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1. A Fortran-Keras Deep Learning Bridge for Scientific Computing

   https://doi.org/10.1155/2020/8888811  

   Ott, Jordan ; Pritchard, Mike ; Best, Natalie ; Linstead, Erik ; Curcic, Milan ; Baldi, Pierre ( August 2020 , Scientific Programming)

   Implementing artificial neural networks is commonly achieved via high-level programming languages such as Python and easy-to-use deep learning libraries such as Keras. These software libraries come preloaded with a variety of network architectures, provide autodifferentiation, and support GPUs for fast and efficient computation. As a result, a deep learning practitioner will favor training a neural network model in Python, where these tools are readily available. However, many large-scale scientific computation projects are written in Fortran, making it difficult to integrate with modern deep learning methods. To alleviate this problem, we introduce a software library, the Fortran-Keras Bridge (FKB). This two-way bridge connects environments where deep learning resources are plentiful with those where they are scarce. The paper describes several unique features offered by FKB, such as customizable layers, loss functions, and network ensembles. The paper concludes with a case study that applies FKB to address open questions about the robustness of an experimental approach to global climate simulation, in which subgrid physics are outsourced to deep neural network emulators. In this context, FKB enables a hyperparameter search of one hundred plus candidate models of subgrid cloud and radiation physics, initially implemented in Keras, to be transferred and used in Fortran. Such a process allows the model’s emergent behavior to be assessed, i.e., when fit imperfections are coupled to explicit planetary-scale fluid dynamics. The results reveal a previously unrecognized strong relationship between offline validation error and online performance, in which the choice of the optimizer proves unexpectedly critical. This in turn reveals many new neural network architectures that produce considerable improvements in climate model stability including some with reduced error, for an especially challenging training dataset. 

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2. TOD: GPU-Accelerated Outlier Detection via Tensor Operations

   https://doi.org/10.14778/3570690.3570703  

   Zhao, Yue ; Chen, George H. ; Jia, Zhihao ( November 2022 , Proceedings of the VLDB Endowment)

   Outlier detection (OD) is a key machine learning task for finding rare and deviant data samples, with many time-critical applications such as fraud detection and intrusion detection. In this work, we propose TOD, the first tensor-based system for efficient and scalable outlier detection on distributed multi-GPU machines. A key idea behind TOD is decomposing complex OD applications into a small collection of basic tensor algebra operators. This decomposition enables TOD to accelerate OD computations by leveraging recent advances in deep learning infrastructure in both hardware and software. Moreover, to deploy memory-intensive OD applications on modern GPUs with limited on-device memory, we introduce two key techniques. First, provable quantization speeds up OD computations and reduces its memory footprint by automatically performing specific floating-point operations in lower precision while provably guaranteeing no accuracy loss. Second, to exploit the aggregated compute resources and memory capacity of multiple GPUs, we introduce automatic batching , which decomposes OD computations into small batches for both sequential execution on a single GPU and parallel execution across multiple GPUs. TOD supports a diverse set of OD algorithms. Evaluation on 11 real-world and 3 synthetic OD datasets shows that TOD is on average 10.9X faster than the leading CPU-based OD system PyOD (with a maximum speedup of 38.9X), and can handle much larger datasets than existing GPU-based OD systems. In addition, TOD allows easy integration of new OD operators, enabling fast prototyping of emerging and yet-to-discovered OD algorithms. 

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3. NAPS : Integrating pose estimation and tag‐based tracking

   https://doi.org/10.1111/2041-210X.14201  

   Wolf, Scott W. ; Ruttenberg, Dee M. ; Knapp, Daniel Y. ; Webb, Andrew E. ; Traniello, Ian M. ; McKenzie‐Smith, Grace C. ; Leheny, Sophie A. ; Shaevitz, Joshua W. ; Kocher, Sarah D. ( August 2023 , Methods in Ecology and Evolution)

   Significant advances in computational ethology have allowed the quantification of behaviour in unprecedented detail. Tracking animals in social groups, however, remains challenging as most existing methods can either capture pose or robustly retain individual identity over time but not both.

   To capture finely resolved behaviours while maintaining individual identity, we built NAPS (NAPS is ArUco Plus SLEAP), a hybrid tracking framework that combines state‐of‐the‐art, deep learning‐based methods for pose estimation (SLEAP) with unique markers for identity persistence (ArUco). We show that this framework allows the exploration of the social dynamics of the common eastern bumblebee (Bombus impatiens).

   We provide a stand‐alone Python package for implementing this framework along with detailed documentation to allow for easy utilization and expansion. We show that NAPS can scale to long timescale experiments at a high frame rate and that it enables the investigation of detailed behavioural variation within individuals in a group.

   Expanding the toolkit for capturing the constituent behaviours of social groups is essential for understanding the structure and dynamics of social networks. NAPS provides a key tool for capturing these behaviours and can provide critical data for understanding how individual variation influences collective dynamics.

    

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4. Tevatron: An Efficient and Flexible Toolkit for Neural Retrieval

   https://doi.org/10.1145/3539618.3591805  

   Gao, Luyu ; Ma, Xueguang ; Lin, Jimmy ; Callan, Jamie ( July 2023 , ACM)

   Recent rapid advances in deep pre-trained language models and the introduction of large datasets have powered research in embedding-based neural retrieval. While many excellent research papers have emerged, most of them come with their own implementations, which are typically optimized for some particular research goals instead of efficiency or code organization. In this paper, we introduce Tevatron, a neural retrieval toolkit that is optimized for efficiency, flexibility, and code simplicity. Tevatron enables model training and evaluation for a variety of ranking components such as dense retrievers, sparse retrievers, and rerankers. It also provides a standardized pipeline that includes text processing, model training, corpus/query encoding, and search. In addition, Tevatron incorporates well-studied methods for improving retriever effectiveness such as hard negative mining and knowledge distillation. We provide an overview of Tevatron in this paper, demonstrating its effectiveness and efficiency on multiple IR and QA datasets. We highlight Tevatron’s flexible design, which enables easy generalization across datasets, model architectures, and accelerator platforms (GPUs and TPUs). Overall, we believe that Tevatron can serve as a solid software foundation for research on neural retrieval systems, including their design, modeling, and optimization. 

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5. Issues in the Reproducibility of Deep Learning Results

   https://doi.org/10.1109/SPMB47826.2019.9037840  

   Jean-Paul, S. ; Elseify, T. ; Obeid, I. ; Picone, J. ( December 2019 , IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. ; Selesnik, I. ; Picone, J. (Ed.)

   The Neuronix high-performance computing cluster allows us to conduct extensive machine learning experiments on big data [1]. This heterogeneous cluster uses innovative scheduling technology, Slurm [2], that manages a network of CPUs and graphics processing units (GPUs). The GPU farm consists of a variety of processors ranging from low-end consumer grade devices such as the Nvidia GTX 970 to higher-end devices such as the GeForce RTX 2080. These GPUs are essential to our research since they allow extremely compute-intensive deep learning tasks to be executed on massive data resources such as the TUH EEG Corpus [2]. We use TensorFlow [3] as the core machine learning library for our deep learning systems, and routinely employ multiple GPUs to accelerate the training process. Reproducible results are essential to machine learning research. Reproducibility in this context means the ability to replicate an existing experiment – performance metrics such as error rates should be identical and floating-point calculations should match closely. Three examples of ways we typically expect an experiment to be replicable are: (1) The same job run on the same processor should produce the same results each time it is run. (2) A job run on a CPU and GPU should produce identical results. (3) A job should produce comparable results if the data is presented in a different order. System optimization requires an ability to directly compare error rates for algorithms evaluated under comparable operating conditions. However, it is a difficult task to exactly reproduce the results for large, complex deep learning systems that often require more than a trillion calculations per experiment [5]. This is a fairly well-known issue and one we will explore in this poster. Researchers must be able to replicate results on a specific data set to establish the integrity of an implementation. They can then use that implementation as a baseline for comparison purposes. A lack of reproducibility makes it very difficult to debug algorithms and validate changes to the system. Equally important, since many results in deep learning research are dependent on the order in which the system is exposed to the data, the specific processors used, and even the order in which those processors are accessed, it becomes a challenging problem to compare two algorithms since each system must be individually optimized for a specific data set or processor. This is extremely time-consuming for algorithm research in which a single run often taxes a computing environment to its limits. Well-known techniques such as cross-validation [5,6] can be used to mitigate these effects, but this is also computationally expensive. These issues are further compounded by the fact that most deep learning algorithms are susceptible to the way computational noise propagates through the system. GPUs are particularly notorious for this because, in a clustered environment, it becomes more difficult to control which processors are used at various points in time. Another equally frustrating issue is that upgrades to the deep learning package, such as the transition from TensorFlow v1.9 to v1.13, can also result in large fluctuations in error rates when re-running the same experiment. Since TensorFlow is constantly updating functions to support GPU use, maintaining an historical archive of experimental results that can be used to calibrate algorithm research is quite a challenge. This makes it very difficult to optimize the system or select the best configurations. The overall impact of all of these issues described above is significant as error rates can fluctuate by as much as 25% due to these types of computational issues. Cross-validation is one technique used to mitigate this, but that is expensive since you need to do multiple runs over the data, which further taxes a computing infrastructure already running at max capacity. GPUs are preferred when training a large network since these systems train at least two orders of magnitude faster than CPUs [7]. Large-scale experiments are simply not feasible without using GPUs. However, there is a tradeoff to gain this performance. Since all our GPUs use the NVIDIA CUDA® Deep Neural Network library (cuDNN) [8], a GPU-accelerated library of primitives for deep neural networks, it adds an element of randomness into the experiment. When a GPU is used to train a network in TensorFlow, it automatically searches for a cuDNN implementation. NVIDIA’s cuDNN implementation provides algorithms that increase the performance and help the model train quicker, but they are non-deterministic algorithms [9,10]. Since our networks have many complex layers, there is no easy way to avoid this randomness. Instead of comparing each epoch, we compare the average performance of the experiment because it gives us a hint of how our model is performing per experiment, and if the changes we make are efficient. In this poster, we will discuss a variety of issues related to reproducibility and introduce ways we mitigate these effects. For example, TensorFlow uses a random number generator (RNG) which is not seeded by default. TensorFlow determines the initialization point and how certain functions execute using the RNG. The solution for this is seeding all the necessary components before training the model. This forces TensorFlow to use the same initialization point and sets how certain layers work (e.g., dropout layers). However, seeding all the RNGs will not guarantee a controlled experiment. Other variables can affect the outcome of the experiment such as training using GPUs, allowing multi-threading on CPUs, using certain layers, etc. To mitigate our problems with reproducibility, we first make sure that the data is processed in the same order during training. Therefore, we save the data from the last experiment and to make sure the newer experiment follows the same order. If we allow the data to be shuffled, it can affect the performance due to how the model was exposed to the data. We also specify the float data type to be 32-bit since Python defaults to 64-bit. We try to avoid using 64-bit precision because the numbers produced by a GPU can vary significantly depending on the GPU architecture [11-13]. Controlling precision somewhat reduces differences due to computational noise even though technically it increases the amount of computational noise. We are currently developing more advanced techniques for preserving the efficiency of our training process while also maintaining the ability to reproduce models. In our poster presentation we will demonstrate these issues using some novel visualization tools, present several examples of the extent to which these issues influence research results on electroencephalography (EEG) and digital pathology experiments and introduce new ways to manage such computational issues. 

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