Multiple instance learning exhibits a powerful approach for whole slide image-based diagnosis in the absence of pixel- or patch-level annotations. In spite of the huge size of hole slide images, the number of individual slides is often rather small, leading to a small number of labeled samples. To improve training, we propose and investigate different data augmentation strategies for multiple instance learning based on the idea of linear interpolations of feature vectors (known as MixUp). Based on state-of-the-art multiple instance learning architectures and two thyroid cancer data sets, an exhaustive study is conducted considering a range of common data augmentation strategies. Whereas a strategy based on to the original MixUp approach showed decreases in accuracy, the use of a novel intra-slide interpolation method led to consistent increases in accuracy.
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Expressive state-of-the-art separation logics rely on step-indexing to model semantically complex features and to support modular reasoning about imperative higher-order concurrent and distributed programs. Step-indexing comes, however, with an inherent cost: it restricts the adequacy theorem of program logics to a fairly simple class of safety properties. In this paper, we explore if and how intensional refinement is a viable methodology for strengthening higher-order concurrent (and distributed) separation logic to prove non-trivial safety and liveness properties. Specifically, we introduce Trillium, a language-agnostic separation logic framework for showing intensional refinement relations between traces of a program and a model. We instantiate Trillium with a concurrent language and develop Fairis, a concurrent separation logic, that we use to show liveness properties of concurrent programs under fair scheduling assumptions through a fair liveness-preserving refinement of a model. We also instantiate Trillium with a distributed language and obtain an extension of Aneris, a distributed separation logic, which we use to show refinement relations between distributed systems and TLA+ models.
Separation logic's compositionality and local reasoning properties have led to significant advances in scalable static analysis. But program analysis has new challenges -- many programs display computational effects and, orthogonally, static analyzers must handle incorrectness too. We present Outcome Separation Logic (OSL), a program logic that is sound for both correctness and incorrectness reasoning in programs with varying effects. OSL has a frame rule -- just like separation logic -- but uses different underlying assumptions that open up local reasoning to a larger class of properties than can be handled by any single existing logic. Building on this foundational theory, we also define symbolic execution algorithms that use bi-abduction to derive specifications for programs with effects. This involves a new tri-abduction procedure to analyze programs whose execution branches due to effects such as nondeterministic or probabilistic choice. This work furthers the compositionality promised by separation logic by opening up the possibility for greater reuse of analysis tools across two dimensions: bug-finding vs verification in programs with varying effects.
The increasingly popular adoption of deep learning models in many critical source code tasks motivates the development of data augmentation (DA) techniques to enhance training data and improve various capabilities (e.g., robustness and generalizability) of these models. Although a series of DA methods have been proposed and tailored for source code models, there lacks a comprehensive survey and examination to understand their effectiveness and implications. This paper fills this gap by conducting a comprehensive and integrative survey of data augmentation for source code, wherein we systematically compile and encapsulate existing literature to provide a comprehensive overview of the field. We start with an introduction of data augmentation in source code and then provide a discussion on major representative approaches. Next, we highlight the general strategies and techniques to optimize the DA quality. Subsequently, we underscore techniques useful in real-world source code scenarios and downstream tasks. Finally, we outline the prevailing challenges and potential opportunities for future research. In essence, we aim to demystify the corpus of existing literature on source code DA for deep learning, and foster further exploration in this sphere. Complementing this, we present a continually updated GitHub repository that hosts a list of update-to-date papers on DA for source code modeling, accessible at \url{//github.com/terryyz/DataAug4Code}.
Task-Adaptive Tokenization: Enhancing Long-Form Text Generation Efficacy in Mental Health and Beyond
We propose task-adaptive tokenization as a way to adapt the generation pipeline to the specifics of a downstream task and enhance long-form generation in mental health. Inspired by insights from cognitive science, our task-adaptive tokenizer samples variable segmentations from multiple outcomes, with sampling probabilities optimized based on task-specific data. We introduce a strategy for building a specialized vocabulary and introduce a vocabulary merging protocol that allows for the integration of task-specific tokens into the pre-trained model's tokenization step. Through extensive experiments on psychological question-answering tasks in both Chinese and English, we find that our task-adaptive tokenization approach brings a significant improvement in generation performance while using up to 60% fewer tokens. Preliminary experiments point to promising results when using our tokenization approach with very large language models.
Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering and recommendation systems, etc. According to the graph types, the existing KGR models can be roughly divided into three categories, \textit{i.e.,} static models, temporal models, and multi-modal models. The early works in this domain mainly focus on static KGR and tend to directly apply general knowledge graph embedding models to the reasoning task. However, these models are not suitable for more complex but practical tasks, such as inductive static KGR, temporal KGR, and multi-modal KGR. To this end, multiple works have been developed recently, but no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the preliminaries, summaries of KGR models, and typical datasets are introduced and discussed consequently. Moreover, we discuss the challenges and potential opportunities. The corresponding open-source repository is shared on GitHub: //github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.
Deep learning-based algorithms have seen a massive popularity in different areas of remote sensing image analysis over the past decade. Recently, transformers-based architectures, originally introduced in natural language processing, have pervaded computer vision field where the self-attention mechanism has been utilized as a replacement to the popular convolution operator for capturing long-range dependencies. Inspired by recent advances in computer vision, remote sensing community has also witnessed an increased exploration of vision transformers for a diverse set of tasks. Although a number of surveys have focused on transformers in computer vision in general, to the best of our knowledge we are the first to present a systematic review of recent advances based on transformers in remote sensing. Our survey covers more than 60 recent transformers-based methods for different remote sensing problems in sub-areas of remote sensing: very high-resolution (VHR), hyperspectral (HSI) and synthetic aperture radar (SAR) imagery. We conclude the survey by discussing different challenges and open issues of transformers in remote sensing. Additionally, we intend to frequently update and maintain the latest transformers in remote sensing papers with their respective code at: //github.com/VIROBO-15/Transformer-in-Remote-Sensing
The incredible development of federated learning (FL) has benefited various tasks in the domains of computer vision and natural language processing, and the existing frameworks such as TFF and FATE has made the deployment easy in real-world applications. However, federated graph learning (FGL), even though graph data are prevalent, has not been well supported due to its unique characteristics and requirements. The lack of FGL-related framework increases the efforts for accomplishing reproducible research and deploying in real-world applications. Motivated by such strong demand, in this paper, we first discuss the challenges in creating an easy-to-use FGL package and accordingly present our implemented package FederatedScope-GNN (FS-G), which provides (1) a unified view for modularizing and expressing FGL algorithms; (2) comprehensive DataZoo and ModelZoo for out-of-the-box FGL capability; (3) an efficient model auto-tuning component; and (4) off-the-shelf privacy attack and defense abilities. We validate the effectiveness of FS-G by conducting extensive experiments, which simultaneously gains many valuable insights about FGL for the community. Moreover, we employ FS-G to serve the FGL application in real-world E-commerce scenarios, where the attained improvements indicate great potential business benefits. We publicly release FS-G, as submodules of FederatedScope, at //github.com/alibaba/FederatedScope to promote FGL's research and enable broad applications that would otherwise be infeasible due to the lack of a dedicated package.
TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classication
Multiple instance learning (MIL) is a powerful tool to solve the weakly supervised classification in whole slide image (WSI) based pathology diagnosis. However, the current MIL methods are usually based on independent and identical distribution hypothesis, thus neglect the correlation among different instances. To address this problem, we proposed a new framework, called correlated MIL, and provided a proof for convergence. Based on this framework, we devised a Transformer based MIL (TransMIL), which explored both morphological and spatial information. The proposed TransMIL can effectively deal with unbalanced/balanced and binary/multiple classification with great visualization and interpretability. We conducted various experiments for three different computational pathology problems and achieved better performance and faster convergence compared with state-of-the-art methods. The test AUC for the binary tumor classification can be up to 93.09% over CAMELYON16 dataset. And the AUC over the cancer subtypes classification can be up to 96.03% and 98.82% over TCGA-NSCLC dataset and TCGA-RCC dataset, respectively.
Visual dialogue is a challenging task that needs to extract implicit information from both visual (image) and textual (dialogue history) contexts. Classical approaches pay more attention to the integration of the current question, vision knowledge and text knowledge, despising the heterogeneous semantic gaps between the cross-modal information. In the meantime, the concatenation operation has become de-facto standard to the cross-modal information fusion, which has a limited ability in information retrieval. In this paper, we propose a novel Knowledge-Bridge Graph Network (KBGN) model by using graph to bridge the cross-modal semantic relations between vision and text knowledge in fine granularity, as well as retrieving required knowledge via an adaptive information selection mode. Moreover, the reasoning clues for visual dialogue can be clearly drawn from intra-modal entities and inter-modal bridges. Experimental results on VisDial v1.0 and VisDial-Q datasets demonstrate that our model outperforms exiting models with state-of-the-art results.
We introduce a multi-task setup of identifying and classifying entities, relations, and coreference clusters in scientific articles. We create SciERC, a dataset that includes annotations for all three tasks and develop a unified framework called Scientific Information Extractor (SciIE) for with shared span representations. The multi-task setup reduces cascading errors between tasks and leverages cross-sentence relations through coreference links. Experiments show that our multi-task model outperforms previous models in scientific information extraction without using any domain-specific features. We further show that the framework supports construction of a scientific knowledge graph, which we use to analyze information in scientific literature.
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