Accurate extraction of breast cancer patients phenotypes is important for clinical decision support and clinical research. Current models do not take full advantage of cancer domain-specific corpus, whether pre-training Bidirectional Encoder Representations from Transformer model on cancer-specific corpus could improve the performances of extracting breast cancer phenotypes from texts data remains to be explored. The objective of this study is to develop and evaluate the CancerBERT model for extracting breast cancer phenotypes from clinical texts in electronic health records. This data used in the study included 21,291 breast cancer patients diagnosed from 2010 to 2020, patients clinical notes and pathology reports were collected from the University of Minnesota Clinical Data Repository (UMN). Results: About 3 million clinical notes and pathology reports in electronic health records for 21,291 breast cancer patients were collected to train the CancerBERT model. 200 pathology reports and 50 clinical notes of breast cancer patients that contain 9,685 sentences and 221,356 tokens were manually annotated by two annotators. 20% of the annotated data was used as a test set. Our CancerBERT model achieved the best performance with macro F1 scores equal to 0.876 (95% CI, 0.896-0.902) for exact match and 0.904 (95% CI, 0.896-0.902) for the lenient match. The NER models we developed would facilitate the automated information extraction from clinical texts to further help clinical decision support. Conclusions and Relevance: In this study, we focused on the breast cancer-related concepts extraction from EHR data and obtained a comprehensive annotated dataset that contains 7 types of breast cancer-related concepts. The CancerBERT model with customized vocabulary could significantly improve the performance for extracting breast cancer phenotypes from clinical texts.
To synthesize a realistic action sequence based on a single human image, it is crucial to model both motion patterns and diversity in the action video. This paper proposes an Action Conditional Temporal Variational AutoEncoder (ACT-VAE) to improve motion prediction accuracy and capture movement diversity. ACT-VAE predicts pose sequences for an action clips from a single input image. It is implemented as a deep generative model that maintains temporal coherence according to the action category with a novel temporal modeling on latent space. Further, ACT-VAE is a general action sequence prediction framework. When connected with a plug-and-play Pose-to-Image (P2I) network, ACT-VAE can synthesize image sequences. Extensive experiments bear out our approach can predict accurate pose and synthesize realistic image sequences, surpassing state-of-the-art approaches. Compared to existing methods, ACT-VAE improves model accuracy and preserves diversity.
Mechanical cloaks are materials engineered to manipulate the elastic response around objects to make them indistinguishable from their homogeneous surroundings. Typically, methods based on material-parameter transformations are used to design optical, thermal and electric cloaks. However, they are not applicable in designing mechanical cloaks, since continuum-mechanics equations are not form-invariant under general coordinate transformations. As a result, existing design methods for mechanical cloaks have so far been limited to a narrow selection of voids with simple shapes. To address this challenge, we present a systematic, data-driven design approach to create mechanical cloaks composed of aperiodic metamaterials using a large pre-computed unit cell database. Our method is flexible to allow the design of cloaks with various boundary conditions, different shapes and numbers of voids, and different homogeneous surroundings. It enables a concurrent optimization of both topology and properties distribution of the cloak. Compared to conventional fixed-shape solutions, this results in an overall better cloaking performance, and offers unparalleled versatility. Experimental measurements on 3D-printed structures further confirm the validity of the proposed approach. Our research illustrates the benefits of data-driven approaches in quickly responding to new design scenarios and resolving the computational challenge associated with multiscale designs of aperiodic metamaterials.
In the field of adversarial robustness, there is a common practice that adopts the single-step adversarial training for quickly developing adversarially robust models. However, the single-step adversarial training is most likely to cause catastrophic overfitting, as after a few training epochs it will be hard to generate strong adversarial examples to continuously boost the adversarial robustness. In this work, we aim to avoid the catastrophic overfitting by introducing multi-step adversarial examples during the single-step adversarial training. Then, to balance the large training overhead of generating multi-step adversarial examples, we propose a Multi-stage Optimization based Adversarial Training (MOAT) method that periodically trains the model on mixed benign examples, single-step adversarial examples, and multi-step adversarial examples stage by stage. In this way, the overall training overhead is reduced significantly, meanwhile, the model could avoid catastrophic overfitting. Extensive experiments on CIFAR-10 and CIFAR-100 datasets demonstrate that under similar amount of training overhead, the proposed MOAT exhibits better robustness than either single-step or multi-step adversarial training methods.
Federated Learning is a distributed machine learning approach which enables model training without data sharing. In this paper, we propose a new federated learning algorithm, Federated Averaging with Client-level Momentum (FedCM), to tackle problems of partial participation and client heterogeneity in real-world federated learning applications. FedCM aggregates global gradient information in previous communication rounds and modifies client gradient descent with a momentum-like term, which can effectively correct the bias and improve the stability of local SGD. We provide theoretical analysis to highlight the benefits of FedCM. We also perform extensive empirical studies and demonstrate that FedCM achieves superior performance in various tasks and is robust to different levels of client numbers, participation rate and client heterogeneity.
We improve one-stage visual grounding by addressing current limitations on grounding long and complex queries. Existing one-stage methods encode the entire language query as a single sentence embedding vector, e.g., taking the embedding from BERT or the hidden state from LSTM. This single vector representation is prone to overlooking the detailed descriptions in the query. To address this query modeling deficiency, we propose a recursive sub-query construction framework, which reasons between image and query for multiple rounds and reduces the referring ambiguity step by step. We show our new one-stage method obtains 5.0%, 4.5%, 7.5%, 12.8% absolute improvements over the state-of-the-art one-stage baseline on ReferItGame, RefCOCO, RefCOCO+, and RefCOCOg, respectively. In particular, superior performances on longer and more complex queries validates the effectiveness of our query modeling.
We address the challenging problem of image captioning by revisiting the representation of image scene graph. At the core of our method lies the decomposition of a scene graph into a set of sub-graphs, with each sub-graph capturing a semantic component of the input image. We design a deep model to select important sub-graphs, and to decode each selected sub-graph into a single target sentence. By using sub-graphs, our model is able to attend to different components of the image. Our method thus accounts for accurate, diverse, grounded and controllable captioning at the same time. We present extensive experiments to demonstrate the benefits of our comprehensive captioning model. Our method establishes new state-of-the-art results in caption diversity, grounding, and controllability, and compares favourably to latest methods in caption quality. Our project website can be found at http://pages.cs.wisc.edu/~yiwuzhong/Sub-GC.html.
Metamaterials are emerging as a new paradigmatic material system to render unprecedented and tailorable properties for a wide variety of engineering applications. However, the inverse design of metamaterial and its multiscale system is challenging due to high-dimensional topological design space, multiple local optima, and high computational cost. To address these hurdles, we propose a novel data-driven metamaterial design framework based on deep generative modeling. A variational autoencoder (VAE) and a regressor for property prediction are simultaneously trained on a large metamaterial database to map complex microstructures into a low-dimensional, continuous, and organized latent space. We show in this study that the latent space of VAE provides a distance metric to measure shape similarity, enable interpolation between microstructures and encode meaningful patterns of variation in geometries and properties. Based on these insights, systematic data-driven methods are proposed for the design of microstructure, graded family, and multiscale system. For microstructure design, the tuning of mechanical properties and complex manipulations of microstructures are easily achieved by simple vector operations in the latent space. The vector operation is further extended to generate metamaterial families with a controlled gradation of mechanical properties by searching on a constructed graph model. For multiscale metamaterial systems design, a diverse set of microstructures can be rapidly generated using VAE for target properties at different locations and then assembled by an efficient graph-based optimization method to ensure compatibility between adjacent microstructures. We demonstrate our framework by designing both functionally graded and heterogeneous metamaterial systems that achieve desired distortion behaviors.
Data-driven design of mechanical metamaterials is an increasingly popular method to combat costly physical simulations and immense, often intractable, geometrical design spaces. Using a precomputed dataset of unit cells, a multiscale structure can be quickly filled via combinatorial search algorithms, and machine learning models can be trained to accelerate the process. However, the dependence on data induces a unique challenge: An imbalanced dataset containing more of certain shapes or physical properties can be detrimental to the efficacy of data-driven approaches. In answer, we posit that a smaller yet diverse set of unit cells leads to scalable search and unbiased learning. To select such subsets, we propose METASET, a methodology that 1) uses similarity metrics and positive semi-definite kernels to jointly measure the closeness of unit cells in both shape and property spaces, and 2) incorporates Determinantal Point Processes for efficient subset selection. Moreover, METASET allows the trade-off between shape and property diversity so that subsets can be tuned for various applications. Through the design of 2D metamaterials with target displacement profiles, we demonstrate that smaller, diverse subsets can indeed improve the search process as well as structural performance. By eliminating inherent overlaps in a dataset of 3D unit cells created with symmetry rules, we also illustrate that our flexible method can distill unique subsets regardless of the metric employed. Our diverse subsets are provided publicly for use by any designer.
It is widely believed that learning good representations is one of the main reasons for the success of deep neural networks. Although highly intuitive, there is a lack of theory and systematic approach quantitatively characterizing what representations do deep neural networks learn. In this work, we move a tiny step towards a theory and better understanding of the representations. Specifically, we study a simpler problem: How similar are the representations learned by two networks with identical architecture but trained from different initializations. We develop a rigorous theory based on the neuron activation subspace match model. The theory gives a complete characterization of the structure of neuron activation subspace matches, where the core concepts are maximum match and simple match which describe the overall and the finest similarity between sets of neurons in two networks respectively. We also propose efficient algorithms to find the maximum match and simple matches. Finally, we conduct extensive experiments using our algorithms. Experimental results suggest that, surprisingly, representations learned by the same convolutional layers of networks trained from different initializations are not as similar as prevalently expected, at least in terms of subspace match.
