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Dec 9

Relightful Harmonization: Lighting-aware Portrait Background Replacement

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.

  • 8 authors
·
Dec 11, 2023

Learning Global-aware Kernel for Image Harmonization

Image harmonization aims to solve the visual inconsistency problem in composited images by adaptively adjusting the foreground pixels with the background as references. Existing methods employ local color transformation or region matching between foreground and background, which neglects powerful proximity prior and independently distinguishes fore-/back-ground as a whole part for harmonization. As a result, they still show a limited performance across varied foreground objects and scenes. To address this issue, we propose a novel Global-aware Kernel Network (GKNet) to harmonize local regions with comprehensive consideration of long-distance background references. Specifically, GKNet includes two parts, \ie, harmony kernel prediction and harmony kernel modulation branches. The former includes a Long-distance Reference Extractor (LRE) to obtain long-distance context and Kernel Prediction Blocks (KPB) to predict multi-level harmony kernels by fusing global information with local features. To achieve this goal, a novel Selective Correlation Fusion (SCF) module is proposed to better select relevant long-distance background references for local harmonization. The latter employs the predicted kernels to harmonize foreground regions with both local and global awareness. Abundant experiments demonstrate the superiority of our method for image harmonization over state-of-the-art methods, \eg, achieving 39.53dB PSNR that surpasses the best counterpart by +0.78dB uparrow; decreasing fMSE/MSE by 11.5\%downarrow/6.7\%downarrow compared with the SoTA method. Code will be available at https://github.com/XintianShen/GKNet{here}.

  • 8 authors
·
May 19, 2023

BlindHarmony: "Blind" Harmonization for MR Images via Flow model

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

  • 4 authors
·
May 18, 2023

Scaling Multimodal Pre-Training via Cross-Modality Gradient Harmonization

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.

  • 6 authors
·
Nov 3, 2022

Lemur: Harmonizing Natural Language and Code for Language Agents

We introduce Lemur and Lemur-Chat, openly accessible language models optimized for both natural language and coding capabilities to serve as the backbone of versatile language agents. The evolution from language chat models to functional language agents demands that models not only master human interaction, reasoning, and planning but also ensure grounding in the relevant environments. This calls for a harmonious blend of language and coding capabilities in the models. Lemur and Lemur-Chat are proposed to address this necessity, demonstrating balanced proficiencies in both domains, unlike existing open-source models that tend to specialize in either. Through meticulous pre-training using a code-intensive corpus and instruction fine-tuning on text and code data, our models achieve state-of-the-art averaged performance across diverse text and coding benchmarks among open-source models. Comprehensive experiments demonstrate Lemur's superiority over existing open-source models and its proficiency across various agent tasks involving human communication, tool usage, and interaction under fully- and partially- observable environments. The harmonization between natural and programming languages enables Lemur-Chat to significantly narrow the gap with proprietary models on agent abilities, providing key insights into developing advanced open-source agents adept at reasoning, planning, and operating seamlessly across environments. https://github.com/OpenLemur/Lemur

  • 16 authors
·
Oct 10, 2023 3

Go-with-the-Flow: Motion-Controllable Video Diffusion Models Using Real-Time Warped Noise

Generative modeling aims to transform random noise into structured outputs. In this work, we enhance video diffusion models by allowing motion control via structured latent noise sampling. This is achieved by just a change in data: we pre-process training videos to yield structured noise. Consequently, our method is agnostic to diffusion model design, requiring no changes to model architectures or training pipelines. Specifically, we propose a novel noise warping algorithm, fast enough to run in real time, that replaces random temporal Gaussianity with correlated warped noise derived from optical flow fields, while preserving the spatial Gaussianity. The efficiency of our algorithm enables us to fine-tune modern video diffusion base models using warped noise with minimal overhead, and provide a one-stop solution for a wide range of user-friendly motion control: local object motion control, global camera movement control, and motion transfer. The harmonization between temporal coherence and spatial Gaussianity in our warped noise leads to effective motion control while maintaining per-frame pixel quality. Extensive experiments and user studies demonstrate the advantages of our method, making it a robust and scalable approach for controlling motion in video diffusion models. Video results are available on our webpage: https://vgenai-netflix-eyeline-research.github.io/Go-with-the-Flow. Source code and model checkpoints are available on GitHub: https://github.com/VGenAI-Netflix-Eyeline-Research/Go-with-the-Flow.

  • 13 authors
·
Jan 14 3

Making Images Real Again: A Comprehensive Survey on Deep Image Composition

As a common image editing operation, image composition (object insertion) aims to combine the foreground from one image and another background image, resulting in a composite image. However, there are many issues that could make the composite images unrealistic. These issues can be summarized as the inconsistency between foreground and background, which includes appearance inconsistency (e.g., incompatible illumination), geometry inconsistency (e.g., unreasonable size), and semantic inconsistency (e.g., mismatched semantic context). Image composition task could be decomposed into multiple sub-tasks, in which each sub-task targets at one or more issues. Specifically, object placement aims to find reasonable scale, location, and shape for the foreground. Image blending aims to address the unnatural boundary between foreground and background. Image harmonization aims to adjust the illumination statistics of foreground. Shadow (resp., reflection) generation aims to generate plausible shadow (resp., reflection) for the foreground. These sub-tasks can be executed sequentially or parallelly to acquire realistic composite images. To the best of our knowledge, there is no previous survey on image composition (object insertion). In this paper, we conduct comprehensive survey over the sub-tasks and combinatorial task of image composition (object insertion). For each one, we summarize the existing methods, available datasets, and common evaluation metrics. We have also contributed the first image composition toolbox libcom, which assembles 10+ image composition related functions (e.g., image blending, image harmonization, object placement, shadow generation, generative composition). The ultimate goal of this toolbox is solving all the problems related to image composition with simple `import libcom'.

  • 7 authors
·
Jun 28, 2021 1

OmniInsert: Mask-Free Video Insertion of Any Reference via Diffusion Transformer Models

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.

  • 11 authors
·
Sep 22 2

Harmonizing the object recognition strategies of deep neural networks with humans

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.

  • 4 authors
·
Nov 8, 2022

On-Policy RL Meets Off-Policy Experts: Harmonizing Supervised Fine-Tuning and Reinforcement Learning via Dynamic Weighting

Supervised Fine-Tuning (SFT) and Reinforcement Learning (RL) are two prominent post-training paradigms for refining the capabilities and aligning the behavior of Large Language Models (LLMs). Existing approaches that integrate SFT and RL often face the risk of disrupting established model patterns and inducing overfitting to expert data. To address this, we present a novel investigation into the unified view of SFT and RL through an off-policy versus on-policy lens. We propose CHORD, a framework for the Controllable Harmonization of On- and Off-Policy Reinforcement Learning via Dynamic Weighting, which reframes SFT not as a separate stage but as a dynamically weighted auxiliary objective within the on-policy RL process. Based on an analysis of off-policy expert data's influence at both holistic and granular levels, we incorporate a dual-control mechanism in CHORD. Specifically, the framework first employs a global coefficient to holistically guide the transition from off-policy imitation to on-policy exploration, and then applies a token-wise weighting function that enables granular learning from expert tokens, which preserves on-policy exploration and mitigates disruption from off-policy data. We conduct extensive experiments on widely used benchmarks, providing empirical evidence that CHORD achieves a stable and efficient learning process. By effectively harmonizing off-policy expert data with on-policy exploration, CHORD demonstrates significant improvements over baselines. We release the implementation at https://github.com/modelscope/Trinity-RFT/tree/main/examples/mix_chord to inspire further research.

  • 8 authors
·
Aug 15 6

tasksource: Structured Dataset Preprocessing Annotations for Frictionless Extreme Multi-Task Learning and Evaluation

The HuggingFace Datasets Hub hosts thousands of datasets. This provides exciting opportunities for language model training and evaluation. However, the datasets for a given type of task are stored with different schemas, and harmonization is harder than it seems (https://xkcd.com/927/). Multi-task training or evaluation requires manual work to fit data into task templates. Various initiatives independently address this problem by releasing the harmonized datasets or harmonization codes to preprocess datasets to the same format. We identify patterns across previous preprocessings, e.g. mapping of column names, and extraction of a specific sub-field from structured data in a column, and propose a structured annotation framework that makes our annotations fully exposed and not buried in unstructured code. We release a dataset annotation framework and dataset annotations for more than 400 English tasks (https://github.com/sileod/tasksource). These annotations provide metadata, like the name of the columns that should be used as input or labels for all datasets, and can save time for future dataset preprocessings, even if they do not use our framework. We fine-tune a multi-task text encoder on all tasksource tasks, outperforming every publicly available text encoder of comparable size on an external evaluation https://hf.co/sileod/deberta-v3-base-tasksource-nli.

  • 1 authors
·
Jan 14, 2023

Image Anything: Towards Reasoning-coherent and Training-free Multi-modal Image Generation

The multifaceted nature of human perception and comprehension indicates that, when we think, our body can naturally take any combination of senses, a.k.a., modalities and form a beautiful picture in our brain. For example, when we see a cattery and simultaneously perceive the cat's purring sound, our brain can construct a picture of a cat in the cattery. Intuitively, generative AI models should hold the versatility of humans and be capable of generating images from any combination of modalities efficiently and collaboratively. This paper presents ImgAny, a novel end-to-end multi-modal generative model that can mimic human reasoning and generate high-quality images. Our method serves as the first attempt in its capacity of efficiently and flexibly taking any combination of seven modalities, ranging from language, audio to vision modalities, including image, point cloud, thermal, depth, and event data. Our key idea is inspired by human-level cognitive processes and involves the integration and harmonization of multiple input modalities at both the entity and attribute levels without specific tuning across modalities. Accordingly, our method brings two novel training-free technical branches: 1) Entity Fusion Branch ensures the coherence between inputs and outputs. It extracts entity features from the multi-modal representations powered by our specially constructed entity knowledge graph; 2) Attribute Fusion Branch adeptly preserves and processes the attributes. It efficiently amalgamates distinct attributes from diverse input modalities via our proposed attribute knowledge graph. Lastly, the entity and attribute features are adaptively fused as the conditional inputs to the pre-trained Stable Diffusion model for image generation. Extensive experiments under diverse modality combinations demonstrate its exceptional capability for visual content creation.

  • 3 authors
·
Jan 31, 2024

A Machine Learning Approach for Identifying Anatomical Biomarkers of Early Mild Cognitive Impairment

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that primarily affects the aging population by impairing cognitive and motor functions. Early detection of AD through accessible methodologies like magnetic resonance imaging (MRI) is vital for developing effective interventions to halt or slow the disease's progression. This study aims to perform a comprehensive analysis of machine learning techniques for selecting MRI-based biomarkers and classifying individuals into healthy controls (HC) and unstable controls (uHC) who later show mild cognitive impairment within five years. The research utilizes MRI data from the Alzheimer's Disease Neuroinformatics Initiative (ADNI) and the Open Access Series of Imaging Studies 3 (OASIS-3), focusing on both HC and uHC participants. The study addresses the challenges of imbalanced data by testing classification methods on balanced and unbalanced datasets, and harmonizes data using polynomial regression to mitigate nuisance variables like age, gender, and intracranial volume. Results indicate that Gaussian Naive Bayes and RusBoost classifiers shows an optimal performance, achieving accuracies of up to 76.46% and 72.48% respectively on the ADNI dataset. For the OASIS-3 dataset, Kernel Naive Bayes and RusBoost yield accuracies ranging from 64.66% to 75.71%, improving further in age-matched datasets. Brain regions like the entorhinal cortex, hippocampus, lateral ventricle, and lateral orbitofrontal cortex are identified as significantly impacted during early cognitive decline. Despite limitations such as small sample sizes, the study's harmonization approach enhances the robustness of biomarker selection, suggesting the potential of this semi-automatic machine learning pipeline for early AD detection using MRI.

  • 6 authors
·
May 29, 2024

Neural Video Compression with Feature Modulation

The emerging conditional coding-based neural video codec (NVC) shows superiority over commonly-used residual coding-based codec and the latest NVC already claims to outperform the best traditional codec. However, there still exist critical problems blocking the practicality of NVC. In this paper, we propose a powerful conditional coding-based NVC that solves two critical problems via feature modulation. The first is how to support a wide quality range in a single model. Previous NVC with this capability only supports about 3.8 dB PSNR range on average. To tackle this limitation, we modulate the latent feature of the current frame via the learnable quantization scaler. During the training, we specially design the uniform quantization parameter sampling mechanism to improve the harmonization of encoding and quantization. This results in a better learning of the quantization scaler and helps our NVC support about 11.4 dB PSNR range. The second is how to make NVC still work under a long prediction chain. We expose that the previous SOTA NVC has an obvious quality degradation problem when using a large intra-period setting. To this end, we propose modulating the temporal feature with a periodically refreshing mechanism to boost the quality. %Besides solving the above two problems, we also design a single model that can support both RGB and YUV colorspaces. Notably, under single intra-frame setting, our codec can achieve 29.7\% bitrate saving over previous SOTA NVC with 16\% MACs reduction. Our codec serves as a notable landmark in the journey of NVC evolution. The codes are at https://github.com/microsoft/DCVC.

  • 3 authors
·
Feb 27, 2024

CHIMERA: Adaptive Cache Injection and Semantic Anchor Prompting for Zero-shot Image Morphing with Morphing-oriented Metrics

Diffusion models exhibit remarkable generative ability, yet achieving smooth and semantically consistent image morphing remains a challenge. Existing approaches often yield abrupt transitions or over-saturated appearances due to the lack of adaptive structural and semantic alignments. We propose CHIMERA, a zero-shot diffusion-based framework that formulates morphing as a cached inversion-guided denoising process. To handle large semantic and appearance disparities, we propose Adaptive Cache Injection and Semantic Anchor Prompting. Adaptive Cache Injection (ACI) caches down, mid, and up blocks features from both inputs during DDIM inversion and re-injects them adaptively during denoising, enabling spatial and semantic alignment in depth- and time-adaptive manners and enabling natural feature fusion and smooth transitions. Semantic Anchor Prompting (SAP) leverages a vision-language model to generate a shared anchor prompt that serves as a semantic anchor, bridging dissimilar inputs and guiding the denoising process toward coherent results. Finally, we introduce the Global-Local Consistency Score (GLCS), a morphing-oriented metric that simultaneously evaluates the global harmonization of the two inputs and the smoothness of the local morphing transition. Extensive experiments and user studies show that CHIMERA achieves smoother and more semantically aligned transitions than existing methods, establishing a new state of the art in image morphing. The code and project page will be publicly released.

  • 4 authors
·
Dec 7

Generative Portrait Shadow Removal

We introduce a high-fidelity portrait shadow removal model that can effectively enhance the image of a portrait by predicting its appearance under disturbing shadows and highlights. Portrait shadow removal is a highly ill-posed problem where multiple plausible solutions can be found based on a single image. While existing works have solved this problem by predicting the appearance residuals that can propagate local shadow distribution, such methods are often incomplete and lead to unnatural predictions, especially for portraits with hard shadows. We overcome the limitations of existing local propagation methods by formulating the removal problem as a generation task where a diffusion model learns to globally rebuild the human appearance from scratch as a condition of an input portrait image. For robust and natural shadow removal, we propose to train the diffusion model with a compositional repurposing framework: a pre-trained text-guided image generation model is first fine-tuned to harmonize the lighting and color of the foreground with a background scene by using a background harmonization dataset; and then the model is further fine-tuned to generate a shadow-free portrait image via a shadow-paired dataset. To overcome the limitation of losing fine details in the latent diffusion model, we propose a guided-upsampling network to restore the original high-frequency details (wrinkles and dots) from the input image. To enable our compositional training framework, we construct a high-fidelity and large-scale dataset using a lightstage capturing system and synthetic graphics simulation. Our generative framework effectively removes shadows caused by both self and external occlusions while maintaining original lighting distribution and high-frequency details. Our method also demonstrates robustness to diverse subjects captured in real environments.

  • 7 authors
·
Oct 7, 2024

MotionDuet: Dual-Conditioned 3D Human Motion Generation with Video-Regularized Text Learning

3D Human motion generation is pivotal across film, animation, gaming, and embodied intelligence. Traditional 3D motion synthesis relies on costly motion capture, while recent work shows that 2D videos provide rich, temporally coherent observations of human behavior. Existing approaches, however, either map high-level text descriptions to motion or rely solely on video conditioning, leaving a gap between generated dynamics and real-world motion statistics. We introduce MotionDuet, a multimodal framework that aligns motion generation with the distribution of video-derived representations. In this dual-conditioning paradigm, video cues extracted from a pretrained model (e.g., VideoMAE) ground low-level motion dynamics, while textual prompts provide semantic intent. To bridge the distribution gap across modalities, we propose Dual-stream Unified Encoding and Transformation (DUET) and a Distribution-Aware Structural Harmonization (DASH) loss. DUET fuses video-informed cues into the motion latent space via unified encoding and dynamic attention, while DASH aligns motion trajectories with both distributional and structural statistics of video features. An auto-guidance mechanism further balances textual and visual signals by leveraging a weakened copy of the model, enhancing controllability without sacrificing diversity. Extensive experiments demonstrate that MotionDuet generates realistic and controllable human motions, surpassing strong state-of-the-art baselines.

  • 7 authors
·
Nov 22

SceneBooth: Diffusion-based Framework for Subject-preserved Text-to-Image Generation

Due to the demand for personalizing image generation, subject-driven text-to-image generation method, which creates novel renditions of an input subject based on text prompts, has received growing research interest. Existing methods often learn subject representation and incorporate it into the prompt embedding to guide image generation, but they struggle with preserving subject fidelity. To solve this issue, this paper approaches a novel framework named SceneBooth for subject-preserved text-to-image generation, which consumes inputs of a subject image, object phrases and text prompts. Instead of learning the subject representation and generating a subject, our SceneBooth fixes the given subject image and generates its background image guided by the text prompts. To this end, our SceneBooth introduces two key components, i.e., a multimodal layout generation module and a background painting module. The former determines the position and scale of the subject by generating appropriate scene layouts that align with text captions, object phrases, and subject visual information. The latter integrates two adapters (ControlNet and Gated Self-Attention) into the latent diffusion model to generate a background that harmonizes with the subject guided by scene layouts and text descriptions. In this manner, our SceneBooth ensures accurate preservation of the subject's appearance in the output. Quantitative and qualitative experimental results demonstrate that SceneBooth significantly outperforms baseline methods in terms of subject preservation, image harmonization and overall quality.

  • 6 authors
·
Jan 6

ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish

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.

  • 5 authors
·
Apr 9, 2024

ATOMMIC: An Advanced Toolbox for Multitask Medical Imaging Consistency to facilitate Artificial Intelligence applications from acquisition to analysis in Magnetic Resonance Imaging

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.

  • 4 authors
·
Apr 30, 2024