arXiv subjects

Vlado Menkovski

Publications and source records attributed to Vlado Menkovski.

At least 55 records · Page 3Linked to original sources

arXiv2022

Towards Learned Simulators for Cell Migration

Simulators driven by deep learning are gaining popularity as a tool for efficiently emulating accurate but expensive numerical simulators. Successful applications of such neural simulators can be found in the domains of physics, chemistry, and structural biology, amongst others. Likewise, a neural simulator for cellular dynamics can augment lab experiments and traditional computational methods to enhance our understanding of a cell's interaction with its physical environment. In this work, we propose an autoregressive probabilistic model that can reproduce spatiotemporal dynamics of single cell migration, traditionally simulated with the Cellular Potts model. We observe that standard single-step training methods do not only lead to inconsistent rollout stability, but also fail to accurately capture the stochastic aspects of the dynamics, and we propose training strategies to mitigate these issues. Our evaluation on two proof-of-concept experimental scenarios shows that neural methods have the potential to faithfully simulate stochastic cellular dynamics at least an order of magnitude faster than a state-of-the-art implementation of the Cellular Potts model.

q-bio.QM↗

arXiv2022

Bridging the Performance Gap between FGSM and PGD Adversarial Training

Deep learning achieves state-of-the-art performance in many tasks but exposes to the underlying vulnerability against adversarial examples. Across existing defense techniques, adversarial training with the projected gradient decent attack (adv.PGD) is considered as one of the most effective ways to achieve moderate adversarial robustness. However, adv.PGD requires too much training time since the projected gradient attack (PGD) takes multiple iterations to generate perturbations. On the other hand, adversarial training with the fast gradient sign method (adv.FGSM) takes much less training time since the fast gradient sign method (FGSM) takes one step to generate perturbations but fails to increase adversarial robustness. In this work, we extend adv.FGSM to make it achieve the adversarial robustness of adv.PGD. We demonstrate that the large curvature along FGSM perturbed direction leads to a large difference in performance of adversarial robustness between adv.FGSM and adv.PGD, and therefore propose combining adv.FGSM with a curvature regularization (adv.FGSMR) in order to bridge the performance gap between adv.FGSM and adv.PGD. The experiments show that adv.FGSMR has higher training efficiency than adv.PGD. In addition, it achieves comparable performance of adversarial robustness on MNIST dataset under white-box attack, and it achieves better performance than adv.PGD under white-box attack and effectively defends the transferable adversarial attack on CIFAR-10 dataset.

cs.CR↗

arXiv2022

Small time asymptotics of the entropy of the heat kernel on a Riemannian manifold

We give an asymptotic expansion of the relative entropy between the heat kernel $q_Z(t,z,w)$ of a compact Riemannian manifold $Z$ and the normalized Riemannian volume for small values of $t$ and for a fixed element $z\in Z$. We prove that coefficients in the expansion can be expressed as universal polynomials in the components of the curvature tensor and its covariant derivatives at $z$, when they are expressed in terms of normal coordinates. We describe a method to compute the coefficients, and we use the method to compute the first three coefficients. The asymptotic expansion is necessary for an unsupervised machine-learning algorithm called the Diffusion Variational Autoencoder.

math.DG↗

arXiv2022

Superposing Many Tickets into One: A Performance Booster for Sparse Neural Network Training

Recent works on sparse neural network training (sparse training) have shown that a compelling trade-off between performance and efficiency can be achieved by training intrinsically sparse neural networks from scratch. Existing sparse training methods usually strive to find the best sparse subnetwork possible in one single run, without involving any expensive dense or pre-training steps. For instance, dynamic sparse training (DST), is capable of reaching a competitive performance of dense training by iteratively evolving the sparse topology during the course of training. In this paper, we argue that it is better to allocate the limited resources to create multiple low-loss sparse subnetworks and superpose them into a stronger one, instead of allocating all resources entirely to find an individual subnetwork. To achieve this, two desiderata are required: (1) efficiently producing many low-loss subnetworks, the so-called cheap tickets, within one training process limited to the standard training time used in dense training; (2) effectively superposing these cheap tickets into one stronger subnetwork. To corroborate our conjecture, we present a novel sparse training approach, termed Sup-tickets, which can satisfy the above two desiderata concurrently in a single sparse-to-sparse training process. Across various modern architectures on CIFAR-10/100 and ImageNet, we show that Sup-tickets integrates seamlessly with the existing sparse training methods and demonstrates consistent performance improvement.

cs.LG↗

arXiv2022

Hop-Count Based Self-Supervised Anomaly Detection on Attributed Networks

Recent years have witnessed an upsurge of interest in the problem of anomaly detection on attributed networks due to its importance in both research and practice. Although various approaches have been proposed to solve this problem, two major limitations exist: (1) unsupervised approaches usually work much less efficiently due to the lack of supervisory signal, and (2) existing anomaly detection methods only use local contextual information to detect anomalous nodes, e.g., one- or two-hop information, but ignore the global contextual information. Since anomalous nodes differ from normal nodes in structures and attributes, it is intuitive that the distance between anomalous nodes and their neighbors should be larger than that between normal nodes and their neighbors if we remove the edges connecting anomalous and normal nodes. Thus, hop counts based on both global and local contextual information can be served as the indicators of anomaly. Motivated by this intuition, we propose a hop-count based model (HCM) to detect anomalies by modeling both local and global contextual information. To make better use of hop counts for anomaly identification, we propose to use hop counts prediction as a self-supervised task. We design two anomaly scores based on the hop counts prediction via HCM model to identify anomalies. Besides, we employ Bayesian learning to train HCM model for capturing uncertainty in learned parameters and avoiding overfitting. Extensive experiments on real-world attributed networks demonstrate that our proposed model is effective in anomaly detection.

cs.SI↗

arXiv2022

Quantifying and Learning Linear Symmetry-Based Disentanglement

The definition of Linear Symmetry-Based Disentanglement (LSBD) formalizes the notion of linearly disentangled representations, but there is currently no metric to quantify LSBD. Such a metric is crucial to evaluate LSBD methods and to compare to previous understandings of disentanglement. We propose $\mathcal{D}_\mathrm{LSBD}$, a mathematically sound metric to quantify LSBD, and provide a practical implementation for $\mathrm{SO}(2)$ groups. Furthermore, from this metric we derive LSBD-VAE, a semi-supervised method to learn LSBD representations. We demonstrate the utility of our metric by showing that (1) common VAE-based disentanglement methods don't learn LSBD representations, (2) LSBD-VAE as well as other recent methods can learn LSBD representations, needing only limited supervision on transformations, and (3) various desirable properties expressed by existing disentanglement metrics are also achieved by LSBD representations.

cs.LG↗

arXiv2022

Semantic-Based Few-Shot Learning by Interactive Psychometric Testing

Few-shot classification tasks aim to classify images in query sets based on only a few labeled examples in support sets. Most studies usually assume that each image in a task has a single and unique class association. Under these assumptions, these algorithms may not be able to identify the proper class assignment when there is no exact matching between support and query classes. For example, given a few images of lions, bikes, and apples to classify a tiger. However, in a more general setting, we could consider the higher-level concept, the large carnivores, to match the tiger to the lion for semantic classification. Existing studies rarely considered this situation due to the incompatibility of label-based supervision with complex conception relationships. In this work, we advance the few-shot learning towards this more challenging scenario, the semantic-based few-shot learning, and propose a method to address the paradigm by capturing the inner semantic relationships using interactive psychometric learning. The experiment results on the CIFAR-100 dataset show the superiority of our method for the semantic-based few-shot learning compared to the baseline.

cs.CV↗

arXiv2021

Direction-Aggregated Attack for Transferable Adversarial Examples

Deep neural networks are vulnerable to adversarial examples that are crafted by imposing imperceptible changes to the inputs. However, these adversarial examples are most successful in white-box settings where the model and its parameters are available. Finding adversarial examples that are transferable to other models or developed in a black-box setting is significantly more difficult. In this paper, we propose the Direction-Aggregated adversarial attacks that deliver transferable adversarial examples. Our method utilizes aggregated direction during the attack process for avoiding the generated adversarial examples overfitting to the white-box model. Extensive experiments on ImageNet show that our proposed method improves the transferability of adversarial examples significantly and outperforms state-of-the-art attacks, especially against adversarial robust models. The best averaged attack success rates of our proposed method reaches 94.6\% against three adversarial trained models and 94.8\% against five defense methods. It also reveals that current defense approaches do not prevent transferable adversarial attacks.

cs.LG↗

arXiv2021

Hierarchical Semantic Segmentation using Psychometric Learning

Assigning meaning to parts of image data is the goal of semantic image segmentation. Machine learning methods, specifically supervised learning is commonly used in a variety of tasks formulated as semantic segmentation. One of the major challenges in the supervised learning approaches is expressing and collecting the rich knowledge that experts have with respect to the meaning present in the image data. Towards this, typically a fixed set of labels is specified and experts are tasked with annotating the pixels, patches or segments in the images with the given labels. In general, however, the set of classes does not fully capture the rich semantic information present in the images. For example, in medical imaging such as histology images, the different parts of cells could be grouped and sub-grouped based on the expertise of the pathologist. To achieve such a precise semantic representation of the concepts in the image, we need access to the full depth of knowledge of the annotator. In this work, we develop a novel approach to collect segmentation annotations from experts based on psychometric testing. Our method consists of the psychometric testing procedure, active query selection, query enhancement, and a deep metric learning model to achieve a patch-level image embedding that allows for semantic segmentation of images. We show the merits of our method with evaluation on the synthetically generated image, aerial image and histology image.

cs.CV↗

arXiv2021

Calibrated Adversarial Training

Adversarial training is an approach of increasing the robustness of models to adversarial attacks by including adversarial examples in the training set. One major challenge of producing adversarial examples is to contain sufficient perturbation in the example to flip the model's output while not making severe changes in the example's semantical content. Exuberant change in the semantical content could also change the true label of the example. Adding such examples to the training set results in adverse effects. In this paper, we present the Calibrated Adversarial Training, a method that reduces the adverse effects of semantic perturbations in adversarial training. The method produces pixel-level adaptations to the perturbations based on novel calibrated robust error. We provide theoretical analysis on the calibrated robust error and derive an upper bound for it. Our empirical results show a superior performance of the Calibrated Adversarial Training over a number of public datasets.

cs.LG↗

arXiv2021

Process Discovery Using Graph Neural Networks

Automatically discovering a process model from an event log is the prime problem in process mining. This task is so far approached as an unsupervised learning problem through graph synthesis algorithms. Algorithmic design decisions and heuristics allow for efficiently finding models in a reduced search space. However, design decisions and heuristics are derived from assumptions about how a given behavioral description - an event log - translates into a process model and were not learned from actual models which introduce biases in the solutions. In this paper, we explore the problem of supervised learning of a process discovery technique D. We introduce a technique for training an ML-based model D using graph convolutional neural networks; D translates a given input event log into a sound Petri net. We show that training D on synthetically generated pairs of input logs and output models allows D to translate previously unseen synthetic and several real-life event logs into sound, arbitrarily structured models of comparable accuracy and simplicity as existing state of the art techniques for discovering imperative process models. We analyze the limitations of the proposed technique and outline alleys for future work.

cs.LG↗

arXiv2021

ProtoInfoMax: Prototypical Networks with Mutual Information Maximization for Out-of-Domain Detection

The ability to detect Out-of-Domain (OOD) inputs has been a critical requirement in many real-world NLP applications. For example, intent classification in dialogue systems. The reason is that the inclusion of unsupported OOD inputs may lead to catastrophic failure of systems. However, it remains an empirical question whether current methods can tackle such problems reliably in a realistic scenario where zero OOD training data is available. In this study, we propose ProtoInfoMax, a new architecture that extends Prototypical Networks to simultaneously process in-domain and OOD sentences via Mutual Information Maximization (InfoMax) objective. Experimental results show that our proposed method can substantially improve performance up to 20% for OOD detection in low resource settings of text classification. We also show that ProtoInfoMax is less prone to typical overconfidence errors of Neural Networks, leading to more reliable prediction results.

cs.CL↗

arXiv2021

VAE-CE: Visual Contrastive Explanation using Disentangled VAEs

The goal of a classification model is to assign the correct labels to data. In most cases, this data is not fully described by the given set of labels. Often a rich set of meaningful concepts exist in the domain that can much more precisely describe each datapoint. Such concepts can also be highly useful for interpreting the model's classifications. In this paper we propose a model, denoted as Variational Autoencoder-based Contrastive Explanation (VAE-CE), that represents data with high-level concepts and uses this representation for both classification and generating explanations. The explanations are produced in a contrastive manner, conveying why a datapoint is assigned to one class rather than an alternative class. An explanation is specified as a set of transformations of the input datapoint, with each step depicting a concept changing towards the contrastive class. We build the model using a disentangled VAE, extended with a new supervised method for disentangling individual dimensions. An analysis on synthetic data and MNIST shows that the approaches to both disentanglement and explanation provide benefits over other methods.

cs.LG↗

arXiv2021

On Generalization of Graph Autoencoders with Adversarial Training

Adversarial training is an approach for increasing model's resilience against adversarial perturbations. Such approaches have been demonstrated to result in models with feature representations that generalize better. However, limited works have been done on adversarial training of models on graph data. In this paper, we raise such a question { does adversarial training improve the generalization of graph representations. We formulate L2 and L1 versions of adversarial training in two powerful node embedding methods: graph autoencoder (GAE) and variational graph autoencoder (VGAE). We conduct extensive experiments on three main applications, i.e. link prediction, node clustering, graph anomaly detection of GAE and VGAE, and demonstrate that both L2 and L1 adversarial training boost the generalization of GAE and VGAE.

cs.LG↗

arXiv2020

A Metric for Linear Symmetry-Based Disentanglement

The definition of Linear Symmetry-Based Disentanglement (LSBD) proposed by (Higgins et al., 2018) outlines the properties that should characterize a disentangled representation that captures the symmetries of data. However, it is not clear how to measure the degree to which a data representation fulfills these properties. We propose a metric for the evaluation of the level of LSBD that a data representation achieves. We provide a practical method to evaluate this metric and use it to evaluate the disentanglement of the data representations obtained for three datasets with underlying $SO(2)$ symmetries.

cs.LG↗

arXiv2020

Plasma Confinement Mode Classification Using a Sequence-to-Sequence Neural Network With Attention

In a typical fusion experiment, the plasma can have several possible confinement modes. At the TCV tokamak, aside from the Low (L) and High (H) confinement modes, an additional mode, dithering (D), is frequently observed. Developing methods that automatically detect these modes is considered to be important for future tokamak operation. Previous work with deep learning methods, particularly convolutional recurrent neural networks (Conv-RNNs), indicates that they are a suitable approach. Nevertheless, those models are sensitive to noise in the temporal alignment of labels, and that model in particular is limited to making individual decisions taking into account only its own hidden state and its input at each time step. In this work, we propose an architecture for a sequence-to-sequence neural network model with attention which solves both of those issues. Using a carefully calibrated dataset, we compare the performance of a Conv-RNN with that of our proposed sequence-to-sequence model, and show two results: one, that the Conv-RNN can be improved upon with new data; two, that the sequence-to-sequence model can improve the results even further, achieving excellent scores on both train and test data.

physics.plasm-ph↗

arXiv2020

Explaining Predictions by Approximating the Local Decision Boundary

Constructing accurate model-agnostic explanations for opaque machine learning models remains a challenging task. Classification models for high-dimensional data, like images, are often inherently complex. To reduce this complexity, individual predictions may be explained locally, either in terms of a simpler local surrogate model or by communicating how the predictions contrast with those of another class. However, existing approaches still fall short in the following ways: a) they measure locality using a (Euclidean) metric that is not meaningful for non-linear high-dimensional data; or b) they do not attempt to explain the decision boundary, which is the most relevant characteristic of classifiers that are optimized for classification accuracy; or c) they do not give the user any freedom in specifying attributes that are meaningful to them. We address these issues in a new procedure for local decision boundary approximation (DBA). To construct a meaningful metric, we train a variational autoencoder to learn a Euclidean latent space of encoded data representations. We impose interpretability by exploiting attribute annotations to map the latent space to attributes that are meaningful to the user. A difficulty in evaluating explainability approaches is the lack of a ground truth. We address this by introducing a new benchmark data set with artificially generated Iris images, and showing that we can recover the latent attributes that locally determine the class. We further evaluate our approach on tabular data and on the CelebA image data set.

cs.LG↗

arXiv2020

Complex Vehicle Routing with Memory Augmented Neural Networks

Complex real-life routing challenges can be modeled as variations of well-known combinatorial optimization problems. These routing problems have long been studied and are difficult to solve at scale. The particular setting may also make exact formulation difficult. Deep Learning offers an increasingly attractive alternative to traditional solutions, which mainly revolve around the use of various heuristics. Deep Learning may provide solutions which are less time-consuming and of higher quality at large scales, as it generally does not need to generate solutions in an iterative manner, and Deep Learning models have shown a surprising capacity for solving complex tasks in recent years. Here we consider a particular variation of the Capacitated Vehicle Routing (CVRP) problem and investigate the use of Deep Learning models with explicit memory components. Such memory components may help in gaining insight into the model's decisions as the memory and operations on it can be directly inspected at any time, and may assist in scaling the method to such a size that it becomes viable for industry settings.

cs.NE↗