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1. A Simple Algorithm for kNN Sampling in General Metrics

   Gardner, Kirk P. ; Sheehy, Donald R. ( January 2020 , Proceedings of the 32nd Canadian Conference on Computational Geometry)

   Keil, Mark ; Mondal, Debajyoti (Ed.)

   Finding the kth nearest neighbor to a query point is a ubiquitous operation in many types of metric computations, especially those in unsupervised machine learning. In many such cases, the distance to k sample points is used as an estimate of the local density of the sample. In this paper, we give an algorithm that takes a finite metric (P,d) and an integer k and produces a subset S ⊆ P with the property that for any q ∈ P, the distance to the second nearest point of S to q is a constant factor approximation to the distance to the kth nearest point of P to q. Thus, the sample S may be used in lieu of P. In addition to being much smaller than P, the distance queries on S only require finding the second nearest neighbor instead of the kth nearest neighbor. This is a significant improvement, especially because theoretical guarantees on kth nearest neighbor methods often require k to grow as a function of the input size n. 

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2. Sketch-and-Lift: Scalable Subsampled Semidefinite Program for K-means Clustering

   Zhuang, Yubo ; Chen, Xiaohui ; Yang, Yun ( March 2022 , International Conference on Artificial Intelligence and Statistics)

   Semidefinite programming (SDP) is a powerful tool for tackling a wide range of computationally hard problems such as clustering. Despite the high accuracy, semidefinite programs are often too slow in practice with poor scalability on large (or even moderate) datasets. In this paper, we introduce a linear time complexity algorithm for approximating an SDP relaxed K-means clustering. The proposed sketch-and-lift (SL) approach solves an SDP on a subsampled dataset and then propagates the solution to all data points by a nearest-centroid rounding procedure. It is shown that the SL approach enjoys a similar exact recovery threshold as the K-means SDP on the full dataset, which is known to be information-theoretically tight under the Gaussian mixture model. The SL method can be made adaptive with enhanced theoretic properties when the cluster sizes are unbalanced. Our simulation experiments demonstrate that the statistical accuracy of the proposed method outperforms state-of-the-art fast clustering algorithms without sacrificing too much computational efficiency, and is comparable to the original K-means SDP with substantially reduced runtime. 

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3. Label consistency in overfitted generalized k-means

   Zhang, Linfan ; Amini, Arash A. ( January 2021 , Advances in neural information processing systems)

   Ranzato, M. ; Beygelzimer, A. ; Dauphin, Y. ; Liang, P.S. ; Vaughan, J. W. (Ed.)

   We provide theoretical guarantees for label consistency in generalized k-means problems, with an emphasis on the overfitted case where the number of clusters used by the algorithm is more than the ground truth. We provide conditions under which the estimated labels are close to a refinement of the true cluster labels. We consider both exact and approximate recovery of the labels. Our results hold for any constant-factor approximation to the k-means problem. The results are also model-free and only based on bounds on the maximum or average distance of the data points to the true cluster centers. These centers themselves are loosely defined and can be taken to be any set of points for which the aforementioned distances can be controlled. We show the usefulness of the results with applications to some manifold clustering problems. 

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4. 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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5. Exact computation of a manifold metric, via Lipschitz Embeddings and Shortest Paths on a Graph

   Chu, T ; Miller, G ; Sheehy, D. ( January 2020 , Proceedings of the annual ACMSIAM symposium on discrete algorithms)

   Data-sensitive metrics adapt distances locally based the density of data points with the goal of aligning distances and some notion of similarity. In this paper, we give the first exact algorithm for computing a data-sensitive metric called the nearest neighbor metric. In fact, we prove the surprising result that a previously published 3-approximation is an exact algorithm. The nearest neighbor metric can be viewed as a special case of a density-based distance used in machine learning, or it can be seen as an example of a manifold metric. Previous computational research on such metrics despaired of computing exact distances on account of the apparent difficulty of minimizing over all continuous paths between a pair of points. We leverage the exact computation of the nearest neighbor metric to compute sparse spanners and persistent homology. We also explore the behavior of the metric built from point sets drawn from an underlying distribution and consider the more general case of inputs that are finite collections of path-connected compact sets. The main results connect several classical theories such as the conformal change of Riemannian metrics, the theory of positive definite functions of Schoenberg, and screw function theory of Schoenberg and Von Neumann. We also develop some novel proof techniques based on the combination of screw functions and Lipschitz extensions that may be of independent interest. 

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