Developing accurate machine learning models for oncology requires large-scale, high-quality multimodal datasets. However, creating such datasets remains challenging due to the complexity and heterogeneity of medical data. To address this challenge, we introduce HoneyBee, a scalable modular framework for building multimodal oncology datasets that leverages foundational models to generate representative embeddings. HoneyBee integrates various data modalities, including clinical records, imaging data, and patient outcomes. It employs data preprocessing techniques and transformer-based architectures to generate embeddings that capture the essential features and relationships within the raw medical data. The generated embeddings are stored in a structured format using Hugging Face datasets and PyTorch dataloaders for accessibility. Vector databases enable efficient querying and retrieval for machine learning applications. We demonstrate the effectiveness of HoneyBee through experiments assessing the quality and representativeness of the embeddings. The framework is designed to be extensible to other medical domains and aims to accelerate oncology research by providing high-quality, machine learning-ready datasets. HoneyBee is an ongoing open-source effort, and the code, datasets, and models are available at the project repository.
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For speech classification tasks, deep learning models often achieve high accuracy but exhibit shortcomings in calibration, manifesting as classifiers exhibiting overconfidence. The significance of calibration lies in its critical role in guaranteeing the reliability of decision-making within deep learning systems. This study explores the effectiveness of Energy-Based Models in calibrating confidence for speech classification tasks by training a joint EBM integrating a discriminative and a generative model, thereby enhancing the classifiers calibration and mitigating overconfidence. Experimental evaluations conducted on three speech classification tasks specifically: age, emotion, and language recognition. Our findings highlight the competitive performance of EBMs in calibrating the speech classification models. This research emphasizes the potential of EBMs in speech classification tasks, demonstrating their ability to enhance calibration without sacrificing accuracy.
Private data, being larger and quality-higher than public data, can greatly improve large language models (LLM). However, due to privacy concerns, this data is often dispersed in multiple silos, making its secure utilization for LLM training a challenge. Federated learning (FL) is an ideal solution for training models with distributed private data, but traditional frameworks like FedAvg are unsuitable for LLM due to their high computational demands on clients. An alternative, split learning, offloads most training parameters to the server while training embedding and output layers locally, making it more suitable for LLM. Nonetheless, it faces significant challenges in security and efficiency. Firstly, the gradients of embeddings are prone to attacks, leading to potential reverse engineering of private data. Furthermore, the server's limitation of handle only one client's training request at a time hinders parallel training, severely impacting training efficiency. In this paper, we propose a Federated Learning framework for LLM, named FL-GLM, which prevents data leakage caused by both server-side and peer-client attacks while improving training efficiency. Specifically, we first place the input block and output block on local client to prevent embedding gradient attacks from server. Secondly, we employ key-encryption during client-server communication to prevent reverse engineering attacks from peer-clients. Lastly, we employ optimization methods like client-batching or server-hierarchical, adopting different acceleration methods based on the actual computational capabilities of the server. Experimental results on NLU and generation tasks demonstrate that FL-GLM achieves comparable metrics to centralized chatGLM model, validating the effectiveness of our federated learning framework.
We introduce Arboretum, the largest publicly accessible dataset designed to advance AI for biodiversity applications. This dataset, curated from the iNaturalist community science platform and vetted by domain experts to ensure accuracy, includes 134.6 million images, surpassing existing datasets in scale by an order of magnitude. The dataset encompasses image-language paired data for a diverse set of species from birds (Aves), spiders/ticks/mites (Arachnida), insects (Insecta), plants (Plantae), fungus/mushrooms (Fungi), snails (Mollusca), and snakes/lizards (Reptilia), making it a valuable resource for multimodal vision-language AI models for biodiversity assessment and agriculture research. Each image is annotated with scientific names, taxonomic details, and common names, enhancing the robustness of AI model training. We showcase the value of Arboretum by releasing a suite of CLIP models trained using a subset of 40 million captioned images. We introduce several new benchmarks for rigorous assessment, report accuracy for zero-shot learning, and evaluations across life stages, rare species, confounding species, and various levels of the taxonomic hierarchy. We anticipate that Arboretum will spur the development of AI models that can enable a variety of digital tools ranging from pest control strategies, crop monitoring, and worldwide biodiversity assessment and environmental conservation. These advancements are critical for ensuring food security, preserving ecosystems, and mitigating the impacts of climate change. Arboretum is publicly available, easily accessible, and ready for immediate use. Please see the \href{//baskargroup.github.io/Arboretum/}{project website} for links to our data, models, and code.
As opposed to evaluating computation and logic-based reasoning, current benchmarks for evaluating large language models (LLMs) in medicine are primarily focused on question-answering involving domain knowledge and descriptive reasoning. While such qualitative capabilities are vital to medical diagnosis, in real-world scenarios, doctors frequently use clinical calculators that follow quantitative equations and rule-based reasoning paradigms for evidence-based decision support. To this end, we propose MedCalc-Bench, a first-of-its-kind dataset focused on evaluating the medical calculation capability of LLMs. MedCalc-Bench contains an evaluation set of over 1000 manually reviewed instances from 55 different medical calculation tasks. Each instance in MedCalc-Bench consists of a patient note, a question requesting to compute a specific medical value, a ground truth answer, and a step-by-step explanation showing how the answer is obtained. While our evaluation results show the potential of LLMs in this area, none of them are effective enough for clinical settings. Common issues include extracting the incorrect entities, not using the correct equation or rules for a calculation task, or incorrectly performing the arithmetic for the computation. We hope our study highlights the quantitative knowledge and reasoning gaps in LLMs within medical settings, encouraging future improvements of LLMs for various clinical calculation tasks.
The usage of medical image data for the training of large-scale machine learning approaches is particularly challenging due to its scarce availability and the costly generation of data annotations, typically requiring the engagement of medical professionals. The rapid development of generative models allows towards tackling this problem by leveraging large amounts of realistic synthetically generated data for the training process. However, randomly choosing synthetic samples, might not be an optimal strategy. In this work, we investigate the targeted generation of synthetic training data, in order to improve the accuracy and robustness of image classification. Therefore, our approach aims to guide the generative model to synthesize data with high epistemic uncertainty, since large measures of epistemic uncertainty indicate underrepresented data points in the training set. During the image generation we feed images reconstructed by an auto encoder into the classifier and compute the mutual information over the class-probability distribution as a measure for uncertainty.We alter the feature space of the autoencoder through an optimization process with the objective of maximizing the classifier uncertainty on the decoded image. By training on such data we improve the performance and robustness against test time data augmentations and adversarial attacks on several classifications tasks.
In settings where only a budgeted amount of labeled data can be afforded, active learning seeks to devise query strategies for selecting the most informative data points to be labeled, aiming to enhance learning algorithms' efficiency and performance. Numerous such query strategies have been proposed and compared in the active learning literature. However, the community still lacks standardized benchmarks for comparing the performance of different query strategies. This particularly holds for the combination of query strategies with different learning algorithms into active learning pipelines and examining the impact of the learning algorithm choice. To close this gap, we propose ALPBench, which facilitates the specification, execution, and performance monitoring of active learning pipelines. It has built-in measures to ensure evaluations are done reproducibly, saving exact dataset splits and hyperparameter settings of used algorithms. In total, ALPBench consists of 86 real-world tabular classification datasets and 5 active learning settings, yielding 430 active learning problems. To demonstrate its usefulness and broad compatibility with various learning algorithms and query strategies, we conduct an exemplary study evaluating 9 query strategies paired with 8 learning algorithms in 2 different settings. We provide ALPBench here: //github.com/ValentinMargraf/ActiveLearningPipelines.
As an effective strategy, data augmentation (DA) alleviates data scarcity scenarios where deep learning techniques may fail. It is widely applied in computer vision then introduced to natural language processing and achieves improvements in many tasks. One of the main focuses of the DA methods is to improve the diversity of training data, thereby helping the model to better generalize to unseen testing data. In this survey, we frame DA methods into three categories based on the diversity of augmented data, including paraphrasing, noising, and sampling. Our paper sets out to analyze DA methods in detail according to the above categories. Further, we also introduce their applications in NLP tasks as well as the challenges.
Data augmentation, the artificial creation of training data for machine learning by transformations, is a widely studied research field across machine learning disciplines. While it is useful for increasing the generalization capabilities of a model, it can also address many other challenges and problems, from overcoming a limited amount of training data over regularizing the objective to limiting the amount data used to protect privacy. Based on a precise description of the goals and applications of data augmentation (C1) and a taxonomy for existing works (C2), this survey is concerned with data augmentation methods for textual classification and aims to achieve a concise and comprehensive overview for researchers and practitioners (C3). Derived from the taxonomy, we divided more than 100 methods into 12 different groupings and provide state-of-the-art references expounding which methods are highly promising (C4). Finally, research perspectives that may constitute a building block for future work are given (C5).
This paper focuses on two fundamental tasks of graph analysis: community detection and node representation learning, which capture the global and local structures of graphs, respectively. In the current literature, these two tasks are usually independently studied while they are actually highly correlated. We propose a probabilistic generative model called vGraph to learn community membership and node representation collaboratively. Specifically, we assume that each node can be represented as a mixture of communities, and each community is defined as a multinomial distribution over nodes. Both the mixing coefficients and the community distribution are parameterized by the low-dimensional representations of the nodes and communities. We designed an effective variational inference algorithm which regularizes the community membership of neighboring nodes to be similar in the latent space. Experimental results on multiple real-world graphs show that vGraph is very effective in both community detection and node representation learning, outperforming many competitive baselines in both tasks. We show that the framework of vGraph is quite flexible and can be easily extended to detect hierarchical communities.
In order to answer natural language questions over knowledge graphs, most processing pipelines involve entity and relation linking. Traditionally, entity linking and relation linking has been performed either as dependent sequential tasks or independent parallel tasks. In this paper, we propose a framework called "EARL", which performs entity linking and relation linking as a joint single task. EARL uses a graph connection based solution to the problem. We model the linking task as an instance of the Generalised Travelling Salesman Problem (GTSP) and use GTSP approximate algorithm solutions. We later develop EARL which uses a pair-wise graph-distance based solution to the problem.The system determines the best semantic connection between all keywords of the question by referring to a knowledge graph. This is achieved by exploiting the "connection density" between entity candidates and relation candidates. The "connection density" based solution performs at par with the approximate GTSP solution.We have empirically evaluated the framework on a dataset with 5000 questions. Our system surpasses state-of-the-art scores for entity linking task by reporting an accuracy of 0.65 to 0.40 from the next best entity linker.
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