An increasing number of public datasets have shown a marked clinical impact on assessing anatomical structures. However, each of the datasets is small, partially labeled, and rarely investigates severe tumor subjects. Moreover, current models are limited to segmenting specific organs/tumors, which can not be extended to novel domains and classes. To tackle these limitations, we introduce embedding learned from Contrastive Language-Image Pre-training (CLIP) to segmentation models, dubbed the CLIP-Driven Universal Model. The Universal Model can better segment 25 organs and 6 types of tumors by exploiting the semantic relationship between abdominal structures. The model is developed from an assembly of 14 datasets with 3,410 CT scans and evaluated on 6,162 external CT scans from 3 datasets. We rank first on the public leaderboard of the Medical Segmentation Decathlon (MSD) and achieve the state-of-the-art results on Beyond The Cranial Vault (BTCV). Compared with dataset-specific models, the Universal Model is computationally more efficient (6x faster), generalizes better to CT scans from varying sites, and shows stronger transfer learning performance on novel tasks. The design of CLIP embedding enables the Universal Model to be easily extended to new classes without catastrophically forgetting the previously learned classes.

Fine-grained classification and counting of bone marrow erythroid cells are vital for evaluating the health status and formulating therapeutic schedules for leukemia or hematopathy. Due to the subtle visual differences between different types of erythroid cells, it is challenging to apply existing image-based deep learning models for fine-grained erythroid cell classification. Moreover, there is no large open-source datasets on erythroid cells to support the model training. In this paper, we introduce BMEC (Bone Morrow Erythroid Cells), the first large fine-grained image dataset of erythroid cells, to facilitate more deep learning research on erythroid cells. BMEC contains 5,666 images of individual erythroid cells, each of which is extracted from the bone marrow erythroid cell smears and professionally annotated to one of the four types of erythroid cells. To distinguish the erythroid cells, one key indicator is the cell shape which is closely related to the cell growth and maturation. Therefore, we design a novel shape-aware image classification network for fine-grained erythroid cell classification. The shape feature is extracted from the shape mask image and aggregated to the raw image feature with a shape attention module. With the shape-attended image feature, our network achieved superior classification performance (81.12\% top-1 accuracy) on the BMEC dataset comparing to the baseline methods. Ablation studies also demonstrate the effectiveness of incorporating the shape information for the fine-grained cell classification. To further verify the generalizability of our method, we tested our network on two additional public white blood cells (WBC) datasets and the results show our shape-aware method can generally outperform recent state-of-the-art works on classifying the WBC. The code and BMEC dataset can be found on https://github.com/wangye8899/BMEC.

With the development of natural language processing techniques(NLP), automatic diagnosis of eye diseases using ophthalmology electronic medical records (OEMR) has become possible. It aims to evaluate the condition of both eyes of a patient respectively, and we formulate it as a particular multi-label classification task in this paper. Although there are a few related studies in other diseases, automatic diagnosis of eye diseases exhibits unique characteristics. First, descriptions of both eyes are mixed up in OEMR documents, with both free text and templated asymptomatic descriptions, resulting in sparsity and clutter of information. Second, OEMR documents contain multiple parts of descriptions and have long document lengths. Third, it is critical to provide explainability to the disease diagnosis model. To overcome those challenges, we present an effective automatic eye disease diagnosis framework, NEEDED. In this framework, a preprocessing module is integrated to improve the density and quality of information. Then, we design a hierarchical transformer structure for learning the contextualized representations of each sentence in the OEMR document. For the diagnosis part, we propose an attention-based predictor that enables traceable diagnosis by obtaining disease-specific information. Experiments on the real dataset and comparison with several baseline models show the advantage and explainability of our framework.

Feature transformation for AI is an essential task to boost the effectiveness and interpretability of machine learning (ML). Feature transformation aims to transform original data to identify an optimal feature space that enhances the performances of a downstream ML model. Existing studies either combines preprocessing, feature selection, and generation skills to empirically transform data, or automate feature transformation by machine intelligence, such as reinforcement learning. However, existing studies suffer from: 1) high-dimensional non-discriminative feature space; 2) inability to represent complex situational states; 3) inefficiency in integrating local and global feature information. To fill the research gap, we formulate the feature transformation task as an iterative, nested process of feature generation and selection, where feature generation is to generate and add new features based on original features, and feature selection is to remove redundant features to control the size of feature space. Finally, we present extensive experiments and case studies to illustrate 24.7\% improvements in F1 scores compared with SOTAs and robustness in high-dimensional data.

With the ever-growing model size and the limited availability of labeled training data, transfer learning has become an increasingly popular approach in many science and engineering domains. For classification problems, this work delves into the mystery of transfer learning through an intriguing phenomenon termed neural collapse (NC), where the last-layer features and classifiers of learned deep networks satisfy: (i) the within-class variability of the features collapses to zero, and (ii) the between-class feature means are maximally and equally separated. Through the lens of NC, our findings for transfer learning are the following: (i) when pre-training models, preventing intra-class variability collapse (to a certain extent) better preserves the intrinsic structures of the input data, so that it leads to better model transferability; (ii) when fine-tuning models on downstream tasks, obtaining features with more NC on downstream data results in better test accuracy on the given task. The above results not only demystify many widely used heuristics in model pre-training (e.g., data augmentation, projection head, self-supervised learning), but also leads to more efficient and principled fine-tuning method on downstream tasks that we demonstrate through extensive experimental results.

Molecular representation learning is crucial for the problem of molecular property prediction, where graph neural networks (GNNs) serve as an effective solution due to their structure modeling capabilities. Since labeled data is often scarce and expensive to obtain, it is a great challenge for GNNs to generalize in the extensive molecular space. Recently, the training paradigm of "pre-train, fine-tune" has been leveraged to improve the generalization capabilities of GNNs. It uses self-supervised information to pre-train the GNN, and then performs fine-tuning to optimize the downstream task with just a few labels. However, pre-training does not always yield statistically significant improvement, especially for self-supervised learning with random structural masking. In fact, the molecular structure is characterized by motif subgraphs, which are frequently occurring and influence molecular properties. To leverage the task-related motifs, we propose a novel paradigm of "pre-train, prompt, fine-tune" for molecular representation learning, named molecule continuous prompt tuning (MolCPT). MolCPT defines a motif prompting function that uses the pre-trained model to project the standalone input into an expressive prompt. The prompt effectively augments the molecular graph with meaningful motifs in the continuous representation space; this provides more structural patterns to aid the downstream classifier in identifying molecular properties. Extensive experiments on several benchmark datasets show that MolCPT efficiently generalizes pre-trained GNNs for molecular property prediction, with or without a few fine-tuning steps.

We study a multi-factor block model for variable clustering and connect it to the regularized subspace clustering by formulating a distributionally robust version of the nodewise regression. To solve the latter problem, we derive a convex relaxation, provide guidance on selecting the size of the robust region, and hence the regularization weighting parameter, based on the data, and propose an ADMM algorithm for implementation. We validate our method in an extensive simulation study. Finally, we propose and apply a variant of our method to stock return data, obtain interpretable clusters that facilitate portfolio selection and compare its out-of-sample performance with other clustering methods in an empirical study.

Dense retrieval aims to map queries and passages into low-dimensional vector space for efficient similarity measuring, showing promising effectiveness in various large-scale retrieval tasks. Since most existing methods commonly adopt pre-trained Transformers (e.g. BERT) for parameter initialization, some work focuses on proposing new pre-training tasks for compressing the useful semantic information from passages into dense vectors, achieving remarkable performances. However, it is still challenging to effectively capture the rich semantic information and relations about passages into the dense vectors via one single particular pre-training task. In this work, we propose a multi-task pre-trained model, MASTER, that unifies and integrates multiple pre-training tasks with different learning objectives under the bottlenecked masked autoencoder architecture. Concretely, MASTER utilizes a multi-decoder architecture to integrate three types of pre-training tasks: corrupted passages recovering, related passage recovering and PLMs outputs recovering. By incorporating a shared deep encoder, we construct a representation bottleneck in our architecture, compressing the abundant semantic information across tasks into dense vectors. The first two types of tasks concentrate on capturing the semantic information of passages and relationships among them within the pre-training corpus. The third one can capture the knowledge beyond the corpus from external PLMs (e.g. GPT-2). Extensive experiments on several large-scale passage retrieval datasets have shown that our approach outperforms the previous state-of-the-art dense retrieval methods. Our code and data are publicly released in https://github.com/microsoft/SimXNS

The geographically weighted regression (GWR) is an essential tool for estimating the spatial variation of relationships between dependent and independent variables in geographical contexts. However, GWR suffers from the problem that classical linear regressions, which compose the GWR model, are more prone to be underfitting, especially for significant volume and complex nonlinear data, causing inferior comparative performance. Nevertheless, some advanced models, such as the decision tree and the support vector machine, can learn features from complex data more effectively while they cannot provide explainable quantification for the spatial variation of localized relationships. To address the above issues, we propose a geographically gradient boosting weighted regression model, GWRBoost, that applies the localized additive model and gradient boosting optimization method to alleviate underfitting problems and retains explainable quantification capability for spatially-varying relationships between geographically located variables. Furthermore, we formulate the computation method of the Akaike information score for the proposed model to conduct the comparative analysis with the classic GWR algorithm. Simulation experiments and the empirical case study are applied to prove the efficient performance and practical value of GWRBoost. The results show that our proposed model can reduce the RMSE by 18.3\% in parameter estimation accuracy and AICc by 67.3\% in the goodness of fit.

Graphic User Interface (GUI) is facing great demand with the popularization and prosperity of mobile apps. Automatic UI code generation from UI design draft dramatically simplifies the development process. However, the nesting layer structure in the design draft affects the quality and usability of the generated code. Few existing GUI automated techniques detect and group the nested layers to improve the accessibility of generated code. In this paper, we proposed our UI Layers Group Detector as a vision-based method that automatically detects images (i.e., basic shapes and visual elements) and text layers that present the same semantic meanings. We propose two plug-in components, text fusion and box attention, that utilize text information from design drafts as a priori information for group localization. We construct a large-scale UI dataset for training and testing, and present a data augmentation approach to boost the detection performance. The experiment shows that the proposed method achieves a decent accuracy regarding layers grouping.