Researchers often spend weeks sifting through decades of unlabeled satellite imagery(on NASA Worldview) in order to develop datasets on which they can start conducting research. We developed an interactive, scalable and fast image similarity search engine (which can take one or more images as the query image) that automatically sifts through the unlabeled dataset reducing dataset generation time from weeks to minutes. In this work, we describe key components of the end to end pipeline. Our similarity search system was created to be able to identify similar images from a potentially petabyte scale database that are similar to an input image, and for this we had to break down each query image into its features, which were generated by a classification layer stripped CNN trained in a supervised manner. To store and search these features efficiently, we had to make several scalability improvements. To improve the speed, reduce the storage, and shrink memory requirements for embedding search, we add a fully connected layer to our CNN make all images into a 128 length vector before entering the classification layers. This helped us compress the size of our image features from 2048 (for ResNet, which was initially tried as our featurizer) to 128 for our new custom model. Additionally, we utilize existing approximate nearest neighbor search libraries to significantly speed up embedding search. Our system currently searches over our entire database of images at 5 seconds per query on a single virtual machine in the cloud. In the future, we would like to incorporate a SimCLR based featurizing model which could be trained without any labelling by a human (since the classification aspect of the model is irrelevant to this use case).
A key capability for autonomous underground mining vehicles is real-time accurate localisation. While significant progress has been made, currently deployed systems have several limitations ranging from dependence on costly additional infrastructure to failure of both visual and range sensor-based techniques in highly aliased or visually challenging environments. In our previous work, we presented a lightweight coarse vision-based localisation system that could map and then localise to within a few metres in an underground mining environment. However, this level of precision is insufficient for providing a cheaper, more reliable vision-based automation alternative to current range sensor-based systems. Here we present a new precision localisation system dubbed "LookUP", which learns a neural-network-based pixel sampling strategy for estimating homographies based on ceiling-facing cameras without requiring any manual labelling. This new system runs in real time on limited computation resource and is demonstrated on two different underground mine sites, achieving real time performance at ~5 frames per second and a much improved average localisation error of ~1.2 metre.
Federated Learning (FL) enables multiple distributed clients (e.g., mobile devices) to collaboratively train a centralized model while keeping the training data locally on the client. Compared to traditional centralized machine learning, FL offers many favorable features such as offloading operations which would usually be performed by a central server and reducing risks of serious privacy leakage. However, Byzantine clients that send incorrect or disruptive updates due to system failures or adversarial attacks may disturb the joint learning process, consequently degrading the performance of the resulting model. In this paper, we propose to mitigate these failures and attacks from a spatial-temporal perspective. Specifically, we use a clustering-based method to detect and exclude incorrect updates by leveraging their geometric properties in the parameter space. Moreover, to further handle malicious clients with time-varying behaviors, we propose to adaptively adjust the learning rate according to momentum-based update speculation. Extensive experiments on 4 public datasets demonstrate that our algorithm achieves enhanced robustness comparing to existing methods under both cross-silo and cross-device FL settings with faulty/malicious clients.
Analyzing time series data is important to predict future events and changes in finance, manufacturing, and administrative decisions. In time series analysis, Gaussian Process (GP) regression methods recently demonstrate competitive performance by decomposing temporal covariance structures. The covariance structure decomposition allows exploiting shared parameters over a set of multiple, selected time series. In this paper, we present two novel GP models which naturally handle multiple time series by placing an Indian Buffet Process (IBP) prior on the presence of shared kernels. We also investigate the well-definedness of the models when infinite latent components are introduced. We present a pragmatic search algorithm which explores a larger structure space efficiently than the existing search algorithm. Experiments are conducted on both synthetic data sets and real-world data sets, showing improved results in term of structure discoveries and predictive performances. We further provide a promising application generating comparison reports from our model results.
The multi-scale, mutli-physics nature of fusion plasmas makes predicting plasma events challenging. Recent advances in deep convolutional neural network architectures (CNN) utilizing dilated convolutions enable accurate predictions on sequences which have long-range, multi-scale characteristics, such as the time-series generated by diagnostic instruments observing fusion plasmas. Here we apply this neural network architecture to the popular problem of disruption prediction in fusion tokamaks, utilizing raw data from a single diagnostic, the Electron Cyclotron Emission imaging (ECEi) diagnostic from the DIII-D tokamak. ECEi measures a fundamental plasma quantity (electron temperature) with high temporal resolution over the entire plasma discharge, making it sensitive to a number of potential pre-disruptions markers with different temporal and spatial scales. Promising, initial disruption prediction results are obtained training a deep CNN with large receptive field (~30k), achieving an $F_1$-score of ~91% on individual time-slices using only the ECEi data.
Clinical machine learning models experience significantly degraded performance in datasets not seen during training, e.g., new hospitals or populations. Recent developments in domain generalization offer a promising solution to this problem by creating models that learn invariances across environments. In this work, we benchmark the performance of eight domain generalization methods on multi-site clinical time series and medical imaging data. We introduce a framework to induce synthetic but realistic domain shifts and sampling bias to stress-test these methods over existing non-healthcare benchmarks. We find that current domain generalization methods do not consistently achieve significant gains in out-of-distribution performance over empirical risk minimization on real-world medical imaging data, in line with prior work on general imaging datasets. However, a subset of realistic induced-shift scenarios in clinical time series data do exhibit limited performance gains. We characterize these scenarios in detail, and recommend best practices for domain generalization in the clinical setting.
Multiplex immunofluorescence and immunohistochemistry benefit patients by allowing cancer pathologists to identify several proteins expressed on the surface of cells, enabling cell classification, better understanding of the tumour micro-environment, more accurate diagnoses, prognoses, and tailored immunotherapy based on the immune status of individual patients. However, they are expensive and time consuming processes which require complex staining and imaging techniques by expert technicians. Hoechst staining is much cheaper and easier to perform, but is not typically used in this case as it binds to DNA rather than to the proteins targeted by immunofluorescent techniques, and it was not previously thought possible to differentiate cells expressing these proteins based only on DNA morphology. In this work we show otherwise, training a deep convolutional neural network to identify cells expressing three proteins (T lymphocyte markers CD3 and CD8, and the B lymphocyte marker CD20) with greater than 90% precision and recall, from Hoechst 33342 stained tissue only. Our model learns previously unknown morphological features associated with expression of these proteins which can be used to accurately differentiate lymphocyte subtypes for use in key prognostic metrics such as assessment of immune cell infiltration,and thereby predict and improve patient outcomes without the need for costly multiplex immunofluorescence.
Topic trajectory information provides crucial insight into the dynamics of topics and their evolutionary relationships over a given time. Also, this information can help to improve our understanding on how new topics have emerged or formed through a sequential or interrelated events of emergence, modification and integration of prior topics. Nevertheless, the implementation of the existing methods for topic trajectory identification is rarely available as usable software. In this paper, we present TopicTracker, a platform for topic trajectory identification and visualisation. The key of Topic Tracker is that it can represent the three facets of information together, given two kinds of input: a time-stamped topic profile consisting of the set of the underlying topics over time, and the evolution strength matrix among them: evolutionary pathways of dynamic topics, evolution states of the topics, and topic importance. TopicTracker is a publicly available software implemented using the R software.
Differential equations in general and neural ODEs in particular are an essential technique in continuous-time system identification. While many deterministic learning algorithms have been designed based on numerical integration via the adjoint method, many downstream tasks such as active learning, exploration in reinforcement learning, robust control, or filtering require accurate estimates of predictive uncertainties. In this work, we propose a novel approach towards estimating epistemically uncertain neural ODEs, avoiding the numerical integration bottleneck. Instead of modeling uncertainty in the ODE parameters, we directly model uncertainties in the state space. Our algorithm - distributional gradient matching (DGM) - jointly trains a smoother and a dynamics model and matches their gradients via minimizing a Wasserstein loss. Our experiments show that, compared to traditional approximate inference methods based on numerical integration, our approach is faster to train, faster at predicting previously unseen trajectories, and in the context of neural ODEs, significantly more accurate.
User intention which often changes dynamically is considered to be an important factor for modeling users in the design of recommendation systems. Recent studies are starting to focus on predicting user intention (what users want) beyond user preference (what users like). In this work, a user intention model is proposed based on deep sequential topic analysis. The model predicts a user's intention in terms of the topic of interest. The Hybrid Topic Model (HTM) comprising Latent Dirichlet Allocation (LDA) and Word2Vec is proposed to derive the topic of interest of users and the history of preferences. HTM finds the true topics of papers estimating word-topic distribution which includes syntactic and semantic correlations among words. Next, to model user intention, a Long Short Term Memory (LSTM) based sequential deep learning model is proposed. This model takes into account temporal context, namely the time difference between clicks of two consecutive papers seen by a user. Extensive experiments with the real-world research paper dataset indicate that the proposed approach significantly outperforms the state-of-the-art methods. Further, the proposed approach introduces a new road map to model a user activity suitable for the design of a research paper recommendation system.