With the increase in available large clinical and experimental datasets, there has been substantial amount of work being done on addressing the challenges in the area of biomedical image analysis. Image segmentation, which is crucial for any quantitative analysis, has especially attracted attention. Recent hardware advancement has led to the success of deep learning approaches. However, although deep learning models are being trained on large datasets, existing methods do not use the information from different learning epochs effectively. In this work, we leverage the information of each training epoch to prune the prediction maps of the subsequent epochs. We propose a novel architecture called feedback attention network (FANet) that unifies the previous epoch mask with the feature map of the current training epoch. The previous epoch mask is then used to provide a hard attention to the learnt feature maps at different convolutional layers. The network also allows to rectify the predictions in an iterative fashion during the test time. We show that our proposed feedback attention model provides a substantial improvement on most segmentation metrics tested on seven publicly available biomedical imaging datasets demonstrating the effectiveness of the proposed FANet.
The application of machine learning algorithms to source code has grown in the past years. Since these algorithms are quite sensitive to input data, it is not surprising that researchers experiment with input representations. Nowadays, a popular starting point to represent code is abstract syntax trees (ASTs). Abstract syntax trees have been used for a long time in various software engineering domains, and in particular in IDEs. The API of modern IDEs allows to manipulate and traverse ASTs, resolve references between code elements, etc. Such algorithms can enrich ASTs with new data and therefore may be useful in ML-based code analysis. In this work, we present PSIMiner - a tool for processing PSI trees from the IntelliJ Platform. PSI trees contain code syntax trees as well as functions to work with them, and therefore can be used to enrich code representation using static analysis algorithms of modern IDEs. To showcase this idea, we use our tool to infer types of identifiers in Java ASTs and extend the code2seq model for the method name prediction problem.
Demand forecasting is a crucial component of demand management. While shortening the forecasting horizon allows for more recent data and less uncertainty, this frequently means lower data aggregation levels and a more significant data sparsity. Sparse demand data usually results in lumpy or intermittent demand patterns, which have sparse and irregular demand intervals. Usual statistical and machine learning models fail to provide good forecasts in such scenarios. Our research shows that competitive demand forecasts can be obtained through two models: predicting the demand occurrence and estimating the demand size. We analyze the usage of local and global machine learning models for both cases and compare results against baseline methods. Finally, we propose a novel evaluation criterion of lumpy and intermittent demand forecasting models' performance. Our research shows that global classification models are the best choice when predicting demand event occurrence. When predicting demand sizes, we achieved the best results using Simple Exponential Smoothing forecast. We tested our approach on real-world data consisting of 516 three-year-long time series corresponding to European automotive original equipment manufacturers' daily demand.
Graph topology inference of network processes with co-evolving and interacting time-series is crucial for network studies. Vector autoregressive models (VAR) are popular approaches for topology inference of directed graphs; however, in large networks with short time-series, topology estimation becomes ill-posed. The present paper proposes a novel nonlinearity-preserving topology inference method for directed networks with co-evolving nodal processes that solves the ill-posedness problem. The proposed method, large-scale kernelized Granger causality (lsKGC), uses kernel functions to transform data into a low-dimensional feature space and solves the autoregressive problem in the feature space, then finds the pre-images in the input space to infer the topology. Extensive simulations on synthetic datasets with nonlinear and linear dependencies and known ground-truth demonstrate significant improvement in the Area Under the receiver operating characteristic Curve ( AUC ) of the receiver operating characteristic for network recovery compared to existing methods. Furthermore, tests on real datasets from a functional magnetic resonance imaging (fMRI) study demonstrate 96.3 percent accuracy in diagnosis tasks of schizophrenia patients, which is the highest in the literature with only brain time-series information.
Our goal is to use overhead imagery to understand patterns in traffic flow, for instance answering questions such as how fast could you traverse Times Square at 3am on a Sunday. A traditional approach for solving this problem would be to model the speed of each road segment as a function of time. However, this strategy is limited in that a significant amount of data must first be collected before a model can be used and it fails to generalize to new areas. Instead, we propose an automatic approach for generating dynamic maps of traffic speeds using convolutional neural networks. Our method operates on overhead imagery, is conditioned on location and time, and outputs a local motion model that captures likely directions of travel and corresponding travel speeds. To train our model, we take advantage of historical traffic data collected from New York City. Experimental results demonstrate that our method can be applied to generate accurate city-scale traffic models.
Recent neural view synthesis methods have achieved impressive quality and realism, surpassing classical pipelines which rely on multi-view reconstruction. State-of-the-Art methods, such as NeRF, are designed to learn a single scene with a neural network and require dense multi-view inputs. Testing on a new scene requires re-training from scratch, which takes 2-3 days. In this work, we introduce Stereo Radiance Fields (SRF), a neural view synthesis approach that is trained end-to-end, generalizes to new scenes, and requires only sparse views at test time. The core idea is a neural architecture inspired by classical multi-view stereo methods, which estimates surface points by finding similar image regions in stereo images. In SRF, we predict color and density for each 3D point given an encoding of its stereo correspondence in the input images. The encoding is implicitly learned by an ensemble of pair-wise similarities -- emulating classical stereo. Experiments show that SRF learns structure instead of overfitting on a scene. We train on multiple scenes of the DTU dataset and generalize to new ones without re-training, requiring only 10 sparse and spread-out views as input. We show that 10-15 minutes of fine-tuning further improve the results, achieving significantly sharper, more detailed results than scene-specific models. The code, model, and videos are available at https://virtualhumans.mpi-inf.mpg.de/srf/.
Precision medicine has the potential to revolutionize healthcare, but much of the data for patients is locked away in unstructured free-text, limiting research and delivery of effective personalized treatments. Generating large annotated datasets for information extraction from clinical notes is often challenging and expensive due to the high level of expertise needed for high quality annotations. To enable natural language processing for small dataset sizes, we develop a novel enriched hierarchical annotation scheme and algorithm, Supervised Line Attention (SLA), and apply this algorithm to predicting categorical tumor attributes from kidney and colon cancer pathology reports from the University of California San Francisco (UCSF). Whereas previous work only annotated document level labels, we in addition ask the annotators to enrich the traditional label by asking them to also highlight the relevant line or potentially lines for the final label, which leads to a 20% increase of annotation time required per document. With the enriched annotations, we develop a simple and interpretable machine learning algorithm that first predicts the relevant lines in the document and then predicts the tumor attribute. Our results show across the small dataset sizes of 32, 64, 128, and 186 labeled documents per cancer, SLA only requires half the number of labeled documents as state-of-the-art methods to achieve similar or better micro-f1 and macro-f1 scores for the vast majority of comparisons that we made. Accounting for the increased annotation time, this leads to a 40% reduction in total annotation time over the state of the art.
Epidemiology models play a key role in understanding and responding to the COVID-19 pandemic. In order to build those models, scientists need to understand contributing factors and their relative importance. A large strand of literature has identified the importance of airflow to mitigate droplets and far-field aerosol transmission risks. However, the specific factors contributing to higher or lower contamination in various settings have not been clearly defined and quantified. As part of the MOAI project (https://moaiapp.com), we are developing a privacy-preserving test and trace app to enable infection cluster investigators to get in touch with patients without having to know their identity. This approach allows involving users in the fight against the pandemic by contributing additional information in the form of anonymous research questionnaires. We first describe how the questionnaire was designed, and the synthetic data was generated based on a review we carried out on the latest available literature. We then present a model to evaluate the risk exposition of a user for a given setting. We finally propose a temporal addition to the model to evaluate the risk exposure over time for a given user.
Deep learned models are now largely adopted in different fields, and they generally provide superior performances with respect to classical signal-based approaches. Notwithstanding this, their actual reliability when working in an unprotected environment is far enough to be proven. In this work, we consider a novel deep neural network architecture, named Neural Ordinary Differential Equations (N-ODE), that is getting particular attention due to an attractive property --- a test-time tunable trade-off between accuracy and efficiency. This paper analyzes the robustness of N-ODE image classifiers when faced against a strong adversarial attack and how its effectiveness changes when varying such a tunable trade-off. We show that adversarial robustness is increased when the networks operate in different tolerance regimes during test time and training time. On this basis, we propose a novel adversarial detection strategy for N-ODE nets based on the randomization of the adaptive ODE solver tolerance. Our evaluation performed on standard image classification benchmarks shows that our detection technique provides high rejection of adversarial examples while maintaining most of the original samples under white-box attacks and zero-knowledge adversaries.
We introduce a general framework for leveraging graph stream data for temporal prediction-based applications. Our proposed framework includes novel methods for learning an appropriate graph time-series representation, modeling and weighting the temporal dependencies, and generalizing existing embedding methods for such data. While previous work on dynamic modeling and embedding has focused on representing a stream of timestamped edges using a time-series of graphs based on a specific time-scale (e.g., 1 month), we propose the notion of an $\epsilon$-graph time-series that uses a fixed number of edges for each graph, and show its superiority over the time-scale representation used in previous work. In addition, we propose a number of new temporal models based on the notion of temporal reachability graphs and weighted temporal summary graphs. These temporal models are then used to generalize existing base (static) embedding methods by enabling them to incorporate and appropriately model temporal dependencies in the data. From the 6 temporal network models investigated (for each of the 7 base embedding methods), we find that the top-3 temporal models are always those that leverage the new $\epsilon$-graph time-series representation. Furthermore, the dynamic embedding methods from the framework almost always achieve better predictive performance than existing state-of-the-art dynamic node embedding methods that are developed specifically for such temporal prediction tasks. Finally, the findings of this work are useful for designing better dynamic embedding methods.