Visualizing Deep Networks by Optimizing with Integrated Gradients

Understanding and interpreting the decisions made by deep learning models is valuable in many domains. In computer vision, computing heatmaps from a deep network is a popular approach for visualizing and understanding deep networks. However, heatmaps that do not correlate with the network may mislead human, hence the performance of heatmaps in providing a faithful explanation to the underlying deep network is crucial. In this paper, we propose I-GOS, which optimizes for a heatmap so that the classification scores on the masked image would maximally decrease. The main novelty of the approach is to compute descent directions based on the integrated gradients instead of the normal gradient, which avoids local optima and speeds up convergence. Compared with previous approaches, our method can flexibly compute heatmaps at any resolution for different user needs. Extensive experiments on several benchmark datasets show that the heatmaps produced by our approach are more correlated with the decision of the underlying deep network, in comparison with other state-of-the-art approaches

Sketch-based Randomized Algorithms for Dynamic Graph Regression

A well-known problem in data science and machine learning is {\em linear regression}, which is recently extended to dynamic graphs. Existing exact algorithms for updating the solution of dynamic graph regression problem require at least a linear time (in terms of $n$: the size of the graph). However, this time complexity might be intractable in practice. In the current paper, we utilize {\em subsampled randomized Hadamard transform} and \textsf{CountSketch} to propose the first randomized algorithms. Suppose that we are given an $n\times m$ matrix embedding $M$ of the graph, where $m \ll n$. Let $r$ be the number of samples required for a guaranteed approximation error, which is a sublinear function of $n$. Our first algorithm reduces time complexity of pre-processing to $O(n(m + 1) + 2n(m + 1) \log_2(r + 1) + rm^2)$. Then after an edge insertion or an edge deletion, it updates the approximate solution in $O(rm)$ time. Our second algorithm reduces time complexity of pre-processing to $O \left( nnz(M) + m^3 \epsilon^{-2} \log^7(m/\epsilon) \right)$, where $nnz(M)$ is the number of nonzero elements of $M$. Then after an edge insertion or an edge deletion or a node insertion or a node deletion, it updates the approximate solution in $O(qm)$ time, with $q=O\left(\frac{m^2}{\epsilon^2} \log^6(m/\epsilon) \right)$. Finally, we show that under some assumptions, if $\ln n < \epsilon^{-1}$ our first algorithm outperforms our second algorithm and if $\ln n \geq \epsilon^{-1}$ our second algorithm outperforms our first algorithm

Kinetic and Dynamic Delaunay tetrahedralizations in three dimensions

We describe the implementation of algorithms to construct and maintain three-dimensional dynamic Delaunay triangulations with kinetic vertices using a three-simplex data structure. The code is capable of constructing the geometric dual, the Voronoi or Dirichlet tessellation. Initially, a given list of points is triangulated. Time evolution of the triangulation is not only governed by kinetic vertices but also by a changing number of vertices. We use three-dimensional simplex flip algorithms, a stochastic visibility walk algorithm for point location and in addition, we propose a new simple method of deleting vertices from an existing three-dimensional Delaunay triangulation while maintaining the Delaunay property. The dual Dirichlet tessellation can be used to solve differential equations on an irregular grid, to define partitions in cell tissue simulations, for collision detection etc.Comment: 29 pg (preprint), 12 figures, 1 table Title changed (mainly nomenclature), referee suggestions included, typos corrected, bibliography update

Fundamental Bounds and Approaches to Sequence Reconstruction from Nanopore Sequencers

Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic analysis of the impact of insertion-deletion (indel) errors in nanopore sequencers. In particular, we consider the following problems: (i) for given indel error characteristics and rate, what is the probability of accurate reconstruction as a function of sequence length; (ii) what is the number of `typical' sequences within the distortion bound induced by indel errors; (iii) using replicated extrusion (the process of passing a DNA strand through the nanopore), what is the number of replicas needed to reduce the distortion bound so that only one typical sequence exists within the distortion bound. Our results provide a number of important insights: (i) the maximum length of a sequence that can be accurately reconstructed in the presence of indel and substitution errors is relatively small; (ii) the number of typical sequences within the distortion bound is large; and (iii) replicated extrusion is an effective technique for unique reconstruction. In particular, we show that the number of replicas is a slow function (logarithmic) of sequence length -- implying that through replicated extrusion, we can sequence large reads using nanopore sequencers. Our model considers indel and substitution errors separately. In this sense, it can be viewed as providing (tight) bounds on reconstruction lengths and repetitions for accurate reconstruction when the two error modes are considered in a single model.Comment: 12 pages, 5 figure

Graph-Controlled Insertion-Deletion Systems

In this article, we consider the operations of insertion and deletion working in a graph-controlled manner. We show that like in the case of context-free productions, the computational power is strictly increased when using a control graph: computational completeness can be obtained by systems with insertion or deletion rules involving at most two symbols in a contextual or in a context-free manner and with the control graph having only four nodes.Comment: In Proceedings DCFS 2010, arXiv:1008.127