The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.
Universal Domain Adaptation aims to transfer the knowledge between the datasets by handling two shifts: domain-shift and category-shift. The main challenge is correctly distinguishing the unknown target samples while adapting the distribution of known class knowledge from source to target. Most existing methods approach this problem by first training the target adapted known classifier and then relying on the single threshold to distinguish unknown target samples. However, this simple threshold-based approach prevents the model from considering the underlying complexities existing between the known and unknown samples in the high-dimensional feature space. In this paper, we propose a new approach in which we use two sets of feature points, namely dual Classifiers for Prototypes and Reciprocals (CPR). Our key idea is to associate each prototype with corresponding known class features while pushing the reciprocals apart from these prototypes to locate them in the potential unknown feature space. The target samples are then classified as unknown if they fall near any reciprocals at test time. To successfully train our framework, we collect the partial, confident target samples that are classified as known or unknown through on our proposed multi-criteria selection. We then additionally apply the entropy loss regularization to them. For further adaptation, we also apply standard consistency regularization that matches the predictions of two different views of the input to make more compact target feature space. We evaluate our proposal, CPR, on three standard benchmarks and achieve comparable or new state-of-the-art results. We also provide extensive ablation experiments to verify our main design choices in our framework.
Colorectal cancer (CRC) is one of the most common causes of cancer and cancer-related mortality worldwide. Performing colon cancer screening in a timely fashion is the key to early detection. Colonoscopy is the primary modality used to diagnose colon cancer. However, the miss rate of polyps, adenomas and advanced adenomas remains significantly high. Early detection of polyps at the precancerous stage can help reduce the mortality rate and the economic burden associated with colorectal cancer. Deep learning-based computer-aided diagnosis (CADx) system may help gastroenterologists to identify polyps that may otherwise be missed, thereby improving the polyp detection rate. Additionally, CADx system could prove to be a cost-effective system that improves long-term colorectal cancer prevention. In this study, we proposed a deep learning-based architecture for automatic polyp segmentation, called Transformer ResU-Net (TransResU-Net). Our proposed architecture is built upon residual blocks with ResNet-50 as the backbone and takes the advantage of transformer self-attention mechanism as well as dilated convolution(s). Our experimental results on two publicly available polyp segmentation benchmark datasets showed that TransResU-Net obtained a highly promising dice score and a real-time speed. With high efficacy in our performance metrics, we concluded that TransResU-Net could be a strong benchmark for building a real-time polyp detection system for the early diagnosis, treatment, and prevention of colorectal cancer. The source code of the proposed TransResU-Net is publicly available at https://github.com/nikhilroxtomar/TransResUNet.
Labelling a large quantity of social media data for the task of supervised machine learning is not only time-consuming but also difficult and expensive. On the other hand, the accuracy of supervised machine learning models is strongly related to the quality of the labelled data on which they train, and automatic sentiment labelling techniques could reduce the time and cost of human labelling. We have compared three automatic sentiment labelling techniques: TextBlob, Vader, and Afinn to assign sentiments to tweets without any human assistance. We compare three scenarios: one uses training and testing datasets with existing ground truth labels; the second experiment uses automatic labels as training and testing datasets; and the third experiment uses three automatic labelling techniques to label the training dataset and uses the ground truth labels for testing. The experiments were evaluated on two Twitter datasets: SemEval-2013 (DS-1) and SemEval-2016 (DS-2). Results show that the Afinn labelling technique obtains the highest accuracy of 80.17% (DS-1) and 80.05% (DS-2) using a BiLSTM deep learning model. These findings imply that automatic text labelling could provide significant benefits, and suggest a feasible alternative to the time and cost of human labelling efforts.
This paper presents a proof-of-concept method for classifying chemical compounds directly from NMR data without doing structure elucidation. This can help to reduce time in finding good structure candidates, as in most cases matching must be done by a human engineer, or at the very least a process for matching must be meaningfully interpreted by one. Therefore, for a long time automation in the area of NMR has been actively sought. The method identified as suitable for the classification is a convolutional neural network (CNN). Other methods, including clustering and image registration, have not been found suitable for the task in a comparative analysis. The result shows that deep learning can offer solutions to automation problems in cheminformatics.
We present an analytical method to estimate the continuous-time collision probability of motion plans for autonomous agents with linear controlled Ito dynamics. Motion plans generated by planning algorithms cannot be perfectly executed by autonomous agents in reality due to the inherent uncertainties in the real world. Estimating end-to-end risk is crucial to characterize the safety of trajectories and plan risk optimal trajectories. In this paper, we derive upper bounds for the continuous-time risk in stochastic robot navigation using the properties of Brownian motion as well as Boole and Hunter's inequalities from probability theory. Using a ground robot navigation example, we numerically demonstrate that our method is considerably faster than the naive Monte Carlo sampling method and the proposed bounds perform better than the discrete-time risk bounds.
Search and rescue, wildfire monitoring, and flood/hurricane impact assessment are mission-critical services for recent IoT networks. Communication synchronization, dependability, and minimal communication jitter are major simulation and system issues for the time-based physics-based ROS simulator, event-based network-based wireless simulator, and complex dynamics of mobile and heterogeneous IoT devices deployed in actual environments. Simulating a heterogeneous multi-robot system before deployment is difficult due to synchronizing physics (robotics) and network simulators. Due to its master-based architecture, most TCP/IP-based synchronization middlewares use ROS1. A real-time ROS2 architecture with masterless packet discovery synchronizes robotics and wireless network simulations. A velocity-aware Transmission Control Protocol (TCP) technique for ground and aerial robots using Data Distribution Service (DDS) publish-subscribe transport minimizes packet loss, synchronization, transmission, and communication jitters. Gazebo and NS-3 simulate and test. Simulator-agnostic middleware. LOS/NLOS and TCP/UDP protocols tested our ROS2-based synchronization middleware for packet loss probability and average latency. A thorough ablation research replaced NS-3 with EMANE, a real-time wireless network simulator, and masterless ROS2 with master-based ROS1. Finally, we tested network synchronization and jitter using one aerial drone (Duckiedrone) and two ground vehicles (TurtleBot3 Burger) on different terrains in masterless (ROS2) and master-enabled (ROS1) clusters. Our middleware shows that a large-scale IoT infrastructure with a diverse set of stationary and robotic devices can achieve low-latency communications (12% and 11% reduction in simulation and real) while meeting mission-critical application reliability (10% and 15% packet loss reduction) and high-fidelity requirements.
Evaluation of intervention in a multi-agent system, e.g., when humans should intervene in autonomous driving systems and when a player should pass to teammates for a good shot, is challenging in various engineering and scientific fields. Estimating the individual treatment effect (ITE) using counterfactual long-term prediction is practical to evaluate such interventions. However, most of the conventional frameworks did not consider the time-varying complex structure of multi-agent relationships and covariate counterfactual prediction. This may sometimes lead to erroneous assessments of ITE and interpretation problems. Here we propose an interpretable, counterfactual recurrent network in multi-agent systems to estimate the effect of the intervention. Our model leverages graph variational recurrent neural networks and theory-based computation with domain knowledge for the ITE estimation framework based on long-term prediction of multi-agent covariates and outcomes, which can confirm under the circumstances under which the intervention is effective. On simulated models of an automated vehicle and biological agents with time-varying confounders, we show that our methods achieved lower estimation errors in counterfactual covariates and the most effective treatment timing than the baselines. Furthermore, using real basketball data, our methods performed realistic counterfactual predictions and evaluated the counterfactual passes in shot scenarios.
This paper introduces a new, highly consequential setting for the use of computer vision for environmental sustainability. Concentrated Animal Feeding Operations (CAFOs) (aka intensive livestock farms or "factory farms") produce significant manure and pollution. Dumping manure in the winter months poses significant environmental risks and violates environmental law in many states. Yet the federal Environmental Protection Agency (EPA) and state agencies have relied primarily on self-reporting to monitor such instances of "land application." Our paper makes four contributions. First, we introduce the environmental, policy, and agricultural setting of CAFOs and land application. Second, we provide a new dataset of high-cadence (daily to weekly) 3m/pixel satellite imagery from 2018-20 for 330 CAFOs in Wisconsin with hand labeled instances of land application (n=57,697). Third, we develop an object detection model to predict land application and a system to perform inference in near real-time. We show that this system effectively appears to detect land application (PR AUC = 0.93) and we uncover several outlier facilities which appear to apply regularly and excessively. Last, we estimate the population prevalence of land application events in Winter 2021/22. We show that the prevalence of land application is much higher than what is self-reported by facilities. The system can be used by environmental regulators and interest groups, one of which piloted field visits based on this system this past winter. Overall, our application demonstrates the potential for AI-based computer vision systems to solve major problems in environmental compliance with near-daily imagery.
Image registration is an essential but challenging task in medical image computing, especially for echocardiography, where the anatomical structures are relatively noisy compared to other imaging modalities. Traditional (non-learning) registration approaches rely on the iterative optimization of a similarity metric which is usually costly in time complexity. In recent years, convolutional neural network (CNN) based image registration methods have shown good effectiveness. In the meantime, recent studies show that the attention-based model (e.g., Transformer) can bring superior performance in pattern recognition tasks. In contrast, whether the superior performance of the Transformer comes from the long-winded architecture or is attributed to the use of patches for dividing the inputs is unclear yet. This work introduces three patch-based frameworks for image registration using MLPs and transformers. We provide experiments on 2D-echocardiography registration to answer the former question partially and provide a benchmark solution. Our results on a large public 2D echocardiography dataset show that the patch-based MLP/Transformer model can be effectively used for unsupervised echocardiography registration. They demonstrate comparable and even better registration performance than a popular CNN registration model. In particular, patch-based models better preserve volume changes in terms of Jacobian determinants, thus generating robust registration fields with less unrealistic deformation. Our results demonstrate that patch-based learning methods, whether with attention or not, can perform high-performance unsupervised registration tasks with adequate time and space complexity. Our codes are available https://gitlab.inria.fr/epione/mlp\_transformer\_registration