The discovery of clinical biomarkers requires large patient cohorts and is aided by a pooled data approach across institutions. In many countries, data protection constraints, especially in the clinical environment, forbid the exchange of individual-level data between different research institutes, impeding the conduct of a joint analyses. To circumvent this problem, only non-disclosive aggregated data is exchanged, which is often done manually and requires explicit permission before transfer, i.e., the number of data calls and the amount of data should be limited. This does not allow for more complex tasks such as variable selection, as only simple aggregated summary statistics are typically transferred. Other methods have been proposed that require more complex aggregated data or use input data perturbation, but these methods can either not deal with a high number of biomarkers or lose information. Here, we propose a multivariable regression approach for identifying biomarkers by automatic variable selection based on aggregated data in iterative calls, which can be implemented under data protection constraints. The approach can be used to jointly analyze data distributed across several locations. To minimize the amount of transferred data and the number of calls, we also provide a heuristic variant of the approach. When performing global data standardization, the proposed method yields the same results as pooled individual-level data analysis. In a simulation study, the information loss introduced by local standardization is seen to be minimal. In a typical scenario, the heuristic decreases the number of data calls from more than 10 to 3, rendering manual data releases feasible. To make our approach widely available for application, we provide an implementation of the heuristic version incorporated in the DataSHIELD framework.\
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Artificial neural networks typically struggle in generalizing to out-of-context examples. One reason for this limitation is caused by having datasets that incorporate only partial information regarding the potential correlational structure of the world. In this work, we propose TIDA (Targeted Image-editing Data Augmentation), a targeted data augmentation method focused on improving models' human-like abilities (e.g., gender recognition) by filling the correlational structure gap using a text-to-image generative model. More specifically, TIDA identifies specific skills in captions describing images (e.g., the presence of a specific gender in the image), changes the caption (e.g., "woman" to "man"), and then uses a text-to-image model to edit the image in order to match the novel caption (e.g., uniquely changing a woman to a man while maintaining the context identical). Based on the Flickr30K benchmark, we show that, compared with the original data set, a TIDA-enhanced dataset related to gender, color, and counting abilities induces better performance in several image captioning metrics. Furthermore, on top of relying on the classical BLEU metric, we conduct a fine-grained analysis of the improvements of our models against the baseline in different ways. We compared text-to-image generative models and found different behaviors of the image captioning models in terms of encoding visual encoding and textual decoding.
While the use of neural radiance fields (NeRFs) in different challenging settings has been explored, only very recently have there been any contributions that focus on the use of NeRF in foggy environments. We argue that the traditional NeRF models are able to replicate scenes filled with fog and propose a method to remove the fog when synthesizing novel views. By calculating the global contrast of a scene, we can estimate a density threshold that, when applied, removes all visible fog. This makes it possible to use NeRF as a way of rendering clear views of objects of interest located in fog-filled environments. Additionally, to benchmark performance on such scenes, we introduce a new dataset that expands some of the original synthetic NeRF scenes through the addition of fog and natural environments. The code, dataset, and video results can be found on our project page: //vegardskui.com/fognerf/
People share stories online for a myriad of purposes, whether as a means of self-disclosure, processing difficult personal experiences, providing needed information or entertainment, or persuading others to share their beliefs. Better understanding of online storytelling can illuminate the dynamics of social movements, sensemaking practices, persuasion strategies, and more. However, unlike other media such as books and visual content where the narrative nature of the content is often overtly signaled at the document level, studying storytelling in online communities is challenging due to the mixture of storytelling and non-storytelling behavior, which can be interspersed within documents and across diverse topics and settings. We introduce a codebook and create the Storytelling in Online Communities Corpus, an expert-annotated dataset of 502 English-language posts and comments with labeled story and event spans. Using our corpus, we train and evaluate an online story detection model, which we use to investigate the role storytelling of in different social contexts. We identify distinctive features of online storytelling, the prevalence of storytelling among different communities, and the conversational patterns of storytelling.
As the scale of machine learning models increases, trends such as scaling laws anticipate consistent downstream improvements in predictive accuracy. However, these trends take the perspective of a single model-provider in isolation, while in reality providers often compete with each other for users. In this work, we demonstrate that competition can fundamentally alter the behavior of these scaling trends, even causing overall predictive accuracy across users to be non-monotonic or decreasing with scale. We define a model of competition for classification tasks, and use data representations as a lens for studying the impact of increases in scale. We find many settings where improving data representation quality (as measured by Bayes risk) decreases the overall predictive accuracy across users (i.e., social welfare) for a marketplace of competing model-providers. Our examples range from closed-form formulas in simple settings to simulations with pretrained representations on CIFAR-10. At a conceptual level, our work suggests that favorable scaling trends for individual model-providers need not translate to downstream improvements in social welfare in marketplaces with multiple model providers.
Based on digital pathology slice scanning technology, artificial intelligence algorithms represented by deep learning have achieved remarkable results in the field of computational pathology. Compared to other medical images, pathology images are more difficult to annotate, and thus, there is an extreme lack of available datasets for conducting supervised learning to train robust deep learning models. In this paper, we propose a self-supervised learning (SSL) model, the global contrast-masked autoencoder (GCMAE), which can train the encoder to have the ability to represent local-global features of pathological images, also significantly improve the performance of transfer learning across data sets. In this study, the ability of the GCMAE to learn migratable representations was demonstrated through extensive experiments using a total of three different disease-specific hematoxylin and eosin (HE)-stained pathology datasets: Camelyon16, NCTCRC and BreakHis. In addition, this study designed an effective automated pathology diagnosis process based on the GCMAE for clinical applications. The source code of this paper is publicly available at //github.com/StarUniversus/gcmae.
Integrating deep learning with clinical expertise holds great potential for addressing healthcare challenges and empowering medical professionals with improved diagnostic tools. However, the need for annotated medical images is often an obstacle to leveraging the full power of machine learning models. Our research demonstrates that by combining synthetic images, generated using diffusion models, with real images, we can enhance nonalcoholic fatty liver disease (NAFLD) classification performance even in low-data regime settings. We evaluate the quality of the synthetic images by comparing two metrics: Inception Score (IS) and Fr\'{e}chet Inception Distance (FID), computed on diffusion- and generative adversarial network (GAN)-generated images. Our results show superior performance for the diffusion-generated images, with a maximum IS score of $1.90$ compared to $1.67$ for GANs, and a minimum FID score of $69.45$ compared to $100.05$ for GANs. Utilizing a partially frozen CNN backbone (EfficientNet v1), our synthetic augmentation method achieves a maximum image-level ROC AUC of $0.904$ on a NAFLD prediction task.
Recent contrastive representation learning methods rely on estimating mutual information (MI) between multiple views of an underlying context. E.g., we can derive multiple views of a given image by applying data augmentation, or we can split a sequence into views comprising the past and future of some step in the sequence. Contrastive lower bounds on MI are easy to optimize, but have a strong underestimation bias when estimating large amounts of MI. We propose decomposing the full MI estimation problem into a sum of smaller estimation problems by splitting one of the views into progressively more informed subviews and by applying the chain rule on MI between the decomposed views. This expression contains a sum of unconditional and conditional MI terms, each measuring modest chunks of the total MI, which facilitates approximation via contrastive bounds. To maximize the sum, we formulate a contrastive lower bound on the conditional MI which can be approximated efficiently. We refer to our general approach as Decomposed Estimation of Mutual Information (DEMI). We show that DEMI can capture a larger amount of MI than standard non-decomposed contrastive bounds in a synthetic setting, and learns better representations in a vision domain and for dialogue generation.
Humans have a natural instinct to identify unknown object instances in their environments. The intrinsic curiosity about these unknown instances aids in learning about them, when the corresponding knowledge is eventually available. This motivates us to propose a novel computer vision problem called: `Open World Object Detection', where a model is tasked to: 1) identify objects that have not been introduced to it as `unknown', without explicit supervision to do so, and 2) incrementally learn these identified unknown categories without forgetting previously learned classes, when the corresponding labels are progressively received. We formulate the problem, introduce a strong evaluation protocol and provide a novel solution, which we call ORE: Open World Object Detector, based on contrastive clustering and energy based unknown identification. Our experimental evaluation and ablation studies analyze the efficacy of ORE in achieving Open World objectives. As an interesting by-product, we find that identifying and characterizing unknown instances helps to reduce confusion in an incremental object detection setting, where we achieve state-of-the-art performance, with no extra methodological effort. We hope that our work will attract further research into this newly identified, yet crucial research direction.
Human doctors with well-structured medical knowledge can diagnose a disease merely via a few conversations with patients about symptoms. In contrast, existing knowledge-grounded dialogue systems often require a large number of dialogue instances to learn as they fail to capture the correlations between different diseases and neglect the diagnostic experience shared among them. To address this issue, we propose a more natural and practical paradigm, i.e., low-resource medical dialogue generation, which can transfer the diagnostic experience from source diseases to target ones with a handful of data for adaptation. It is capitalized on a commonsense knowledge graph to characterize the prior disease-symptom relations. Besides, we develop a Graph-Evolving Meta-Learning (GEML) framework that learns to evolve the commonsense graph for reasoning disease-symptom correlations in a new disease, which effectively alleviates the needs of a large number of dialogues. More importantly, by dynamically evolving disease-symptom graphs, GEML also well addresses the real-world challenges that the disease-symptom correlations of each disease may vary or evolve along with more diagnostic cases. Extensive experiment results on the CMDD dataset and our newly-collected Chunyu dataset testify the superiority of our approach over state-of-the-art approaches. Besides, our GEML can generate an enriched dialogue-sensitive knowledge graph in an online manner, which could benefit other tasks grounded on knowledge graph.
The aim of this work is to develop a fully-distributed algorithmic framework for training graph convolutional networks (GCNs). The proposed method is able to exploit the meaningful relational structure of the input data, which are collected by a set of agents that communicate over a sparse network topology. After formulating the centralized GCN training problem, we first show how to make inference in a distributed scenario where the underlying data graph is split among different agents. Then, we propose a distributed gradient descent procedure to solve the GCN training problem. The resulting model distributes computation along three lines: during inference, during back-propagation, and during optimization. Convergence to stationary solutions of the GCN training problem is also established under mild conditions. Finally, we propose an optimization criterion to design the communication topology between agents in order to match with the graph describing data relationships. A wide set of numerical results validate our proposal. To the best of our knowledge, this is the first work combining graph convolutional neural networks with distributed optimization.
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