) that contain humans risk physically amplifying malignant stereotypes in general; and that merely correcting disparities will be insufficient for the complexity and scale of the problem. Instead, we recommend that robot learning methods that physically manifest stereotypes or other harmful outcomes be paused, reworked, or even wound down when appropriate, until outcomes can be proven safe, effective, and just. Finally, we discuss comprehensive policy changes and the potential of new interdisciplinary research on topics like Identity Safety Assessment Frameworks and Design Justice to better understand and address these harms., Comment: 30 pages, 10 figures, 5 tables. Website: https://sites.google.com/view/robots-enact-stereotypes . Published in the 2022 ACM Conference on Fairness, Accountability, and Transparency (FAccT 22), June 21-24, 2022, Seoul, Republic of Korea. ACM, DOI: https://doi.org/10.1145/3531146.3533138 . FAccT22 Submission dates: Abstract Dec 13, 2021; Submitted Jan 22, 2022; Accepted Apr 7, 2022

The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is commonly facilitated by constructing index data structures which allow for efficient querying of substrings. Recent metagenomic classification pipelines annotate reads with taxonomic labels by analyzing their $k$-mer histograms with respect to a reference genome database. CPU-based index construction is often performed in a preprocessing phase due to the relatively high cost of building irregular data structures such as hash maps. However, the rapidly growing amount of available reference genomes establishes the need for index construction and querying at interactive speeds. In this paper, we introduce MetaCache-GPU -- an ultra-fast metagenomic short read classifier specifically tailored to fit the characteristics of CUDA-enabled accelerators. Our approach employs a novel hash table variant featuring efficient minhash fingerprinting of reads for locality-sensitive hashing and their rapid insertion using warp-aggregated operations. Our performance evaluation shows that MetaCache-GPU is able to build large reference databases in a matter of seconds, enabling instantaneous operability, while popular CPU-based tools such as Kraken2 require over an hour for index construction on the same data. In the context of an ever-growing number of reference genomes, MetaCache-GPU is the first metagenomic classifier that makes analysis pipelines with on-demand composition of large-scale reference genome sets practical. The source code is publicly available at https://github.com/muellan/metacache ., Comment: 11 pages. To be published in ICPP 2021

Hash tables are ubiquitous. Properties such as an amortized constant time complexity for insertion and querying as well as a compact memory layout make them versatile associative data structures with manifold applications. The rapidly growing amount of data emerging in many fields motivated the need for accelerated hash tables designed for modern parallel architectures. In this work, we exploit the fast memory interface of modern GPUs together with a parallel hashing scheme tailored to improve global memory access patterns, to design WarpCore -- a versatile library of hash table data structures. Unique device-sided operations allow for building high performance data processing pipelines entirely on the GPU. Our implementation achieves up to 1.6 billion inserts and up to 4.3 billion retrievals per second on a single GV100 GPU thereby outperforming the state-of-the-art solutions cuDPP, SlabHash, and NVIDIA RAPIDS cuDF. This performance advantage becomes even more pronounced for high load factors of over $90\%$. To overcome the memory limitation of a single GPU, we scale our approach over a dense NVLink topology which gives us close-to-optimal weak scaling on DGX servers. We further show how WarpCore can be used for accelerating a real world bioinformatics application (metagenomic classification) with speedups of over two orders-of-magnitude against state-of-the-art CPU-based solutions. WC is written in C++/CUDA-C and is openly available at https://github.com/sleeepyjack/warpcore., Comment: To be published in HiPC 2020 (best paper award winner)