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During the COVID-19 pandemic, a major driver of new surges has been the emergence of new variants. When a new variant emerges in one or more countries, other nations monitor its spread in preparation for its potential arrival. The impact of the new variant and the timings of epidemic peaks in a country highly depend on when the variant arrives. The current methods for predicting the spread of new variants rely on statistical modeling, however, these methods work only when the new variant has already arrived in the region of interest and has a significant prevalence. Can we predict when a variant existing elsewhere will arrive in a given region? To address this question, we propose a variant-dynamics-informed Graph Neural Network (GNN) approach. First, we derive the dynamics of variant prevalence across pairs of regions (countries) that apply to a large class of epidemic models. The dynamics motivate the introduction of certain features in the GNN. We demonstrate that our proposed dynamics-informed GNN outperforms all the baselines, including the currently pervasive framework of Physics-Informed Neural Networks (PINNs). To advance research in this area, we introduce a benchmarking tool to assess a user-defined model's prediction performance across 87 countries and 36 variants.

Measuring distance or similarity between time-series data is a fundamental aspect of many applications including classification and clustering. Existing measures may fail to capture similarities due to local trends (shapes) and may even produce misleading results. Our goal is to develop a measure that looks for similar trends occurring around similar times and is easily interpretable for researchers in applied domains. This is particularly useful for applications where time-series have a sequence of meaningful local trends that are ordered, such as in epidemics (a surge to an increase to a peak to a decrease). We propose a novel measure, DTW+S, which creates an interpretable "closeness-preserving" matrix representation of the time-series, where each column represents local trends, and then it applies Dynamic Time Warping to compute distances between these matrices. We present a theoretical analysis that supports the choice of this representation. We demonstrate the utility of DTW+S in ensemble building and clustering of epidemic curves. We also demonstrate that our approach results in better classification compared to Dynamic Time Warping for a class of datasets, particularly when local trends rather than scale play a decisive role., Comment: 11 pages, 13 figures

Acoustic-to-articulatory inversion (AAI) involves mapping from the acoustic to the articulatory space. Signal-processing features like the MFCCs, have been widely used for the AAI task. For subjects with dysarthric speech, AAI is challenging because of an imprecise and indistinct pronunciation. In this work, we perform AAI for dysarthric speech using representations from pre-trained self-supervised learning (SSL) models. We demonstrate the impact of different pre-trained features on this challenging AAI task, at low-resource conditions. In addition, we also condition x-vectors to the extracted SSL features to train a BLSTM network. In the seen case, we experiment with three AAI training schemes (subject-specific, pooled, and fine-tuned). The results, consistent across training schemes, reveal that DeCoAR, in the fine-tuned scheme, achieves a relative improvement of the Pearson Correlation Coefficient (CC) by ~1.81% and ~4.56% for healthy controls and patients, respectively, over MFCCs. We observe similar average trends for different SSL features in the unseen case. Overall, SSL networks like wav2vec, APC, and DeCoAR, trained with feature reconstruction or future timestep prediction tasks, perform well in predicting dysarthric articulatory trajectories., Comment: Accepted to IEEE ICASSP Workshops 2024

The traditional methods for detecting autism spectrum disorder (ASD) are expensive, subjective, and time-consuming, often taking years for a diagnosis, with many children growing well into adolescence and even adulthood before finally confirming the disorder. Recently, graph-based learning techniques have demonstrated impressive results on resting-state functional magnetic resonance imaging (rs-fMRI) data from the Autism Brain Imaging Data Exchange (ABIDE). We introduce IMAGIN, a multI-granular, Multi-Atlas spatio-temporal attention Graph Isomorphism Network, which we use to learn graph representations of dynamic functional brain connectivity (chronnectome), as opposed to static connectivity (connectome). The experimental results demonstrate that IMAGIN achieves a 5-fold cross-validation accuracy of 79.25%, which surpasses the current state-of-the-art by 1.5%. In addition, analysis of the spatial and temporal attention scores provides further validation for the neural basis of autism., Comment: 6 pages, 2 figures

Forecasting the hospitalizations caused by the Influenza virus is vital for public health planning so that hospitals can be better prepared for an influx of patients. Many forecasting methods have been used in real-time during the Influenza seasons and submitted to the CDC for public communication. The forecasting models range from mechanistic models, and auto-regression models to machine learning models. We hypothesize that we can improve forecasting by using multiple mechanistic models to produce potential trajectories and use machine learning to learn how to combine those trajectories into an improved forecast. We propose a Tree Ensemble model design that utilizes the individual predictors of our baseline model SIkJalpha to improve its performance. Each predictor is generated by changing a set of hyper-parameters. We compare our prospective forecasts deployed for the FluSight challenge (2022) to all the other submitted approaches. Our approach is fully automated and does not require any manual tuning. We demonstrate that our Random Forest-based approach is able to improve upon the forecasts of the individual predictors in terms of mean absolute error, coverage, and weighted interval score. Our method outperforms all other models in terms of the mean absolute error and the weighted interval score based on the mean across all weekly submissions in the current season (2022). Explainability of the Random Forest (through analysis of the trees) enables us to gain insights into how it improves upon the individual predictors.

Data Prefetching is a technique that can hide memory latency by fetching data before it is needed by a program. Prefetching relies on accurate memory access prediction, to which task machine learning based methods are increasingly applied. Unlike previous approaches that learn from deltas or offsets and perform one access prediction, we develop TransforMAP, based on the powerful Transformer model, that can learn from the whole address space and perform multiple cache line predictions. We propose to use the binary of memory addresses as model input, which avoids information loss and saves a token table in hardware. We design a block index bitmap to collect unordered future page offsets under the current page address as learning labels. As a result, our model can learn temporal patterns as well as spatial patterns within a page. In a practical implementation, this approach has the potential to hide prediction latency because it prefetches multiple cache lines likely to be used in a long horizon. We show that our approach achieves 35.67% MPKI improvement and 20.55% IPC improvement in simulation, higher than state-of-the-art Best-Offset prefetcher and ISB prefetcher.

Machine learning algorithms have shown potential to improve prefetching performance by accurately predicting future memory accesses. Existing approaches are based on the modeling of text prediction, considering prefetching as a classification problem for sequence prediction. However, the vast and sparse memory address space leads to large vocabulary, which makes this modeling impractical. The number and order of outputs for multiple cache line prefetching are also fundamentally different from text prediction. We propose TransFetch, a novel way to model prefetching. To reduce vocabulary size, we use fine-grained address segmentation as input. To predict unordered sets of future addresses, we use delta bitmaps for multiple outputs. We apply an attention-based network to learn the mapping between input and output. Prediction experiments demonstrate that address segmentation achieves 26% - 36% higher F1-score than delta inputs and 15% - 24% higher F1-score than page & offset inputs for SPEC 2006, SPEC 2017, and GAP benchmarks. Simulation results show that TransFetch achieves 38.75% IPC improvement compared with no prefetching, outperforming the best-performing rule-based prefetcher BOP by 10.44%, and ML-based prefetcher Voyager by 6.64%.

State-of-the-art Graph Neural Networks (GNNs) have limited scalability with respect to the graph and model sizes. On large graphs, increasing the model depth often means exponential expansion of the scope (i.e., receptive field). Beyond just a few layers, two fundamental challenges emerge: 1. degraded expressivity due to oversmoothing, and 2. expensive computation due to neighborhood explosion. We propose a design principle to decouple the depth and scope of GNNs -- to generate representation of a target entity (i.e., a node or an edge), we first extract a localized subgraph as the bounded-size scope, and then apply a GNN of arbitrary depth on top of the subgraph. A properly extracted subgraph consists of a small number of critical neighbors, while excluding irrelevant ones. The GNN, no matter how deep it is, smooths the local neighborhood into informative representation rather than oversmoothing the global graph into "white noise". Theoretically, decoupling improves the GNN expressive power from the perspectives of graph signal processing (GCN), function approximation (GraphSAGE) and topological learning (GIN). Empirically, on seven graphs (with up to 110M nodes) and six backbone GNN architectures, our design achieves significant accuracy improvement with orders of magnitude reduction in computation and hardware cost., Comment: Accepted to NeurIPS 2021

Graph Neural Networks (GNNs) are proven to be powerful models to generate node embedding for downstream applications. However, due to the high computation complexity of GNN inference, it is hard to deploy GNNs for large-scale or real-time applications. In this paper, we propose to accelerate GNN inference by pruning the dimensions in each layer with negligible accuracy loss. Our pruning framework uses a novel LASSO regression formulation for GNNs to identify feature dimensions (channels) that have high influence on the output activation. We identify two inference scenarios and design pruning schemes based on their computation and memory usage for each. To further reduce the inference complexity, we effectively store and reuse hidden features of visited nodes, which significantly reduces the number of supporting nodes needed to compute the target embedding. We evaluate the proposed method with the node classification problem on five popular datasets and a real-time spam detection application. We demonstrate that the pruned GNN models greatly reduce computation and memory usage with little accuracy loss. For full inference, the proposed method achieves an average of 3.27x speedup with only 0.002 drop in F1-Micro on GPU. For batched inference, the proposed method achieves an average of 6.67x speedup with only 0.003 drop in F1-Micro on CPU. To the best of our knowledge, we are the first to accelerate large scale real-time GNN inference through channel pruning.

During the COVID-19 pandemic, a significant effort has gone into developing ML-driven epidemic forecasting techniques. However, benchmarks do not exist to claim if a new AI/ML technique is better than the existing ones. The "covid-forecast-hub" is a collection of more than 30 teams, including us, that submit their forecasts weekly to the CDC. It is not possible to declare whether one method is better than the other using those forecasts because each team's submission may correspond to different techniques over the period and involve human interventions as the teams are continuously changing/tuning their approach. Such forecasts may be considered "human-expert" forecasts and do not qualify as AI/ML approaches, although they can be used as an indicator of human expert performance. We are interested in supporting AI/ML research in epidemic forecasting which can lead to scalable forecasting without human intervention. Which modeling technique, learning strategy, and data pre-processing technique work well for epidemic forecasting is still an open problem. To help advance the state-of-the-art AI/ML applied to epidemiology, a benchmark with a collection of performance points is needed and the current "state-of-the-art" techniques need to be identified. We propose EpiBench a platform consisting of community-driven benchmarks for AI/ML applied to epidemic forecasting to standardize the challenge with a uniform evaluation protocol. In this paper, we introduce a prototype of EpiBench which is currently running and accepting submissions for the task of forecasting COVID-19 cases and deaths in the US states and We demonstrate that we can utilize the prototype to develop an ensemble relying on fully automated epidemic forecasts (no human intervention) that reaches human-expert level ensemble currently being used by the CDC., Comment: 8 pages, 6 figures. Accepted at the 5th International Workshop on Health Intelligence in conjunction with the Thirty-Fifth AAAI Conference on Artificial Intelligence (AAAI-21)

While Graph Neural Networks (GNNs) are powerful models for learning representations on graphs, most state-of-the-art models do not have significant accuracy gain beyond two to three layers. Deep GNNs fundamentally need to address: 1). expressivity challenge due to oversmoothing, and 2). computation challenge due to neighborhood explosion. We propose a simple "deep GNN, shallow sampler" design principle to improve both the GNN accuracy and efficiency -- to generate representation of a target node, we use a deep GNN to pass messages only within a shallow, localized subgraph. A properly sampled subgraph may exclude irrelevant or even noisy nodes, and still preserve the critical neighbor features and graph structures. The deep GNN then smooths the informative local signals to enhance feature learning, rather than oversmoothing the global graph signals into just "white noise". We theoretically justify why the combination of deep GNNs with shallow samplers yields the best learning performance. We then propose various sampling algorithms and neural architecture extensions to achieve good empirical results. On the largest public graph dataset, ogbn-papers100M, we achieve state-of-the-art accuracy with an order of magnitude reduction in hardware cost., Comment: The complete version of this paper is accepted to NeurIPS 2021, available on arXiv under the new title "Decoupling the depth and scope of graph neural networks" (arXiv:2201.07858). This version, "Deep graph neural networks with shallow subgraph samplers", is a short version and we withdraw it to avoid confusion. Please always refer to arXiv:2201.07858

Graph Neural Networks (GNNs) are powerful deep learning models to generate node embeddings on graphs. When applying deep GNNs on large graphs, it is still challenging to perform training in an efficient and scalable way. We propose a novel parallel training framework. Through sampling small subgraphs as minibatches, we reduce training workload by orders of magnitude compared with state-of-the-art minibatch methods. We then parallelize the key computation steps on tightly-coupled shared memory systems. For graph sampling, we exploit parallelism within and across sampler instances, and propose an efficient data structure supporting concurrent accesses from samplers. The parallel sampler theoretically achieves near-linear speedup with respect to number of processing units. For feature propagation within subgraphs, we improve cache utilization and reduce DRAM traffic by data partitioning. Our partitioning is a 2-approximation strategy for minimizing the communication cost compared to the optimal. We further develop a runtime scheduler to reorder the training operations and adjust the minibatch subgraphs to improve parallel performance. Finally, we generalize the above parallelization strategies to support multiple types of GNN models and graph samplers. The proposed training outperforms the state-of-the-art in scalability, efficiency and accuracy simultaneously. On a 40-core Xeon platform, we achieve 60x speedup (with AVX) in the sampling step and 20x speedup in the feature propagation step, compared to the serial implementation. Our algorithm enables fast training of deeper GNNs, as demonstrated by orders of magnitude speedup compared to the Tensorflow implementation. We open-source our code at https://github.com/GraphSAINT/GraphSAINT., Comment: 43 pages, 8 figures. arXiv admin note: text overlap with arXiv:1810.11899

Forecasting the effect of COVID-19 is essential to design policies that may prepare us to handle the pandemic. Many methods have already been proposed, particularly, to forecast reported cases and deaths at country-level and state-level. Many of these methods are based on traditional epidemiological model which rely on simulations or Bayesian inference to simultaneously learn many parameters at a time. This makes them prone to over-fitting and slow execution. We propose an extension to our model SIkJ$\alpha$ to forecast deaths and show that it can consider the effect of many complexities of the epidemic process and yet be simplified to a few parameters that are learned using fast linear regressions. We also present an evaluation of our method against seven approaches currently being used by the CDC, based on their two weeks forecast at various times during the pandemic. We demonstrate that our method achieves better root mean squared error compared to these seven approaches during majority of the evaluation period. Further, on a 2 core desktop machine, our approach takes only 3.18s to tune hyper-parameters, learn parameters and generate 100 days of forecasts of reported cases and deaths for all the states in the US. The total execution time for 184 countries is 11.83s and for all the US counties ($>$ 3000) is 101.03s., Comment: Fixed a typo

Accurate forecasts for COVID-19 are necessary for better preparedness and resource management. Specifically, deciding the response over months or several months requires accurate long-term forecasts which is particularly challenging as the model errors accumulate with time. A critical factor that can hinder accurate long-term forecasts, is the number of unreported/asymptomatic cases. While there have been early serology tests to estimate this number, more tests need to be conducted for more reliable results. To identify the number of unreported/asymptomatic cases, we take an epidemiology data-driven approach. We show that we can identify lower bounds on this ratio or upper bound on actual cases as a factor of reported cases. To do so, we propose an extension of our prior heterogeneous infection rate model, incorporating unreported/asymptomatic cases. We prove that the number of unreported cases can be reliably estimated only from a certain time period of the epidemic data. In doing so, we construct an algorithm called Fixed Infection Rate method, which identifies a reliable bound on the learned ratio. We also propose two heuristics to learn this ratio and show their effectiveness on simulated data. We use our approaches to identify the upper bounds on the ratio of actual to reported cases for New York City and several US states. Our results demonstrate with high confidence that the actual number of cases cannot be more than 35 times in New York, 40 times in Illinois, 38 times in Massachusetts and 29 times in New Jersey, than the reported cases., Comment: Fixed a typo

Accurate forecasts of COVID-19 is central to resource management and building strategies to deal with the epidemic. We propose a heterogeneous infection rate model with human mobility for epidemic modeling, a preliminary version of which we have successfully used during DARPA Grand Challenge 2014. By linearizing the model and using weighted least squares, our model is able to quickly adapt to changing trends and provide extremely accurate predictions of confirmed cases at the level of countries and states of the United States. We show that during the earlier part of the epidemic, using travel data increases the predictions. Training the model to forecast also enables learning characteristics of the epidemic. In particular, we show that changes in model parameters over time can help us quantify how well a state or a country has responded to the epidemic. The variations in parameters also allow us to forecast different scenarios such as what would happen if we were to disregard social distancing suggestions., Comment: 12 pages, 8 figures. Added a figure

Writing high-performance code requires significant expertise in the programming language, compiler optimizations, and hardware knowledge. This often leads to poor productivity and portability and is inconvenient for a non-programmer domain-specialist such as a Physicist. More desirable is a high-level language where the domain-specialist simply specifies the workload in terms of high-level operations (e.g., matrix-multiply(A, B)), and the compiler identifies the best implementation fully utilizing the heterogeneous platform. For creating a compiler that supports productivity, portability, and performance simultaneously, it is crucial to predict the performance of various available implementations (variants) of the dominant operations (kernels) contained in the workload on various hardware to decide (a) which variant should be chosen for each kernel in the workload, and (b) on which hardware resource the variant should run. To enable the performance prediction, we propose lightweight augmented neural networks for arbitrary combinations of kernel-variant-hardware. A key innovation is utilizing the mathematical complexity of the kernels as a feature to achieve higher accuracy. These models are compact to reduce training time and fast inference during compile-time and run-time. Using models with less than 75 parameters, and only 250 training data instances, we are able to obtain a low MAPE of 3%, significantly outperforming traditional feed-forward neural networks on 48 kernel-variant-hardware combinations. We further demonstrate that our variant-selection approach can be used in Halide implementations to obtain up to 1.7x speedup over Halide's auto-scheduler.

One of the first things to do while planning a trip is to book a good place to stay. Booking a hotel online can be an overwhelming task with thousands of hotels to choose from, for every destination. Motivated by the importance of these situations, we decided to work on the task of recommending hotels to users. We used Expedia's hotel recommendation dataset, which has a variety of features that helped us achieve a deep understanding of the process that makes a user choose certain hotels over others. The aim of this hotel recommendation task is to predict and recommend five hotel clusters to a user that he/she is more likely to book given hundred distinct clusters., Comment: arXiv admin note: text overlap with arXiv:1703.02915 by other authors

Graph Convolutional Networks (GCNs) are powerful models for learning representations of attributed graphs. To scale GCNs to large graphs, state-of-the-art methods use various layer sampling techniques to alleviate the "neighbor explosion" problem during minibatch training. We propose GraphSAINT, a graph sampling based inductive learning method that improves training efficiency and accuracy in a fundamentally different way. By changing perspective, GraphSAINT constructs minibatches by sampling the training graph, rather than the nodes or edges across GCN layers. Each iteration, a complete GCN is built from the properly sampled subgraph. Thus, we ensure fixed number of well-connected nodes in all layers. We further propose normalization technique to eliminate bias, and sampling algorithms for variance reduction. Importantly, we can decouple the sampling from the forward and backward propagation, and extend GraphSAINT with many architecture variants (e.g., graph attention, jumping connection). GraphSAINT demonstrates superior performance in both accuracy and training time on five large graphs, and achieves new state-of-the-art F1 scores for PPI (0.995) and Reddit (0.970)., Comment: Published at ICLR 2020; Code release: github.com/GraphSAINT/GraphSAINT

The Graph Convolutional Network (GCN) model and its variants are powerful graph embedding tools for facilitating classification and clustering on graphs. However, a major challenge is to reduce the complexity of layered GCNs and make them parallelizable and scalable on very large graphs -- state-of the art techniques are unable to achieve scalability without losing accuracy and efficiency. In this paper, we propose novel parallelization techniques for graph sampling-based GCNs that achieve superior scalable performance on very large graphs without compromising accuracy. Specifically, our GCN guarantees work-efficient training and produces order of magnitude savings in computation and communication. To scale GCN training on tightly-coupled shared memory systems, we develop parallelization strategies for the key steps in training: For the graph sampling step, we exploit parallelism within and across multiple sampling instances, and devise an efficient data structure for concurrent accesses that provides theoretical guarantee of near-linear speedup with number of processing units. For the feature propagation step within the sampled graph, we improve cache utilization and reduce DRAM communication by data partitioning. We prove that our partitioning strategy is a 2-approximation for minimizing the communication time compared to the optimal strategy. We demonstrate that our parallel graph embedding outperforms state-of-the-art methods in scalability (with respect to number of processors, graph size and GCN model size), efficiency and accuracy on several large datasets. On a 40-core Xeon platform, our parallel training achieves $64\times$ speedup (with AVX) in the sampling step and $25\times$ speedup in the feature propagation step, compared to the serial implementation, resulting in a net speedup of $21\times$., Comment: 10 pages. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS)