We assess costs and efficiency of state-of-the-art high performance cloud computing compared to a traditional on-premises compute cluster. Our use case are atomistic simulations carried out with the GROMACS molecular dynamics (MD) toolkit with a focus on alchemical protein-ligand binding free energy calculations. We set up a compute cluster in the Amazon Web Services (AWS) cloud that incorporates various different instances with Intel, AMD, and ARM CPUs, some with GPU acceleration. Using representative biomolecular simulation systems we benchmark how GROMACS performs on individual instances and across multiple instances. Thereby we assess which instances deliver the highest performance and which are the most cost-efficient ones for our use case. We find that, in terms of total costs including hardware, personnel, room, energy and cooling, producing MD trajectories in the cloud can be as cost-efficient as an on-premises cluster given that optimal cloud instances are chosen. Further, we find that high-throughput ligand-screening for protein-ligand binding affinity estimation can be accelerated dramatically by using global cloud resources. For a ligand screening study consisting of 19,872 independent simulations, we used all hardware that was available in the cloud at the time of the study. The computations scaled-up to reach peak performances using more than 10,000 instances, 140,000 cores, and 3,000 GPUs simultaneously around the globe. Our simulation ensemble finished in about two days in the cloud, while weeks would be required to complete the task on a typical on-premises cluster consisting of several hundred nodes. We demonstrate that the costs of such and similar studies can be drastically reduced with a checkpoint-restart protocol that allows to use cheap Spot pricing and by using instance types with optimal cost-efficiency.
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Interactive machine learning (IML) is a field of research that explores how to leverage both human and computational abilities in decision making systems. IML represents a collaboration between multiple complementary human and machine intelligent systems working as a team, each with their own unique abilities and limitations. This teamwork might mean that both systems take actions at the same time, or in sequence. Two major open research questions in the field of IML are: "How should we design systems that can learn to make better decisions over time with human interaction?" and "How should we evaluate the design and deployment of such systems?" A lack of appropriate consideration for the humans involved can lead to problematic system behaviour, and issues of fairness, accountability, and transparency. Thus, our goal with this work is to present a human-centred guide to designing and evaluating IML systems while mitigating risks. This guide is intended to be used by machine learning practitioners who are responsible for the health, safety, and well-being of interacting humans. An obligation of responsibility for public interaction means acting with integrity, honesty, fairness, and abiding by applicable legal statutes. With these values and principles in mind, we as a machine learning research community can better achieve goals of augmenting human skills and abilities. This practical guide therefore aims to support many of the responsible decisions necessary throughout the iterative design, development, and dissemination of IML systems.
Given its status as a classic problem and its importance to both theoreticians and practitioners, edit distance provides an excellent lens through which to understand how the theoretical analysis of algorithms impacts practical implementations. From an applied perspective, the goals of theoretical analysis are to predict the empirical performance of an algorithm and to serve as a yardstick to design novel algorithms that perform well in practice. In this paper, we systematically survey the types of theoretical analysis techniques that have been applied to edit distance and evaluate the extent to which each one has achieved these two goals. These techniques include traditional worst-case analysis, worst-case analysis parametrized by edit distance or entropy or compressibility, average-case analysis, semi-random models, and advice-based models. We find that the track record is mixed. On one hand, two algorithms widely used in practice have been born out of theoretical analysis and their empirical performance is captured well by theoretical predictions. On the other hand, all the algorithms developed using theoretical analysis as a yardstick since then have not had any practical relevance. We conclude by discussing the remaining open problems and how they can be tackled.
Silicon-photonic neural networks (SPNNs) have emerged as promising successors to electronic artificial intelligence (AI) accelerators by offering orders of magnitude lower latency and higher energy efficiency. Nevertheless, the underlying silicon photonic devices in SPNNs are sensitive to inevitable fabrication-process variations (FPVs) stemming from optical lithography imperfections. Consequently, the inferencing accuracy in an SPNN can be highly impacted by FPVs -- e.g., can drop to below 10% -- the impact of which is yet to be fully studied. In this paper, we, for the first time, model and explore the impact of FPVs in the waveguide width and silicon-on-insulator (SOI) thickness in coherent SPNNs that use Mach-Zehnder Interferometers (MZIs). Leveraging such models, we propose a novel variation-aware, design-time optimization solution to improve MZI tolerance to different FPVs in SPNNs. Simulation results for two example SPNNs of different scales under realistic and correlated FPVs indicate that the optimized MZIs can improve the inferencing accuracy by up to 93.95% for the MNIST handwritten digit dataset -- considered as an example in this paper -- which corresponds to a <0.5% accuracy loss compared to the variation-free case. The proposed one-time optimization method imposes low area overhead, and hence is applicable even to resource-constrained designs
Common tasks encountered in epidemiology, including disease incidence estimation and causal inference, rely on predictive modeling. Constructing a predictive model can be thought of as learning a prediction function, i.e., a function that takes as input covariate data and outputs a predicted value. Many strategies for learning these functions from data are available, from parametric regressions to machine learning algorithms. It can be challenging to choose an approach, as it is impossible to know in advance which one is the most suitable for a particular dataset and prediction task at hand. The super learner (SL) is an algorithm that alleviates concerns over selecting the one "right" strategy while providing the freedom to consider many of them, such as those recommended by collaborators, used in related research, or specified by subject-matter experts. It is an entirely pre-specified and data-adaptive strategy for predictive modeling. To ensure the SL is well-specified for learning the prediction function, the analyst does need to make a few important choices. In this Education Corner article, we provide step-by-step guidelines for making these choices, walking the reader through each of them and providing intuition along the way. In doing so, we aim to empower the analyst to tailor the SL specification to their prediction task, thereby ensuring their SL performs as well as possible. A flowchart provides a concise, easy-to-follow summary of key suggestions and heuristics, based on our accumulated experience, and guided by theory.
In a sports competition, a team might lose a powerful incentive to exert full effort if its final rank does not depend on the outcome of the matches still to be played. Therefore, the organiser should reduce the probability of such a situation to the extent possible. Our paper provides a classification scheme to identify these weakly (where one team is indifferent) or strongly (where both teams are indifferent) stakeless games. A statistical model is estimated to simulate the UEFA Champions League groups and compare the candidate schedules used in the 2021/22 season according to the competitiveness of the matches played in the last round(s). The option followed in four of the eight groups is found to be optimal under a wide set of parameters. Minimising the number of strongly stakeless matches is verified to be a likely goal in the computer draw of the fixture that remains hidden from the public.
We consider M-estimation problems, where the target value is determined using a minimizer of an expected functional of a Levy process. With discrete observations from the Levy process, we can produce a "quasi-path" by shuffling increments of the Levy process, we call it a quasi-process. Under a suitable sampling scheme, a quasi-process can converge weakly to the true process according to the properties of the stationary and independent increments. Using this resampling technique, we can estimate objective functionals similar to those estimated using the Monte Carlo simulations, and it is available as a contrast function. The M-estimator based on these quasi-processes can be consistent and asymptotically normal.
Locating 3D objects from a single RGB image via Perspective-n-Points (PnP) is a long-standing problem in computer vision. Driven by end-to-end deep learning, recent studies suggest interpreting PnP as a differentiable layer, so that 2D-3D point correspondences can be partly learned by backpropagating the gradient w.r.t. object pose. Yet, learning the entire set of unrestricted 2D-3D points from scratch fails to converge with existing approaches, since the deterministic pose is inherently non-differentiable. In this paper, we propose the EPro-PnP, a probabilistic PnP layer for general end-to-end pose estimation, which outputs a distribution of pose on the SE(3) manifold, essentially bringing categorical Softmax to the continuous domain. The 2D-3D coordinates and corresponding weights are treated as intermediate variables learned by minimizing the KL divergence between the predicted and target pose distribution. The underlying principle unifies the existing approaches and resembles the attention mechanism. EPro-PnP significantly outperforms competitive baselines, closing the gap between PnP-based method and the task-specific leaders on the LineMOD 6DoF pose estimation and nuScenes 3D object detection benchmarks.
Hardware vulnerabilities are generally considered more difficult to fix than software ones because they are persistent after fabrication. Thus, it is crucial to assess the security and fix the vulnerabilities at earlier design phases, such as Register Transfer Level (RTL) and gate level. The focus of the existing security assessment techniques is mainly twofold. First, they check the security of Intellectual Property (IP) blocks separately. Second, they aim to assess the security against individual threats considering the threats are orthogonal. We argue that IP-level security assessment is not sufficient. Eventually, the IPs are placed in a platform, such as a system-on-chip (SoC), where each IP is surrounded by other IPs connected through glue logic and shared/private buses. Hence, we must develop a methodology to assess the platform-level security by considering both the IP-level security and the impact of the additional parameters introduced during platform integration. Another important factor to consider is that the threats are not always orthogonal. Improving security against one threat may affect the security against other threats. Hence, to build a secure platform, we must first answer the following questions: What additional parameters are introduced during the platform integration? How do we define and characterize the impact of these parameters on security? How do the mitigation techniques of one threat impact others? This paper aims to answer these important questions and proposes techniques for quantifiable assurance by quantitatively estimating and measuring the security of a platform at the pre-silicon stages. We also touch upon the term security optimization and present the challenges for future research directions.
Many mathematical objects can be represented as functors from finitely-presented categories $\mathsf{C}$ to $\mathsf{Set}$. For instance, graphs are functors to $\mathsf{Set}$ from the category with two parallel arrows. Such functors are known informally as $\mathsf{C}$-sets. In this paper, we describe and implement an extension of $\mathsf{C}$-sets having data attributes with fixed types, such as graphs with labeled vertices or real-valued edge weights. We call such structures "acsets," short for "attributed $\mathsf{C}$-sets." Derived from previous work on algebraic databases, acsets are a joint generalization of graphs and data frames. They also encompass more elaborate graph-like objects such as wiring diagrams and Petri nets with rate constants. We develop the mathematical theory of acsets and then describe a generic implementation in the Julia programming language, which uses advanced language features to achieve performance comparable with specialized data structures.
The quest to understand consciousness, once the purview of philosophers and theologians, is now actively pursued by scientists of many stripes. We examine consciousness from the perspective of theoretical computer science (TCS), a branch of mathematics concerned with understanding the underlying principles of computation and complexity, including the implications and surprising consequences of resource limitations. In the spirit of Alan Turing's simple yet powerful definition of a computer, the Turing Machine (TM), and perspective of computational complexity theory, we formalize a modified version of the Global Workspace Theory (GWT) of consciousness originated by cognitive neuroscientist Bernard Baars and further developed by him, Stanislas Dehaene, Jean-Pierre Changeaux and others. We are not looking for a complex model of the brain nor of cognition, but for a simple computational model of (the admittedly complex concept of) consciousness. We do this by defining the Conscious Turing Machine (CTM), also called a conscious AI, and then we define consciousness and related notions in the CTM. While these are only mathematical (TCS) definitions, we suggest why the CTM has the feeling of consciousness. The TCS perspective provides a simple formal framework to employ tools from computational complexity theory and machine learning to help us understand consciousness and related concepts. Previously we explored high level explanations for the feelings of pain and pleasure in the CTM. Here we consider three examples related to vision (blindsight, inattentional blindness, and change blindness), followed by discussions of dreams, free will, and altered states of consciousness.
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