Daily Papers

Data harmonization is an essential task that entails integrating datasets from diverse sources. Despite years of research in this area, it remains a time-consuming and challenging task due to schema mismatches, varying terminologies, and differences in data collection methodologies. This paper presents the case for agentic data harmonization as a means to both empower experts to harmonize their data and to streamline the process. We introduce Harmonia, a system that combines LLM-based reasoning, an interactive user interface, and a library of data harmonization primitives to automate the synthesis of data harmonization pipelines. We demonstrate Harmonia in a clinical data harmonization scenario, where it helps to interactively create reusable pipelines that map datasets to a standard format. Finally, we discuss challenges and open problems, and suggest research directions for advancing our vision.

Electronic health records (EHRs) contain vast amounts of complex data, but harmonizing and processing this information remains a challenging and costly task requiring significant clinical expertise. While large language models (LLMs) have shown promise in various healthcare applications, their potential for abstracting medical concepts from EHRs remains largely unexplored. We introduce EHRmonize, a framework leveraging LLMs to abstract medical concepts from EHR data. Our study uses medication data from two real-world EHR databases to evaluate five LLMs on two free-text extraction and six binary classification tasks across various prompting strategies. GPT-4o's with 10-shot prompting achieved the highest performance in all tasks, accompanied by Claude-3.5-Sonnet in a subset of tasks. GPT-4o achieved an accuracy of 97% in identifying generic route names, 82% for generic drug names, and 100% in performing binary classification of antibiotics. While EHRmonize significantly enhances efficiency, reducing annotation time by an estimated 60%, we emphasize that clinician oversight remains essential. Our framework, available as a Python package, offers a promising tool to assist clinicians in EHR data abstraction, potentially accelerating healthcare research and improving data harmonization processes.

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.

The Russian Financial Statements Database (RFSD) is an open, harmonized collection of annual unconsolidated financial statements of the universe of Russian firms in 2011-2023. It is the first open data set with information on every active firm in the country, including non-filing firms. With 56.6 million geolocated firm-year observations gathered from two official sources, the RFSD features multiple end-user quality-of-life improvements such as data imputation, statement articulation, harmonization across data providers and formats, and data enrichment. Extensive internal and external validation shows that most statements articulate well while their aggregates display higher correlation with the regional GDP than the previous gridded GDP data products. We also examine the direction and magnitude of the reporting bias by comparing the universe of firms that are required to file with the actual filers. The RFSD can be used in various economic applications as diverse as calibration of micro-founded models, estimation of markups and productivity, or assessing industry organization and market power.

Training and evaluating language models increasingly requires the construction of meta-datasets --diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization by transforming existing, supervised datasets into a diversity of novel pretraining tasks, highlighting the benefits of meta-dataset curation. While successful in general-domain text, translating these data-centric approaches to biomedical language modeling remains challenging, as labeled biomedical datasets are significantly underrepresented in popular data hubs. To address this challenge, we introduce BigBIO a community library of 126+ biomedical NLP datasets, currently covering 12 task categories and 10+ languages. BigBIO facilitates reproducible meta-dataset curation via programmatic access to datasets and their metadata, and is compatible with current platforms for prompt engineering and end-to-end few/zero shot language model evaluation. We discuss our process for task schema harmonization, data auditing, contribution guidelines, and outline two illustrative use cases: zero-shot evaluation of biomedical prompts and large-scale, multi-task learning. BigBIO is an ongoing community effort and is available at https://github.com/bigscience-workshop/biomedical

Portrait harmonization aims to composite a subject into a new background, adjusting its lighting and color to ensure harmony with the background scene. Existing harmonization techniques often only focus on adjusting the global color and brightness of the foreground and ignore crucial illumination cues from the background such as apparent lighting direction, leading to unrealistic compositions. We introduce Relightful Harmonization, a lighting-aware diffusion model designed to seamlessly harmonize sophisticated lighting effect for the foreground portrait using any background image. Our approach unfolds in three stages. First, we introduce a lighting representation module that allows our diffusion model to encode lighting information from target image background. Second, we introduce an alignment network that aligns lighting features learned from image background with lighting features learned from panorama environment maps, which is a complete representation for scene illumination. Last, to further boost the photorealism of the proposed method, we introduce a novel data simulation pipeline that generates synthetic training pairs from a diverse range of natural images, which are used to refine the model. Our method outperforms existing benchmarks in visual fidelity and lighting coherence, showing superior generalization in real-world testing scenarios, highlighting its versatility and practicality.

Self-supervised pre-training recently demonstrates success on large-scale multimodal data, and state-of-the-art contrastive learning methods often enforce the feature consistency from cross-modality inputs, such as video/audio or video/text pairs. Despite its convenience to formulate and leverage in practice, such cross-modality alignment (CMA) is only a weak and noisy supervision, since two modalities can be semantically misaligned even they are temporally aligned. For example, even in the commonly adopted instructional videos, a speaker can sometimes refer to something that is not visually present in the current frame; and the semantic misalignment would only be more unpredictable for the raw videos from the internet. We conjecture that might cause conflicts and biases among modalities, and may hence prohibit CMA from scaling up to training with larger and more heterogeneous data. This paper first verifies our conjecture by observing that, even in the latest VATT pre-training using only instructional videos, there exist strong gradient conflicts between different CMA losses within the same video, audio, text triplet, indicating them as the noisy source of supervision. We then propose to harmonize such gradients, via two techniques: (i) cross-modality gradient realignment: modifying different CMA loss gradients for each sample triplet, so that their gradient directions are more aligned; and (ii) gradient-based curriculum learning: leveraging the gradient conflict information on an indicator of sample noisiness, to develop a curriculum learning strategy to prioritize training on less noisy sample triplets. Applying those techniques to pre-training VATT on the HowTo100M dataset, we consistently improve its performance on different downstream tasks. Moreover, we are able to scale VATT pre-training to more complicated non-narrative Youtube8M dataset to further improve the state-of-the-arts.

In MRI, images of the same contrast (e.g., T_1) from the same subject can exhibit noticeable differences when acquired using different hardware, sequences, or scan parameters. These differences in images create a domain gap that needs to be bridged by a step called image harmonization, to process the images successfully using conventional or deep learning-based image analysis (e.g., segmentation). Several methods, including deep learning-based approaches, have been proposed to achieve image harmonization. However, they often require datasets from multiple domains for deep learning training and may still be unsuccessful when applied to images from unseen domains. To address this limitation, we propose a novel concept called `Blind Harmonization', which utilizes only target domain data for training but still has the capability to harmonize images from unseen domains. For the implementation of blind harmonization, we developed BlindHarmony using an unconditional flow model trained on target domain data. The harmonized image is optimized to have a correlation with the input source domain image while ensuring that the latent vector of the flow model is close to the center of the Gaussian distribution. BlindHarmony was evaluated on both simulated and real datasets and compared to conventional methods. BlindHarmony demonstrated noticeable performance on both datasets, highlighting its potential for future use in clinical settings. The source code is available at: https://github.com/SNU-LIST/BlindHarmony

The many successes of deep neural networks (DNNs) over the past decade have largely been driven by computational scale rather than insights from biological intelligence. Here, we explore if these trends have also carried concomitant improvements in explaining the visual strategies humans rely on for object recognition. We do this by comparing two related but distinct properties of visual strategies in humans and DNNs: where they believe important visual features are in images and how they use those features to categorize objects. Across 84 different DNNs trained on ImageNet and three independent datasets measuring the where and the how of human visual strategies for object recognition on those images, we find a systematic trade-off between DNN categorization accuracy and alignment with human visual strategies for object recognition. State-of-the-art DNNs are progressively becoming less aligned with humans as their accuracy improves. We rectify this growing issue with our neural harmonizer: a general-purpose training routine that both aligns DNN and human visual strategies and improves categorization accuracy. Our work represents the first demonstration that the scaling laws that are guiding the design of DNNs today have also produced worse models of human vision. We release our code and data at https://serre-lab.github.io/Harmonization to help the field build more human-like DNNs.

Advances in natural language processing techniques, such as named entity recognition and normalization to widely used standardized terminologies like UMLS or SNOMED-CT, along with the digitalization of electronic health records, have significantly advanced clinical text analysis. This study presents ClinLinker, a novel approach employing a two-phase pipeline for medical entity linking that leverages the potential of in-domain adapted language models for biomedical text mining: initial candidate retrieval using a SapBERT-based bi-encoder and subsequent re-ranking with a cross-encoder, trained by following a contrastive-learning strategy to be tailored to medical concepts in Spanish. This methodology, focused initially on content in Spanish, substantially outperforming multilingual language models designed for the same purpose. This is true even for complex scenarios involving heterogeneous medical terminologies and being trained on a subset of the original data. Our results, evaluated using top-k accuracy at 25 and other top-k metrics, demonstrate our approach's performance on two distinct clinical entity linking Gold Standard corpora, DisTEMIST (diseases) and MedProcNER (clinical procedures), outperforming previous benchmarks by 40 points in DisTEMIST and 43 points in MedProcNER, both normalized to SNOMED-CT codes. These findings highlight our approach's ability to address language-specific nuances and set a new benchmark in entity linking, offering a potent tool for enhancing the utility of digital medical records. The resulting system is of practical value, both for large scale automatic generation of structured data derived from clinical records, as well as for exhaustive extraction and harmonization of predefined clinical variables of interest.

Novel-view synthesis techniques achieve impressive results for static scenes but struggle when faced with the inconsistencies inherent to casual capture settings: varying illumination, scene motion, and other unintended effects that are difficult to model explicitly. We present an approach for leveraging generative video models to simulate the inconsistencies in the world that can occur during capture. We use this process, along with existing multi-view datasets, to create synthetic data for training a multi-view harmonization network that is able to reconcile inconsistent observations into a consistent 3D scene. We demonstrate that our world-simulation strategy significantly outperforms traditional augmentation methods in handling real-world scene variations, thereby enabling highly accurate static 3D reconstructions in the presence of a variety of challenging inconsistencies. Project page: https://alextrevithick.github.io/simvs

This paper describes a novel nonparametric model for modeling diffusion MRI signals in q-space. In q-space, diffusion MRI signal is measured for a sequence of magnetic strengths (b-values) and magnetic gradient directions (b-vectors). We propose a Poly-RBF model, which employs a bidirectional framework with polynomial bases to model the signal along the b-value direction and Gaussian radial bases across the b-vectors. The model can accommodate sparse data on b-values and moderately dense data on b-vectors. The utility of Poly-RBF is inspected for two applications: 1) prediction of the dMRI signal, and 2) harmonization of dMRI data collected under different acquisition protocols with different scanners. Our results indicate that the proposed Poly-RBF model can more accurately predict the unmeasured diffusion signal than its competitors such as the Gaussian process model in {\tt Eddy} of FSL. Applying it to harmonizing the diffusion signal can significantly improve the reproducibility of derived white matter microstructure measures.

Recent advances in video insertion based on diffusion models are impressive. However, existing methods rely on complex control signals but struggle with subject consistency, limiting their practical applicability. In this paper, we focus on the task of Mask-free Video Insertion and aim to resolve three key challenges: data scarcity, subject-scene equilibrium, and insertion harmonization. To address the data scarcity, we propose a new data pipeline InsertPipe, constructing diverse cross-pair data automatically. Building upon our data pipeline, we develop OmniInsert, a novel unified framework for mask-free video insertion from both single and multiple subject references. Specifically, to maintain subject-scene equilibrium, we introduce a simple yet effective Condition-Specific Feature Injection mechanism to distinctly inject multi-source conditions and propose a novel Progressive Training strategy that enables the model to balance feature injection from subjects and source video. Meanwhile, we design the Subject-Focused Loss to improve the detailed appearance of the subjects. To further enhance insertion harmonization, we propose an Insertive Preference Optimization methodology to optimize the model by simulating human preferences, and incorporate a Context-Aware Rephraser module during reference to seamlessly integrate the subject into the original scenes. To address the lack of a benchmark for the field, we introduce InsertBench, a comprehensive benchmark comprising diverse scenes with meticulously selected subjects. Evaluation on InsertBench indicates OmniInsert outperforms state-of-the-art closed-source commercial solutions. The code will be released.