Nima Tajbakhsh

Shengzhi Li, Nima Tajbakhsh

In this work, we present SciGraphQA, a synthetic multi-turn question-answer dataset related to academic graphs. SciGraphQA is 13 times larger than ChartVQA, the previously largest chart-visual question-answering dataset. It is also the largest open-sourced chart VQA dataset with non-synthetic charts. To build our dataset, we selected 290,000 Computer Science or Machine Learning ArXiv papers published between 2010 and 2020, and then used Palm-2 to generate 295K samples of open-vocabulary multi-turn question-answering dialogues about the graphs. As context, we provided the text-only Palm-2 with paper title, abstract, paragraph mentioning the graph, and rich text contextual data from the graph itself, obtaining dialogues with an average 2.23 question-answer turns for each graph. We asked GPT-4 to assess the matching quality of our question-answer turns given the paper's context, obtaining an average rating of 8.7/10 on our 3K test set. We evaluated the 0-shot capability of the most popular MLLM models such as LLaVa, mPLUGowl, BLIP-2, and openFlamingo's on our dataset, finding LLaVA-13B being the most performant with a CIDEr score of 0.08. We further enriched the question prompts for LLAVA by including the serialized data tables extracted from the graphs using the DePlot model, boosting LLaVA's 0-shot CIDEr to 0.15. To verify the validity of our dataset, we also fine-tuned LLaVa using our dataset, reaching a substantially higher CIDEr score of 0.26. We anticipate further accuracy improvement by including segmentation mask tokens and leveraging larger LLM backbones coupled with emergent prompting techniques. Our code and data are open-sourced.

Felix Abecassis, Anjulie Agrusa, Dong Ahn et al. · nvidia

Large Language Models (LLMs) today are powerful problem solvers across many domains, and they continue to get stronger as they scale in model size, training set size, and training set quality, as shown by extensive research and experimentation across the industry. Training a frontier model today requires on the order of tens to hundreds of yottaflops, which is a massive investment of time, compute, and energy. Improving pretraining efficiency is therefore essential to enable the next generation of even more capable LLMs. While 8-bit floating point (FP8) training is now widely adopted, transitioning to even narrower precision, such as 4-bit floating point (FP4), could unlock additional improvements in computational speed and resource utilization. However, quantization at this level poses challenges to training stability, convergence, and implementation, notably for large-scale models trained on long token horizons. In this study, we introduce a novel approach for stable and accurate training of large language models (LLMs) using the NVFP4 format. Our method integrates Random Hadamard transforms (RHT) to bound block-level outliers, employs a two-dimensional quantization scheme for consistent representations across both the forward and backward passes, utilizes stochastic rounding for unbiased gradient estimation, and incorporates selective high-precision layers. We validate our approach by training a 12-billion-parameter model on 10 trillion tokens -- the longest publicly documented training run in 4-bit precision to date. Our results show that the model trained with our NVFP4-based pretraining technique achieves training loss and downstream task accuracies comparable to an FP8 baseline. These findings highlight that NVFP4, when combined with our training approach, represents a major step forward in narrow-precision LLM training algorithms.

Amala Sanjay Deshmukh, Kateryna Chumachenko, Tuomas Rintamaki et al. · amazon-science, nvidia

We introduce Nemotron 3 Nano Omni, the latest model in the Nemotron multimodal series and the first to natively support audio inputs alongside text, images, and video. Nemotron 3 Nano Omni delivers consistent accuracy improvements over its predecessor, Nemotron Nano V2 VL, across all modalities, enabled by advances in architecture, training data and recipes. In particular, Nemotron 3 delivers leading results in real-world document understanding, long audio-video comprehension, and agentic computer use. Built on the highly efficient Nemotron 3 Nano 30B-A3B backbone, Nemotron 3 Nano Omni further incorporates innovative multimodal token-reduction techniques to deliver substantially lower inference latency and higher throughput than other models of similar size. We are releasing model checkpoints in BF16, FP8, and FP4 formats, along with portions of the training data and codebase to facilitate further research and development.

Yashaswi Karnati, Kamran Jafari, Akash Mehra et al.

Foundation model training is becoming multimodal, from post-training pipelines to large-scale pretraining. As modality coverage broadens, context windows grow, and encoder LLM scales diverge, a single LLM-centric TP/CP/PP/DP/EP layout increasingly limits throughput. This coupling forces encoders to inherit LLM-driven sharding and placement choices that can add communication, limit encoder parallelism, or constrain the LLM schedule; the mismatch is most pronounced at long contexts, where LLM context parallelism is needed for the fused multimodal sequence but encoder inputs remain bounded. We present heterogeneous parallelism for multimodal large language model training, an abstraction that lets modules in one end-to-end graph use independent layouts and rank placements, supporting colocated execution on shared GPUs and non-colocated execution on disjoint rank sets. The key challenge is preserving boundary tensor semantics across independent layouts: forward activations must be materialized for the destination layout, while backward gradients must be routed back to the source layout. We address this with boundary communicators that implement forward and backward layout transforms, plus scheduling extensions for both placement modes. We evaluate optimized homogeneous, colocated heterogeneous, and non-colocated heterogeneous configurations across multimodal workloads and GPU scales to characterize when added layout and placement freedom exposes a better operating point. Across this sweep, colocated heterogeneity improves TFLOPS/GPU by up to 49.3%, while non-colocated heterogeneity improves aggregate token throughput by up to 13.0% and TFLOPS/GPU by up to 9.6%. We validate loss convergence parity against homogeneous baselines and release the system as an open-source Megatron-LM extension.

Mikail Khona, Aditya Vavre, Boxiang Wang et al.

Higher-order optimizers such as Muon and SOAP offer faster convergence than AdamW, but their computational cost and numerical stability challenges have limited adoption at scale. In this work, we adapt and enhance preconditioned gradient methods to overcome the practical challenges of large-scale LLM pretraining. We first identify instabilities in SOAP at large batch sizes and propose algorithmic modifications including per-step QR orthogonalization and improved preconditioning strategies that eliminate loss spikes and enable stable training in these regimes. We then present a unified empirical study of SOAP, Muon, and AdamW using update-RMS matching to ensure fair learning rate transfer across optimizers. As part of this analysis, we empirically evaluate the orthogonalization quality of Muon. Our experiments on multi-billion-parameter models trained on trillions of tokens reveal that SOAP and Muon consistently outperform AdamW at the scales we tested. Notably, at batch sizes of up to 100M tokens for next-token prediction, these optimizers maintain training stability and quality while AdamW degrades. To enable efficient training at large scale, we introduce a layer-wise distributed optimizer compatible with Megatron-LM. Our implementation balances memory and hides communication while avoiding approximations to the optimizer computations, thus retaining their convergence benefits. Additionally, we identify and build specific system-level improvements to further accelerate our layer-wise implementation. To support the research community, we release a codebase that contains emerging algorithms for optimization: https://github.com/NVIDIA-NeMo/Emerging-Optimizers

Rohit Jena, Ali Taghibakhshi, Sahil Jain et al.

Text-to-image (T2I) diffusion models have become prominent tools for generating high-fidelity images from text prompts. However, when trained on unfiltered internet data, these models can produce unsafe, incorrect, or stylistically undesirable images that are not aligned with human preferences. To address this, recent approaches have incorporated human preference datasets to fine-tune T2I models or to optimize reward functions that capture these preferences. Although effective, these methods are vulnerable to reward hacking, where the model overfits to the reward function, leading to a loss of diversity in the generated images. In this paper, we prove the inevitability of reward hacking and study natural regularization techniques like KL divergence and LoRA scaling, and their limitations for diffusion models. We also introduce Annealed Importance Guidance (AIG), an inference-time regularization inspired by Annealed Importance Sampling, which retains the diversity of the base model while achieving Pareto-Optimal reward-diversity tradeoffs. Our experiments demonstrate the benefits of AIG for Stable Diffusion models, striking the optimal balance between reward optimization and image diversity. Furthermore, a user study confirms that AIG improves diversity and quality of generated images across different model architectures and reward functions.

Yonggan Fu, Lexington Whalen, Abhinav Garg et al.

We introduce Nemotron-Labs-Diffusion, a tri-mode language model (LM) that unifies AR, diffusion, and self-speculation decoding within a single architecture. Trained with a joint AR-diffusion objective, Nemotron-Labs-Diffusion can switch modes to sustain high throughput across deployment settings and concurrency levels. Our study shows that (1) AR and diffusion objectives are complementary: diffusion improves lookahead planning, while AR provides left-to-right linguistic priors. (2) In self-speculation mode, diffusion drafts while AR verifies, outperforming multi-token prediction (MTP) methods in both acceptance rate and real-device efficiency. (3) A speed-of-light analysis further demonstrates diffusion's long-term potential, with up to 76.5% more tokens per forward pass than self-speculation under an optimal sampler. Scaling to 3B, 8B, and 14B parameters, our Nemotron-Labs-Diffusion family, including base, instruct, and vision-language models, consistently outperforms state-of-the-art open-source AR and diffusion LMs in both accuracy and speed. For example, Nemotron-Labs-Diffusion-8B decodes 6x more tokens per forward than Qwen3-8B with comparable accuracy, translating to 4x higher throughput on SPEED-Bench with SGLang on a GB200 GPU.

Ali Taghibakhshi, Ruisi Cai, Saurav Muralidharan et al.

Training a family of large language models (LLMs), either from scratch or via iterative compression, is prohibitively expensive and inefficient, requiring separate training runs for each model in the family. In this paper, we introduce Star Elastic, a novel LLM post-training method that adds N nested submodels to a given parent reasoning model using the compute of one run (N-fold savings) via a single post-training job. Beyond reducing training costs, Star Elastic also addresses a fundamental limitation of efficient reasoning: the rigidity of static architectures, which forces the allocation of constant resources regardless of token difficulty. By unlocking elastic budget control, Star Elastic enables a novel inference scheme that uses different submodels for each reasoning phase (thinking and answering). Star Elastic supports (1) nesting along the SSM, embedding channel, MoE, and FFN axes, (2) learning nested submodels via an end-to-end trainable router, and (3) curriculum-based knowledge distillation. Building on the Nemotron Elastic framework, we apply Star Elastic to the NVIDIA Nemotron Nano models, with a particular focus on hybrid Mixture-of-Experts (MoE) architectures: from Nemotron Nano v3 (30B/3.6A), we generate 23B (2.8A) and 12B (2.0A) variants with 160B training tokens. All nested models match or outperform independently trained baselines of comparable size and achieve a 360x reduction versus pretraining from scratch and a 7x reduction over state-of-the-art compression. Crucially, elastic budget control advances the accuracy-latency Pareto frontier, achieving up to 16% higher accuracy and 1.9x lower latency via dynamic per-phase model selection. We further extend Star Elastic to quantized regimes via Quantization-Aware Distillation (QAD), producing nested NVFP4 and FP8 elastic checkpoints that preserve zero-shot slicing while delivering smaller deployment footprints.

Weinan Song, Gaurav Fotedar, Nima Tajbakhsh et al.

Deep learning models tend to underperform in the presence of domain shifts. Domain transfer has recently emerged as a promising approach wherein images exhibiting a domain shift are transformed into other domains for augmentation or adaptation. However, with the absence of paired and annotated images, models merely learned by adversarial loss and cycle consistency loss could result in poor consistency of anatomy structures during the translation. Additionally, the complexity of learning multi-domain transfer could significantly increase with the number of target domains and source images. In this paper, we propose a multi-domain transfer network, named MDT-Net, to address the limitations above through perceptual supervision. Specifically, our model consists of a single encoder-decoder network and multiple domain-specific transfer modules to disentangle feature representations of the anatomy content and domain variance. Owing to this architecture, the model could significantly reduce the complexity when the translation is conducted among multiple domains. To demonstrate the performance of our method, we evaluate our model qualitatively and quantitatively on RETOUCH, an OCT dataset comprising scans from three different scanner devices (domains). Furthermore, we take the transfer results as additional training data for fluid segmentation to prove the advantage of our model indirectly, i.e., in the task of data adaptation and augmentation. Experimental results show that our method could bring universal improvement in these segmentation tasks, which demonstrates the effectiveness and efficiency of MDT-Net in multi-domain transfer.

Akhiad Bercovich, Talor Abramovich, Daniel Afrimi et al.

We present Nemotron-Labs-3-Puzzle-75B-A9B, a compressed variant of Nemotron-3-Super optimized for interactive deployment. We designed the model to maximize server throughput under high user throughput constraints. In interactive serving workloads on a single 8xB200 node, Puzzle-75B-A9B achieves approximately 2x higher server throughput than Nemotron-3-Super at matched user throughput constraints. In ultra-long-context deployment on a single H100 GPU, the compressed model increases 1M-token concurrency from 1 request to 8 requests. Puzzle-75B-A9B is constructed using a multi-stage pipeline that combines the Iterative Puzzle compression framework with knowledge distillation, reinforcement learning, quantization, and a Multi-Token Prediction head. The compression process jointly optimizes heterogeneous MoE pruning, active parameter budget, and Mamba pruning to improve inference efficiency while preserving model quality. We evaluate Puzzle-75B-A9B on a broad suite of reasoning, coding, multilingual, long-context, and agentic benchmarks. Despite substantial compression, the model retains strong downstream accuracy relative to the parent model across a wide range of tasks. These results demonstrate that large hybrid MoE models can be substantially optimized for deployment efficiency while maintaining strong downstream capability.

Zongwei Zhou, Md Mahfuzur Rahman Siddiquee, Nima Tajbakhsh et al.

The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance segmentation, by (1) alleviating the unknown network depth with an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision; (2) redesigning skip connections to aggregate features of varying semantic scales at the decoder sub-networks, leading to a highly flexible feature fusion scheme; and (3) devising a pruning scheme to accelerate the inference speed of UNet++. We have evaluated UNet++ using six different medical image segmentation datasets, covering multiple imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and electron microscopy (EM), and demonstrating that (1) UNet++ consistently outperforms the baseline models for the task of semantic segmentation across different datasets and backbone architectures; (2) UNet++ enhances segmentation quality of varying-size objects -- an improvement over the fixed-depth U-Net; (3) Mask RCNN++ (Mask R-CNN with UNet++ design) outperforms the original Mask R-CNN for the task of instance segmentation; and (4) pruned UNet++ models achieve significant speedup while showing only modest performance degradation. Our implementation and pre-trained models are available at https://github.com/MrGiovanni/UNetPlusPlus.

Zongwei Zhou, Vatsal Sodha, Md Mahfuzur Rahman Siddiquee et al.

Transfer learning from natural image to medical image has established as one of the most practical paradigms in deep learning for medical image analysis. However, to fit this paradigm, 3D imaging tasks in the most prominent imaging modalities (e.g., CT and MRI) have to be reformulated and solved in 2D, losing rich 3D anatomical information and inevitably compromising the performance. To overcome this limitation, we have built a set of models, called Generic Autodidactic Models, nicknamed Models Genesis, because they are created ex nihilo (with no manual labeling), self-taught (learned by self-supervision), and generic (served as source models for generating application-specific target models). Our extensive experiments demonstrate that our Models Genesis significantly outperform learning from scratch in all five target 3D applications covering both segmentation and classification. More importantly, learning a model from scratch simply in 3D may not necessarily yield performance better than transfer learning from ImageNet in 2D, but our Models Genesis consistently top any 2D approaches including fine-tuning the models pre-trained from ImageNet as well as fine-tuning the 2D versions of our Models Genesis, confirming the importance of 3D anatomical information and significance of our Models Genesis for 3D medical imaging. This performance is attributed to our unified self-supervised learning framework, built on a simple yet powerful observation: the sophisticated yet recurrent anatomy in medical images can serve as strong supervision signals for deep models to learn common anatomical representation automatically via self-supervision. As open science, all pre-trained Models Genesis are available at https://github.com/MrGiovanni/ModelsGenesis.

Md Mahfuzur Rahman Siddiquee, Zongwei Zhou, Nima Tajbakhsh et al.

Generative adversarial networks (GANs) have ushered in a revolution in image-to-image translation. The development and proliferation of GANs raises an interesting question: can we train a GAN to remove an object, if present, from an image while otherwise preserving the image? Specifically, can a GAN "virtually heal" anyone by turning his medical image, with an unknown health status (diseased or healthy), into a healthy one, so that diseased regions could be revealed by subtracting those two images? Such a task requires a GAN to identify a minimal subset of target pixels for domain translation, an ability that we call fixed-point translation, which no GAN is equipped with yet. Therefore, we propose a new GAN, called Fixed-Point GAN, trained by (1) supervising same-domain translation through a conditional identity loss, and (2) regularizing cross-domain translation through revised adversarial, domain classification, and cycle consistency loss. Based on fixed-point translation, we further derive a novel framework for disease detection and localization using only image-level annotation. Qualitative and quantitative evaluations demonstrate that the proposed method outperforms the state of the art in multi-domain image-to-image translation and that it surpasses predominant weakly-supervised localization methods in both disease detection and localization. Implementation is available at https://github.com/jlianglab/Fixed-Point-GAN.

Ali Taghibakhshi, Sharath Turuvekere Sreenivas, Saurav Muralidharan et al.

Hybrid LLM architectures that combine Attention and State Space Models (SSMs) achieve state-of-the-art accuracy and runtime performance. Recent work has demonstrated that applying compression and distillation to Attention-only models yields smaller, more accurate models at a fraction of the training cost. In this work, we explore the effectiveness of compressing Hybrid architectures. We introduce a novel group-aware pruning strategy that preserves the structural integrity of SSM blocks and their sequence modeling capabilities. Furthermore, we demonstrate the necessity of such SSM pruning to achieve improved accuracy and inference speed compared to traditional approaches. Our compression recipe combines SSM, FFN, embedding dimension, and layer pruning, followed by knowledge distillation-based retraining, similar to the MINITRON technique. Using this approach, we compress the Nemotron-H 8B Hybrid model down to 4B parameters with up to 40x fewer training tokens. The resulting model surpasses the accuracy of similarly-sized models while achieving 2x faster inference, significantly advancing the Pareto frontier.

Aditya Vavre, Ethan He, Dennis Liu et al. · nvidia

Scaling large language models (LLMs) significantly improves performance but comes with prohibitive computational costs. Mixture-of-Experts (MoE) models offer an efficient alternative, increasing capacity without a proportional rise in compute requirements. However, training MoE models from scratch poses challenges like overfitting and routing instability. We present an efficient training recipe leveraging pre-trained dense checkpoints, training an 8-Expert Top-2 MoE model from Llama 3-8B with less than $1\%$ of typical pre-training compute. Our approach enhances downstream performance on academic benchmarks, achieving a $\textbf{2%}$ improvement in 0-shot accuracy on MMLU, while reaching a Model FLOPs Utilization (MFU) of $\textbf{46.8%}$ during training using our framework. We also integrate online upcycling in NeMo for seamless use of pre-trained weights, enabling cost-effective development of high-capacity MoE models.

Meng Xin, Sweta Priyadarshi, Jingyu Xin et al.

This technical report presents quantization-aware distillation (QAD) and our best practices for recovering accuracy of NVFP4-quantized large language models (LLMs) and vision-language models (VLMs). QAD distills a full-precision teacher model into a quantized student model using a KL divergence loss. While applying distillation to quantized models is not a new idea, we observe key advantages of QAD for today's LLMs: 1. It shows remarkable effectiveness and stability for models trained through multi-stage post-training pipelines, including supervised fine-tuning (SFT), reinforcement learning (RL), and model merging, where traditional quantization-aware training (QAT) suffers from engineering complexity and training instability; 2. It is robust to data quality and coverage, enabling accuracy recovery without full training data. We evaluate QAD across multiple post-trained models including AceReason Nemotron, Nemotron 3 Nano, Nemotron Nano V2, Nemotron Nano V2 VL (VLM), and Llama Nemotron Super v1, showing consistent recovery to near-BF16 accuracy.

Ali Taghibakhshi, Sharath Turuvekere Sreenivas, Saurav Muralidharan et al.

Training a family of large language models targeting multiple scales and deployment objectives is prohibitively expensive, requiring separate training runs for each different size. Recent work on model compression through pruning and knowledge distillation has reduced this cost; however, this process still incurs hundreds of billions of tokens worth of training cost per compressed model. In this paper, we present Nemotron Elastic, a framework for building reasoning-oriented LLMs, including hybrid Mamba-Attention architectures, that embed multiple nested submodels within a single parent model, each optimized for different deployment configurations and budgets. Each of these submodels shares weights with the parent model and can be extracted zero-shot during deployment without additional training or fine-tuning. We enable this functionality through an end-to-end trained router, tightly coupled to a two-stage training curriculum designed specifically for reasoning models. We additionally introduce group-aware SSM elastification that preserves Mamba's structural constraints, heterogeneous MLP elastification, normalized MSE-based layer importance for improved depth selection, and knowledge distillation enabling simultaneous multi-budget optimization. We apply Nemotron Elastic to the Nemotron Nano V2 12B model, simultaneously producing a 9B and a 6B model using only 110B training tokens; this results in over 360x cost reduction compared to training model families from scratch, and around 7x compared to SoTA compression techniques. Each of the nested models performs on par or better than the SoTA in accuracy. Moreover, unlike other compression methods, the nested capability of our approach allows having a many-in-one reasoning model that has constant deployment memory against the number of models in the family.

Qinji Yu, Kang Dang, Nima Tajbakhsh et al.

Despite the tremendous success of deep neural networks in medical image segmentation, they typically require a large amount of costly, expert-level annotated data. Few-shot segmentation approaches address this issue by learning to transfer knowledge from limited quantities of labeled examples. Incorporating appropriate prior knowledge is critical in designing high-performance few-shot segmentation algorithms. Since strong spatial priors exist in many medical imaging modalities, we propose a prototype-based method -- namely, the location-sensitive local prototype network -- that leverages spatial priors to perform few-shot medical image segmentation. Our approach divides the difficult problem of segmenting the entire image with global prototypes into easily solvable subproblems of local region segmentation with local prototypes. For organ segmentation experiments on the VISCERAL CT image dataset, our method outperforms the state-of-the-art approaches by 10% in the mean Dice coefficient. Extensive ablation studies demonstrate the substantial benefits of incorporating spatial information and confirm the effectiveness of our approach.

Gaurav Fotedar, Nima Tajbakhsh, Shilpa Ananth et al.

Supervised learning has proved effective for medical image analysis. However, it can utilize only the small labeled portion of data; it fails to leverage the large amounts of unlabeled data that is often available in medical image datasets. Supervised models are further handicapped by domain shifts, when the labeled dataset, despite being large enough, fails to cover different protocols or ethnicities. In this paper, we introduce \emph{extreme consistency}, which overcomes the above limitations, by maximally leveraging unlabeled data from the same or a different domain in a teacher-student semi-supervised paradigm. Extreme consistency is the process of sending an extreme transformation of a given image to the student network and then constraining its prediction to be consistent with the teacher network's prediction for the untransformed image. The extreme nature of our consistency loss distinguishes our method from related works that yield suboptimal performance by exercising only mild prediction consistency. Our method is 1) auto-didactic, as it requires no extra expert annotations; 2) versatile, as it handles both domain shift and limited annotation problems; 3) generic, as it is readily applicable to classification, segmentation, and detection tasks; and 4) simple to implement, as it requires no adversarial training. We evaluate our method for the tasks of lesion and retinal vessel segmentation in skin and fundus images. Our experiments demonstrate a significant performance gain over both modern supervised networks and recent semi-supervised models. This performance is attributed to the strong regularization enforced by extreme consistency, which enables the student network to learn how to handle extreme variants of both labeled and unlabeled images. This enhances the network's ability to tackle the inevitable same- and cross-domain data variability during inference.

Germán González, Daniel Jimenez-Carretero, Sara Rodríguez-López et al.

Rationale: Computer aided detection (CAD) algorithms for Pulmonary Embolism (PE) algorithms have been shown to increase radiologists' sensitivity with a small increase in specificity. However, CAD for PE has not been adopted into clinical practice, likely because of the high number of false positives current CAD software produces. Objective: To generate a database of annotated computed tomography pulmonary angiographies, use it to compare the sensitivity and false positive rate of current algorithms and to develop new methods that improve such metrics. Methods: 91 Computed tomography pulmonary angiography scans were annotated by at least one radiologist by segmenting all pulmonary emboli visible on the study. 20 annotated CTPAs were open to the public in the form of a medical image analysis challenge. 20 more were kept for evaluation purposes. 51 were made available post-challenge. 8 submissions, 6 of them novel, were evaluated on the 20 evaluation CTPAs. Performance was measured as per embolus sensitivity vs. false positives per scan curve. Results: The best algorithms achieved a per-embolus sensitivity of 75% at 2 false positives per scan (fps) or of 70% at 1 fps, outperforming the state of the art. Deep learning approaches outperformed traditional machine learning ones, and their performance improved with the number of training cases. Significance: Through this work and challenge we have improved the state-of-the art of computer aided detection algorithms for pulmonary embolism. An open database and an evaluation benchmark for such algorithms have been generated, easing the development of further improvements. Implications on clinical practice will need further research.

Nima Tajbakhsh, Brian Lai, Shilpa Ananth et al.

Deep convolutional neural networks have proved effective in segmenting lesions and anatomies in various medical imaging modalities. However, in the presence of small sample size and domain shift problems, these models often produce masks with non-intuitive segmentation mistakes. In this paper, we propose a segmentation framework called ErrorNet, which learns to correct these segmentation mistakes through the repeated process of injecting systematic segmentation errors to the segmentation result based on a learned shape prior, followed by attempting to predict the injected error. During inference, ErrorNet corrects the segmentation mistakes by adding the predicted error map to the initial segmentation result. ErrorNet has advantages over alternatives based on domain adaptation or CRF-based post processing, because it requires neither domain-specific parameter tuning nor any data from the target domains. We have evaluated ErrorNet using five public datasets for the task of retinal vessel segmentation. The selected datasets differ in size and patient population, allowing us to evaluate the effectiveness of ErrorNet in handling small sample size and domain shift problems. Our experiments demonstrate that ErrorNet outperforms a base segmentation model, a CRF-based post processing scheme, and a domain adaptation method, with a greater performance gain in the presence of the aforementioned dataset limitations.

Nima Tajbakhsh, Laura Jeyaseelan, Qian Li et al.

The medical imaging literature has witnessed remarkable progress in high-performing segmentation models based on convolutional neural networks. Despite the new performance highs, the recent advanced segmentation models still require large, representative, and high quality annotated datasets. However, rarely do we have a perfect training dataset, particularly in the field of medical imaging, where data and annotations are both expensive to acquire. Recently, a large body of research has studied the problem of medical image segmentation with imperfect datasets, tackling two major dataset limitations: scarce annotations where only limited annotated data is available for training, and weak annotations where the training data has only sparse annotations, noisy annotations, or image-level annotations. In this article, we provide a detailed review of the solutions above, summarizing both the technical novelties and empirical results. We further compare the benefits and requirements of the surveyed methodologies and provide our recommended solutions. We hope this survey article increases the community awareness of the techniques that are available to handle imperfect medical image segmentation datasets.

Abdullah-Al-Zubaer Imran, Ali Hatamizadeh, Shilpa P. Ananth et al.

Reliable and automatic segmentation of lung lobes is important for diagnosis, assessment, and quantification of pulmonary diseases. The existing techniques are prohibitively slow, undesirably rely on prior (airway/vessel) segmentation, and/or require user interactions for optimal results. This work presents a reliable, fast, and fully automated lung lobe segmentation based on a progressive dense V-network (PDV-Net). The proposed method can segment lung lobes in one forward pass of the network, with an average runtime of 2 seconds using 1 Nvidia Titan XP GPU, eliminating the need for any prior atlases, lung segmentation or any subsequent user intervention. We evaluated our model using 84 chest CT scans from the LIDC and 154 pathological cases from the LTRC datasets. Our model achieved a Dice score of $0.939 \pm 0.02$ for the LIDC test set and $0.950 \pm 0.01$ for the LTRC test set, significantly outperforming a 2D U-net model and a 3D dense V-net. We further evaluated our model against 55 cases from the LOLA11 challenge, obtaining an average Dice score of 0.935---a performance level competitive to the best performing team with an average score of 0.938. Our extensive robustness analyses also demonstrate that our model can reliably segment both healthy and pathological lung lobes in CT scans from different vendors, and that our model is robust against configurations of CT scan reconstruction.

Nima Tajbakhsh, Yufei Hu, Junli Cao et al.

We investigate the effectiveness of a simple solution to the common problem of deep learning in medical image analysis with limited quantities of labeled training data. The underlying idea is to assign artificial labels to abundantly available unlabeled medical images and, through a process known as surrogate supervision, pre-train a deep neural network model for the target medical image analysis task lacking sufficient labeled training data. In particular, we employ 3 surrogate supervision schemes, namely rotation, reconstruction, and colorization, in 4 different medical imaging applications representing classification and segmentation for both 2D and 3D medical images. 3 key findings emerge from our research: 1) pre-training with surrogate supervision is effective for small training sets; 2) deep models trained from initial weights pre-trained through surrogate supervision outperform the same models when trained from scratch, suggesting that pre-training with surrogate supervision should be considered prior to training any deep 3D models; 3) pre-training models in the medical domain with surrogate supervision is more effective than transfer learning from an unrelated domain (e.g., natural images), indicating the practical value of abundant unlabeled medical image data.

Zongwei Zhou, Md Mahfuzur Rahman Siddiquee, Nima Tajbakhsh et al.

In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively.

Jae Y. Shin, Nima Tajbakhsh, R. Todd Hurst et al.

Cardiovascular disease (CVD) is the leading cause of mortality yet largely preventable, but the key to prevention is to identify at-risk individuals before adverse events. For predicting individual CVD risk, carotid intima-media thickness (CIMT), a noninvasive ultrasound method, has proven to be valuable, offering several advantages over CT coronary artery calcium score. However, each CIMT examination includes several ultrasound videos, and interpreting each of these CIMT videos involves three operations: (1) select three end-diastolic ultrasound frames (EUF) in the video, (2) localize a region of interest (ROI) in each selected frame, and (3) trace the lumen-intima interface and the media-adventitia interface in each ROI to measure CIMT. These operations are tedious, laborious, and time consuming, a serious limitation that hinders the widespread utilization of CIMT in clinical practice. To overcome this limitation, this paper presents a new system to automate CIMT video interpretation. Our extensive experiments demonstrate that the suggested system significantly outperforms the state-of-the-art methods. The superior performance is attributable to our unified framework based on convolutional neural networks (CNNs) coupled with our informative image representation and effective post-processing of the CNN outputs, which are uniquely designed for each of the above three operations.

Nima Tajbakhsh, Jae Y. Shin, Suryakanth R. Gurudu et al.

Training a deep convolutional neural network (CNN) from scratch is difficult because it requires a large amount of labeled training data and a great deal of expertise to ensure proper convergence. A promising alternative is to fine-tune a CNN that has been pre-trained using, for instance, a large set of labeled natural images. However, the substantial differences between natural and medical images may advise against such knowledge transfer. In this paper, we seek to answer the following central question in the context of medical image analysis: \emph{Can the use of pre-trained deep CNNs with sufficient fine-tuning eliminate the need for training a deep CNN from scratch?} To address this question, we considered 4 distinct medical imaging applications in 3 specialties (radiology, cardiology, and gastroenterology) involving classification, detection, and segmentation from 3 different imaging modalities, and investigated how the performance of deep CNNs trained from scratch compared with the pre-trained CNNs fine-tuned in a layer-wise manner. Our experiments consistently demonstrated that (1) the use of a pre-trained CNN with adequate fine-tuning outperformed or, in the worst case, performed as well as a CNN trained from scratch; (2) fine-tuned CNNs were more robust to the size of training sets than CNNs trained from scratch; (3) neither shallow tuning nor deep tuning was the optimal choice for a particular application; and (4) our layer-wise fine-tuning scheme could offer a practical way to reach the best performance for the application at hand based on the amount of available data.