Prostate cancer is the most common cancer in men worldwide and the second leading cause of cancer death in the United States. One of the prognostic features in prostate cancer is the Gleason grading of histopathology images. The Gleason grade is assigned based on tumor architecture on Hematoxylin and Eosin (H&E) stained whole slide images (WSI) by the pathologists. This process is time-consuming and has known interobserver variability. In the past few years, deep learning algorithms have been used to analyze histopathology images, delivering promising results for grading prostate cancer. However, most of the algorithms rely on the fully annotated datasets which are expensive to generate. In this work, we proposed a novel weakly-supervised algorithm to classify prostate cancer grades. The proposed algorithm consists of three steps: (1) extracting discriminative areas in a histopathology image by employing the Multiple Instance Learning (MIL) algorithm based on Transformers, (2) representing the image by constructing a graph using the discriminative patches, and (3) classifying the image into its Gleason grades by developing a Graph Convolutional Neural Network (GCN) based on the gated attention mechanism. We evaluated our algorithm using publicly available datasets, including TCGAPRAD, PANDA, and Gleason 2019 challenge datasets. We also cross validated the algorithm on an independent dataset. Results show that the proposed model achieved state-of-the-art performance in the Gleason grading task in terms of accuracy, F1 score, and cohen-kappa. The code is available at https://github.com/NabaviLab/Prostate-Cancer.

Our situated environment is full of uncertainty and highly dynamic, thus hindering the widespread adoption of machine-led Intelligent Decision-Making (IDM) in real world scenarios. This means IDM should have the capability of continuously learning new skills and efficiently generalizing across wider applications. IDM benefits from any new approaches and theoretical breakthroughs that exhibit Artificial General Intelligence (AGI) breaking the barriers between tasks and applications. Recent research has well-examined neural architecture, Transformer, as a backbone foundation model and its generalization to various tasks, including computer vision, natural language processing, and reinforcement learning. We therefore argue that a foundation decision model (FDM) can be established by formulating various decision-making tasks as a sequence decoding task using the Transformer architecture; this would be a promising solution to advance the applications of IDM in more complex real world tasks. In this paper, we elaborate on how a foundation decision model improves the efficiency and generalization of IDM. We also discuss potential applications of a FDM in multi-agent game AI, production scheduling, and robotics tasks. Finally, through a case study, we demonstrate our realization of the FDM, DigitalBrain (DB1) with 1.2 billion parameters, which achieves human-level performance over 453 tasks, including text generation, images caption, video games playing, robotic control, and traveling salesman problems. As a foundation decision model, DB1 would be a baby step towards more autonomous and efficient real world IDM applications.

While deep learning succeeds in a wide range of tasks, it highly depends on the massive collection of annotated data which is expensive and time-consuming. To lower the cost of data annotation, active learning has been proposed to interactively query an oracle to annotate a small proportion of informative samples in an unlabeled dataset. Inspired by the fact that the samples with higher loss are usually more informative to the model than the samples with lower loss, in this paper we present a novel deep active learning approach that queries the oracle for data annotation when the unlabeled sample is believed to incorporate high loss. The core of our approach is a measurement Temporal Output Discrepancy (TOD) that estimates the sample loss by evaluating the discrepancy of outputs given by models at different optimization steps. Our theoretical investigation shows that TOD lower-bounds the accumulated sample loss thus it can be used to select informative unlabeled samples. On basis of TOD, we further develop an effective unlabeled data sampling strategy as well as an unsupervised learning criterion for active learning. Due to the simplicity of TOD, our methods are efficient, flexible, and task-agnostic. Extensive experimental results demonstrate that our approach achieves superior performances than the state-of-the-art active learning methods on image classification and semantic segmentation tasks. In addition, we show that TOD can be utilized to select the best model of potentially the highest testing accuracy from a pool of candidate models.

Robots are traditionally bounded by a fixed embodiment during their operational lifetime, which limits their ability to adapt to their surroundings. Co-optimizing control and morphology of a robot, however, is often inefficient due to the complex interplay between the controller and morphology. In this paper, we propose a learning-based control method that can inherently take morphology into consideration such that once the control policy is trained in the simulator, it can be easily deployed to robots with different embodiments in the real world. In particular, we present the Embodiment-aware Transformer (EAT), an architecture that casts this control problem as conditional sequence modeling. EAT outputs the optimal actions by leveraging a causally masked Transformer. By conditioning an autoregressive model on the desired robot embodiment, past states, and actions, our EAT model can generate future actions that best fit the current robot embodiment. Experimental results show that EAT can outperform all other alternatives in embodiment-varying tasks, and succeed in an example of real-world evolution tasks: stepping down a stair through updating the morphology alone. We hope that EAT will inspire a new push toward real-world evolution across many domains, where algorithms like EAT can blaze a trail by bridging the field of evolutionary robotics and big data sequence modeling.

Recently, there has been increasing interest in synthesizing data to improve downstream text-to-SQL tasks. In this paper, we first examined the existing synthesized datasets and discovered that state-of-the-art text-to-SQL algorithms did not further improve on popular benchmarks when trained with augmented synthetic data. We observed two shortcomings: illogical synthetic SQL queries from independent column sampling and arbitrary table joins. To address these issues, we propose a novel synthesis framework that incorporates key relationships from schema, imposes strong typing, and conducts schema-distance-weighted column sampling. We also adopt an intermediate representation (IR) for the SQL-to-text task to further improve the quality of the generated natural language questions. When existing powerful semantic parsers are pre-finetuned on our high-quality synthesized data, our experiments show that these models have significant accuracy boosts on popular benchmarks, including new state-of-the-art performance on Spider.

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.

Deep reinforcement learning has recently emerged as an appealing alternative for legged locomotion over multiple terrains by training a policy in physical simulation and then transferring it to the real world (i.e., sim-to-real transfer). Despite considerable progress, the capacity and scalability of traditional neural networks are still limited, which may hinder their applications in more complex environments. In contrast, the Transformer architecture has shown its superiority in a wide range of large-scale sequence modeling tasks, including natural language processing and decision-making problems. In this paper, we propose Terrain Transformer (TERT), a high-capacity Transformer model for quadrupedal locomotion control on various terrains. Furthermore, to better leverage Transformer in sim-to-real scenarios, we present a novel two-stage training framework consisting of an offline pretraining stage and an online correction stage, which can naturally integrate Transformer with privileged training. Extensive experiments in simulation demonstrate that TERT outperforms state-of-the-art baselines on different terrains in terms of return, energy consumption and control smoothness. In further real-world validation, TERT successfully traverses nine challenging terrains, including sand pit and stair down, which can not be accomplished by strong baselines.

Distantly-Supervised Named Entity Recognition (DS-NER) effectively alleviates the data scarcity problem in NER by automatically generating training samples. Unfortunately, the distant supervision may induce noisy labels, thus undermining the robustness of the learned models and restricting the practical application. To relieve this problem, recent works adopt self-training teacher-student frameworks to gradually refine the training labels and improve the generalization ability of NER models. However, we argue that the performance of the current self-training frameworks for DS-NER is severely underestimated by their plain designs, including both inadequate student learning and coarse-grained teacher updating. Therefore, in this paper, we make the first attempt to alleviate these issues by proposing: (1) adaptive teacher learning comprised of joint training of two teacher-student networks and considering both consistent and inconsistent predictions between two teachers, thus promoting comprehensive student learning. (2) fine-grained student ensemble that updates each fragment of the teacher model with a temporal moving average of the corresponding fragment of the student, which enhances consistent predictions on each model fragment against noise. To verify the effectiveness of our proposed method, we conduct experiments on four DS-NER datasets. The experimental results demonstrate that our method significantly surpasses previous SOTA methods.

Photometric differences are widely used as supervision signals to train neural networks for estimating depth and camera pose from unlabeled monocular videos. However, this approach is detrimental for model optimization because occlusions and moving objects in a scene violate the underlying static scenario assumption. In addition, pixels in textureless regions or less discriminative pixels hinder model training. To solve these problems, in this paper, we deal with moving objects and occlusions utilizing the difference of the flow fields and depth structure generated by affine transformation and view synthesis, respectively. Secondly, we mitigate the effect of textureless regions on model optimization by measuring differences between features with more semantic and contextual information without adding networks. In addition, although the bidirectionality component is used in each sub-objective function, a pair of images are reasoned about only once, which helps reduce overhead. Extensive experiments and visual analysis demonstrate the effectiveness of the proposed method, which outperform existing state-of-the-art self-supervised methods under the same conditions and without introducing additional auxiliary information.

Recently, density map regression-based methods have dominated in crowd counting owing to their excellent fitting ability on density distribution. However, further improvement tends to saturate mainly because of the confusing background noise and the large density variation. In this paper, we propose a Hierarchically Decoupled Network (HDNet) to solve the above two problems within a unified framework. Specifically, a background classification sub-task is decomposed from the density map prediction task, which is then assigned to a Density Decoupling Module (DDM) to exploit its highly discriminative ability. For the remaining foreground prediction sub-task, it is further hierarchically decomposed to several density-specific sub-tasks by the DDM, which are then solved by the regression-based experts in a Foreground Density Estimation Module (FDEM). Although the proposed strategy effectively reduces the hypothesis space so as to relieve the optimization for those task-specific experts, the high correlation of these sub-tasks are ignored. Therefore, we introduce three types of interaction strategies to unify the whole framework, which are Feature Interaction, Gradient Interaction, and Scale Interaction. Integrated with the above spirits, HDNet achieves state-of-the-art performance on several popular counting benchmarks.