Finding Meaningful Distributions of ML Black-boxes under Forensic Investigation

Given a poorly documented neural network model, we take the perspective of a forensic investigator who wants to find out the model's data domain (e.g. whether on face images or traffic signs). Although existing methods such as membership inference and model inversion can be used to uncover some information about an unknown model, they still require knowledge of the data domain to start with. In this paper, we propose solving this problem by leveraging on comprehensive corpus such as ImageNet to select a meaningful distribution that is close to the original training distribution and leads to high performance in follow-up investigations. The corpus comprises two components, a large dataset of samples and meta information such as hierarchical structure and textual information on the samples. Our goal is to select a set of samples from the corpus for the given model. The core of our method is an objective function that considers two criteria on the selected samples: the model functional properties (derived from the dataset), and semantics (derived from the metadata). We also give an algorithm to efficiently search the large space of all possible subsets w.r.t. the objective function. Experimentation results show that the proposed method is effective. For example, cloning a given model (originally trained with CIFAR-10) by using Caltech 101 can achieve 45.5% accuracy. By using datasets selected by our method, the accuracy is improved to 72.0%.

An End-to-End Breast Tumour Classification Model Using Context-Based Patch Modelling- A BiLSTM Approach for Image Classification

Researchers working on computational analysis of Whole Slide Images (WSIs) in histopathology have primarily resorted to patch-based modelling due to large resolution of each WSI. The large resolution makes WSIs infeasible to be fed directly into the machine learning models due to computational constraints. However, due to patch-based analysis, most of the current methods fail to exploit the underlying spatial relationship among the patches. In our work, we have tried to integrate this relationship along with feature-based correlation among the extracted patches from the particular tumorous region. For the given task of classification, we have used BiLSTMs to model both forward and backward contextual relationship. RNN based models eliminate the limitation of sequence size by allowing the modelling of variable size images within a deep learning model. We have also incorporated the effect of spatial continuity by exploring different scanning techniques used to sample patches. To establish the efficiency of our approach, we trained and tested our model on two datasets, microscopy images and WSI tumour regions. After comparing with contemporary literature we achieved the better performance with accuracy of 90% for microscopy image dataset. For WSI tumour region dataset, we compared the classification results with deep learning networks such as ResNet, DenseNet, and InceptionV3 using maximum voting technique. We achieved the highest performance accuracy of 84%. We found out that BiLSTMs with CNN features have performed much better in modelling patches into an end-to-end Image classification network. Additionally, the variable dimensions of WSI tumour regions were used for classification without the need for resizing. This suggests that our method is independent of tumour image size and can process large dimensional images without losing the resolution details.

Automated Deep Learning Analysis of Angiography Video Sequences for Coronary Artery Disease

The evaluation of obstructions (stenosis) in coronary arteries is currently done by a physician's visual assessment of coronary angiography video sequences. It is laborious, and can be susceptible to interobserver variation. Prior studies have attempted to automate this process, but few have demonstrated an integrated suite of algorithms for the end-to-end analysis of angiograms. We report an automated analysis pipeline based on deep learning to rapidly and objectively assess coronary angiograms, highlight coronary vessels of interest, and quantify potential stenosis. We propose a 3-stage automated analysis method consisting of key frame extraction, vessel segmentation, and stenosis measurement. We combined powerful deep learning approaches such as ResNet and U-Net with traditional image processing and geometrical analysis. We trained and tested our algorithms on the Left Anterior Oblique (LAO) view of the right coronary artery (RCA) using anonymized angiograms obtained from a tertiary cardiac institution, then tested the generalizability of our technique to the Right Anterior Oblique (RAO) view. We demonstrated an overall improvement on previous work, with key frame extraction top-5 precision of 98.4%, vessel segmentation F1-Score of 0.891 and stenosis measurement 20.7% Type I Error rate.

Machine-Learning Study using Improved Correlation Configuration and Application to Quantum Monte Carlo Simulation

We use the Fortuin-Kasteleyn representation based improved estimator of the correlation configuration as an alternative to the ordinary correlation configuration in the machine-learning study of the phase classification of spin models. The phases of classical spin models are classified using the improved estimators, and the method is also applied to the quantum Monte Carlo simulation using the loop algorithm. We analyze the Berezinskii-Kosterlitz-Thouless (BKT) transition of the spin 1/2 quantum XY model on the square lattice. We classify the BKT phase and the paramagnetic phase of the quantum XY model using the machine-learning approach. We show that the classification of the quantum XY model can be performed by using the training data of the classical XY model.

Studying The Effect of MIL Pooling Filters on MIL Tasks

There are different multiple instance learning (MIL) pooling filters used in MIL models. In this paper, we study the effect of different MIL pooling filters on the performance of MIL models in real world MIL tasks. We designed a neural network based MIL framework with 5 different MIL pooling filters: `max', `mean', `attention', `distribution' and `distribution with attention'. We also formulated 5 different MIL tasks on a real world lymph node metastases dataset. We found that the performance of our framework in a task is different for different filters. We also observed that the performances of the five pooling filters are also different from task to task. Hence, the selection of a correct MIL pooling filter for each MIL task is crucial for better performance. Furthermore, we noticed that models with `distribution' and `distribution with attention' pooling filters consistently perform well in almost all of the tasks. We attribute this phenomena to the amount of information captured by `distribution' based pooling filters. While point estimate based pooling filters, like `max' and `mean', produce point estimates of distributions, `distribution' based pooling filters capture the full information in distributions. Lastly, we compared the performance of our neural network model with `distribution' pooling filter with the performance of the best MIL methods in the literature on classical MIL datasets and our model outperformed the others.

Detection and Recovery of Adversarial Attacks with Injected Attractors

Many machine learning adversarial attacks find adversarial samples of a victim model ${\mathcal M}$ by following the gradient of some functions, either explicitly or implicitly. To detect and recover from such attacks, we take the proactive approach that modifies those functions with the goal of misleading the attacks to some local minimals, or to some designated regions that can be easily picked up by a forensic analyzer. To achieve the goal, we propose adding a large number of artifacts, which we called $attractors$, onto the otherwise smooth function. An attractor is a point in the input space, which has a neighborhood of samples with gradients pointing toward it. We observe that decoders of watermarking schemes exhibit properties of attractors, and give a generic method that injects attractors from a watermark decoder into the victim model ${\mathcal M}$. This principled approach allows us to leverage on known watermarking schemes for scalability and robustness. Experimental studies show that our method has competitive performance. For instance, for un-targeted attacks on CIFAR-10 dataset, we can reduce the overall attack success rate of DeepFool to 1.9%, whereas known defence LID, FS and MagNet can reduce the rate to 90.8%, 98.5% and 78.5% respectively.

Regional Registration of Whole Slide Image Stacks Containing Highly Deformed Artefacts

Motivation: High resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, however, requires accurate reconstruction of the tissue volume from the 2D image stack. This task is not trivial due to the distortions that each individual tissue slice experiences while cutting and mounting the tissue on the glass slide. Performing registration for the whole tissue slices may be adversely affected by the deformed tissue regions. Consequently, regional registration is found to be more effective. In this paper, we propose an accurate and robust regional registration algorithm for whole slide images which incrementally focuses registration on the area around the region of interest. Results: Using mean similarity index as the metric, the proposed algorithm (mean $\pm$ std: $0.84 \pm 0.11$) followed by a fine registration algorithm ($0.86 \pm 0.08$) outperformed the state-of-the-art linear whole tissue registration algorithm ($0.74 \pm 0.19$) and the regional version of this algorithm ($0.81 \pm 0.15$). The proposed algorithm also outperforms the state-of-the-art nonlinear registration algorithm (original : $0.82 \pm 0.12$, regional : $0.77 \pm 0.22$) for whole slide images and a recently proposed patch-based registration algorithm (patch size 256: $0.79 \pm 0.16$ , patch size 512: $0.77 \pm 0.16$) for medical images. Availability: The C++ implementation code is available online at the github repository: https://github.com/MahsaPaknezhad/WSIRegistration

Cribriform pattern detection in prostate histopathological images using deep learning models

Architecture, size, and shape of glands are most important patterns used by pathologists for assessment of cancer malignancy in prostate histopathological tissue slides. Varying structures of glands along with cumbersome manual observations may result in subjective and inconsistent assessment. Cribriform gland with irregular border is an important feature in Gleason pattern 4. We propose using deep neural networks for cribriform pattern classification in prostate histopathological images. $163708$ Hematoxylin and Eosin (H\&E) stained images were extracted from histopathologic tissue slides of $19$ patients with prostate cancer and annotated for cribriform patterns. Our automated image classification system analyses the H\&E images to classify them as either `Cribriform' or `Non-cribriform'. Our system uses various deep learning approaches and hand-crafted image pixel intensity-based features. We present our results for cribriform pattern detection across various parameters and configuration allowed by our system. The combination of fine-tuned deep learning models outperformed the state-of-art nuclei feature based methods. Our image classification system achieved the testing accuracy of $85.93~\pm~7.54$ (cross-validated) and $88.04~\pm~5.63$ ( additional unseen test set) across three folds. In this paper, we present an annotated cribriform dataset along with analysis of deep learning models and hand-crafted features for cribriform pattern detection in prostate histopathological images.

A Weakly Supervised Learning Based Clustering Framework

A weakly supervised learning based clustering framework is proposed in this paper. As the core of this framework, we introduce a novel multiple instance learning task based on a bag level label called unique class count ($ucc$), which is the number of unique classes among all instances inside the bag. In this task, no annotations on individual instances inside the bag are needed during training of the models. We mathematically prove that a perfect $ucc$ classifier, in principle, can be used to perfectly cluster individual instances inside the bags. In other words, perfect clustering of individual instances is possible even when no annotations on individual instances are given during training. We have constructed a neural network based $ucc$ classifier and experimentally shown that the clustering performance of our framework with our $ucc$ classifier is comparable to that of fully supervised learning models. We have also observed that our $ucc$ classifiers can potentially be used for zero-shot learning as they learn better semantic features than fully supervised models for `unseen classes', which have never been input into the models during training.

Enhancing Transformation-based Defenses using a Distribution Classifier

Adversarial attacks on convolutional neural networks (CNN) have gained significant attention and research efforts have focused on defense methods that make the classifiers more robust. Stochastic input transformation methods have been proposed, where the idea is to randomly transform the input images to try to recover from the adversarial attacks. While these transformation-based methods have shown considerable success at recovering from adversarial images, the performance on clean images deteriorates as the magnitude of the transformation increases. In this paper, we propose a defense mechanism that can be integrated with existing transformation-based defenses and reduce the deterioration of performance on clean images. Exploiting the fact that the transformation methods are stochastic, our method samples a population of transformed images and performs the final classification on distributions of softmax probabilities. We train a separate compact distribution classifier to recognize distinctive features in the distributions of softmax probabilities of transformed clean images. Without retraining the original CNN, our distribution classifier improves the performance of transformation-based defenses on both clean and adversarial images, even though the distribution classifier was never trained on distributions obtained from the adversarial images. Our method is generic and can be integrated with existing transformation-based methods.