Yucheng Zhao, Chong Luo, Chuanxin Tang, Dongdong Chen, Noel Codella, Zheng-Jun Zha
Video understanding tasks have traditionally been modeled by two separate architectures, specially tailored for two distinct tasks. Sequence-based video tasks, such as action recognition, use a video backbone to directly extract spatiotemporal features, while frame-based video tasks, such as multiple object tracking (MOT), rely on single fixed-image backbone to extract spatial features. In contrast, we propose to unify video understanding tasks into one novel streaming video architecture, referred to as Streaming Vision Transformer (S-ViT). S-ViT first produces frame-level features with a memory-enabled temporally-aware spatial encoder to serve the frame-based video tasks. Then the frame features are input into a task-related temporal decoder to obtain spatiotemporal features for sequence-based tasks. The efficiency and efficacy of S-ViT is demonstrated by the state-of-the-art accuracy in the sequence-based action recognition task and the competitive advantage over conventional architecture in the frame-based MOT task. We believe that the concept of streaming video model and the implementation of S-ViT are solid steps towards a unified deep learning architecture for video understanding. Code will be available at https://github.com/yuzhms/Streaming-Video-Model.
Pouya Bashivan, Irina Rish, Mohammed Yeasin, Noel Codella
One of the challenges in modeling cognitive events from electroencephalogram (EEG) data is finding representations that are invariant to inter- and intra-subject differences, as well as to inherent noise associated with such data. Herein, we propose a novel approach for learning such representations from multi-channel EEG time-series, and demonstrate its advantages in the context of mental load classification task. First, we transform EEG activities into a sequence of topology-preserving multi-spectral images, as opposed to standard EEG analysis techniques that ignore such spatial information. Next, we train a deep recurrent-convolutional network inspired by state-of-the-art video classification to learn robust representations from the sequence of images. The proposed approach is designed to preserve the spatial, spectral, and temporal structure of EEG which leads to finding features that are less sensitive to variations and distortions within each dimension. Empirical evaluation on the cognitive load classification task demonstrated significant improvements in classification accuracy over current state-of-the-art approaches in this field.
Stephanie L. Hyland, Shruthi Bannur, Kenza Bouzid, Daniel C. Castro, Mercy Ranjit, Anton Schwaighofer, Fernando Pérez-García, Valentina Salvatelli, Shaury Srivastav, Anja Thieme, Noel Codella, Matthew P. Lungren, Maria Teodora Wetscherek, Ozan Oktay, Javier Alvarez-Valle
We present a radiology-specific multimodal model for the task for generating radiological reports from chest X-rays (CXRs). Our work builds on the idea that large language model(s) can be equipped with multimodal capabilities through alignment with pre-trained vision encoders. On natural images, this has been shown to allow multimodal models to gain image understanding and description capabilities. Our proposed model (MAIRA-1) leverages a CXR-specific image encoder in conjunction with a fine-tuned large language model based on Vicuna-7B, and text-based data augmentation, to produce reports with state-of-the-art quality. In particular, MAIRA-1 significantly improves on the radiologist-aligned RadCliQ metric and across all lexical metrics considered. Manual review of model outputs demonstrates promising fluency and accuracy of generated reports while uncovering failure modes not captured by existing evaluation practices. More information and resources can be found on the project website: https://aka.ms/maira.
Noel Codella, Veronica Rotemberg, Philipp Tschandl, M. Emre Celebi, Stephen Dusza, David Gutman, Brian Helba, Aadi Kalloo, Konstantinos Liopyris, Michael Marchetti, Harald Kittler, Allan Halpern
This work summarizes the results of the largest skin image analysis challenge in the world, hosted by the International Skin Imaging Collaboration (ISIC), a global partnership that has organized the world's largest public repository of dermoscopic images of skin. The challenge was hosted in 2018 at the Medical Image Computing and Computer Assisted Intervention (MICCAI) conference in Granada, Spain. The dataset included over 12,500 images across 3 tasks. 900 users registered for data download, 115 submitted to the lesion segmentation task, 25 submitted to the lesion attribute detection task, and 159 submitted to the disease classification task. Novel evaluation protocols were established, including a new test for segmentation algorithm performance, and a test for algorithm ability to generalize. Results show that top segmentation algorithms still fail on over 10% of images on average, and algorithms with equal performance on test data can have different abilities to generalize. This is an important consideration for agencies regulating the growing set of machine learning tools in the healthcare domain, and sets a new standard for future public challenges in healthcare.
Noel Codella, Quoc-Bao Nguyen, Sharath Pankanti, David Gutman, Brian Helba, Allan Halpern, John R. Smith
Melanoma is the deadliest form of skin cancer. While curable with early detection, only highly trained specialists are capable of accurately recognizing the disease. As expertise is in limited supply, automated systems capable of identifying disease could save lives, reduce unnecessary biopsies, and reduce costs. Toward this goal, we propose a system that combines recent developments in deep learning with established machine learning approaches, creating ensembles of methods that are capable of segmenting skin lesions, as well as analyzing the detected area and surrounding tissue for melanoma detection. The system is evaluated using the largest publicly available benchmark dataset of dermoscopic images, containing 900 training and 379 testing images. New state-of-the-art performance levels are demonstrated, leading to an improvement in the area under receiver operating characteristic curve of 7.5% (0.843 vs. 0.783), in average precision of 4% (0.649 vs. 0.624), and in specificity measured at the clinically relevant 95% sensitivity operating point 2.9 times higher than the previous state-of-the-art (36.8% specificity compared to 12.5%). Compared to the average of 8 expert dermatologists on a subset of 100 test images, the proposed system produces a higher accuracy (76% vs. 70.5%), and specificity (62% vs. 59%) evaluated at an equivalent sensitivity (82%).
Veronica Rotemberg, Nicholas Kurtansky, Brigid Betz-Stablein, Liam Caffery, Emmanouil Chousakos, Noel Codella, Marc Combalia, Stephen Dusza, Pascale Guitera, David Gutman, Allan Halpern, Harald Kittler, Kivanc Kose, Steve Langer, Konstantinos Lioprys, Josep Malvehy, Shenara Musthaq, Jabpani Nanda, Ofer Reiter, George Shih, Alexander Stratigos, Philipp Tschandl, Jochen Weber, H. Peter Soyer
Prior skin image datasets have not addressed patient-level information obtained from multiple skin lesions from the same patient. Though artificial intelligence classification algorithms have achieved expert-level performance in controlled studies examining single images, in practice dermatologists base their judgment holistically from multiple lesions on the same patient. The 2020 SIIM-ISIC Melanoma Classification challenge dataset described herein was constructed to address this discrepancy between prior challenges and clinical practice, providing for each image in the dataset an identifier allowing lesions from the same patient to be mapped to one another. This patient-level contextual information is frequently used by clinicians to diagnose melanoma and is especially useful in ruling out false positives in patients with many atypical nevi. The dataset represents 2,056 patients from three continents with an average of 16 lesions per patient, consisting of 33,126 dermoscopic images and 584 histopathologically confirmed melanomas compared with benign melanoma mimickers.
Yunhui Guo, Noel C. Codella, Leonid Karlinsky, James V. Codella, John R. Smith, Kate Saenko, Tajana Rosing, Rogerio Feris
Recent progress on few-shot learning largely relies on annotated data for meta-learning: base classes sampled from the same domain as the novel classes. However, in many applications, collecting data for meta-learning is infeasible or impossible. This leads to the cross-domain few-shot learning problem, where there is a large shift between base and novel class domains. While investigations of the cross-domain few-shot scenario exist, these works are limited to natural images that still contain a high degree of visual similarity. No work yet exists that examines few-shot learning across different imaging methods seen in real world scenarios, such as aerial and medical imaging. In this paper, we propose the Broader Study of Cross-Domain Few-Shot Learning (BSCD-FSL) benchmark, consisting of image data from a diverse assortment of image acquisition methods. This includes natural images, such as crop disease images, but additionally those that present with an increasing dissimilarity to natural images, such as satellite images, dermatology images, and radiology images. Extensive experiments on the proposed benchmark are performed to evaluate state-of-art meta-learning approaches, transfer learning approaches, and newer methods for cross-domain few-shot learning. The results demonstrate that state-of-art meta-learning methods are surprisingly outperformed by earlier meta-learning approaches, and all meta-learning methods underperform in relation to simple fine-tuning by 12.8% average accuracy. Performance gains previously observed with methods specialized for cross-domain few-shot learning vanish in this more challenging benchmark. Finally, accuracy of all methods tend to correlate with dataset similarity to natural images, verifying the value of the benchmark to better represent the diversity of data seen in practice and guiding future research.
Asma Ben Abacha, Alberto Santamaria-Pang, Ho Hin Lee, Jameson Merkow, Qin Cai, Surya Teja Devarakonda, Abdullah Islam, Julia Gong, Matthew P. Lungren, Thomas Lin, Noel C Codella, Ivan Tarapov
The increasing use of medical imaging in healthcare settings presents a significant challenge due to the increasing workload for radiologists, yet it also offers opportunity for enhancing healthcare outcomes if effectively leveraged. 3D image retrieval holds potential to reduce radiologist workloads by enabling clinicians to efficiently search through diagnostically similar or otherwise relevant cases, resulting in faster and more precise diagnoses. However, the field of 3D medical image retrieval is still emerging, lacking established evaluation benchmarks, comprehensive datasets, and thorough studies. This paper attempts to bridge this gap by introducing a novel benchmark for 3D Medical Image Retrieval (3D-MIR) that encompasses four different anatomies imaged with computed tomography. Using this benchmark, we explore a diverse set of search strategies that use aggregated 2D slices, 3D volumes, and multi-modal embeddings from popular multi-modal foundation models as queries. Quantitative and qualitative assessments of each approach are provided alongside an in-depth discussion that offers insight for future research. To promote the advancement of this field, our benchmark, dataset, and code are made publicly available.
Shruthi Bannur, Kenza Bouzid, Daniel C. Castro, Anton Schwaighofer, Anja Thieme, Sam Bond-Taylor, Maximilian Ilse, Fernando Pérez-García, Valentina Salvatelli, Harshita Sharma, Felix Meissen, Mercy Ranjit, Shaury Srivastav, Julia Gong, Noel C. F. Codella, Fabian Falck, Ozan Oktay, Matthew P. Lungren, Maria Teodora Wetscherek, Javier Alvarez-Valle, Stephanie L. Hyland
Radiology reporting is a complex task requiring detailed medical image understanding and precise language generation, for which generative multimodal models offer a promising solution. However, to impact clinical practice, models must achieve a high level of both verifiable performance and utility. We augment the utility of automated report generation by incorporating localisation of individual findings on the image - a task we call grounded report generation - and enhance performance by incorporating realistic reporting context as inputs. We design a novel evaluation framework (RadFact) leveraging the logical inference capabilities of large language models (LLMs) to quantify report correctness and completeness at the level of individual sentences, while supporting the new task of grounded reporting. We develop MAIRA-2, a large radiology-specific multimodal model designed to generate chest X-ray reports with and without grounding. MAIRA-2 achieves state of the art on existing report generation benchmarks and establishes the novel task of grounded report generation.
Noel C. F. Codella, David Gutman, M. Emre Celebi, Brian Helba, Michael A. Marchetti, Stephen W. Dusza, Aadi Kalloo, Konstantinos Liopyris, Nabin Mishra, Harald Kittler, Allan Halpern
This article describes the design, implementation, and results of the latest installment of the dermoscopic image analysis benchmark challenge. The goal is to support research and development of algorithms for automated diagnosis of melanoma, the most lethal skin cancer. The challenge was divided into 3 tasks: lesion segmentation, feature detection, and disease classification. Participation involved 593 registrations, 81 pre-submissions, 46 finalized submissions (including a 4-page manuscript), and approximately 50 attendees, making this the largest standardized and comparative study in this field to date. While the official challenge duration and ranking of participants has concluded, the dataset snapshots remain available for further research and development.
Marc Combalia, Noel C. F. Codella, Veronica Rotemberg, Brian Helba, Veronica Vilaplana, Ofer Reiter, Cristina Carrera, Alicia Barreiro, Allan C. Halpern, Susana Puig, Josep Malvehy
This article summarizes the BCN20000 dataset, composed of 19424 dermoscopic images of skin lesions captured from 2010 to 2016 in the facilities of the Hospital Clínic in Barcelona. With this dataset, we aim to study the problem of unconstrained classification of dermoscopic images of skin cancer, including lesions found in hard-to-diagnose locations (nails and mucosa), large lesions which do not fit in the aperture of the dermoscopy device, and hypo-pigmented lesions. The BCN20000 will be provided to the participants of the ISIC Challenge 2019, where they will be asked to train algorithms to classify dermoscopic images of skin cancer automatically.
Michael Hind, Dennis Wei, Murray Campbell, Noel C. F. Codella, Amit Dhurandhar, Aleksandra Mojsilović, Karthikeyan Natesan Ramamurthy, Kush R. Varshney
Artificial intelligence systems are being increasingly deployed due to their potential to increase the efficiency, scale, consistency, fairness, and accuracy of decisions. However, as many of these systems are opaque in their operation, there is a growing demand for such systems to provide explanations for their decisions. Conventional approaches to this problem attempt to expose or discover the inner workings of a machine learning model with the hope that the resulting explanations will be meaningful to the consumer. In contrast, this paper suggests a new approach to this problem. It introduces a simple, practical framework, called Teaching Explanations for Decisions (TED), that provides meaningful explanations that match the mental model of the consumer. We illustrate the generality and effectiveness of this approach with two different examples, resulting in highly accurate explanations with no loss of prediction accuracy for these two examples.
Newton M. Kinyanjui, Timothy Odonga, Celia Cintas, Noel C. F. Codella, Rameswar Panda, Prasanna Sattigeri, Kush R. Varshney
Recent advances in computer vision and deep learning have led to breakthroughs in the development of automated skin image analysis. In particular, skin cancer classification models have achieved performance higher than trained expert dermatologists. However, no attempt has been made to evaluate the consistency in performance of machine learning models across populations with varying skin tones. In this paper, we present an approach to estimate skin tone in benchmark skin disease datasets, and investigate whether model performance is dependent on this measure. Specifically, we use individual typology angle (ITA) to approximate skin tone in dermatology datasets. We look at the distribution of ITA values to better understand skin color representation in two benchmark datasets: 1) the ISIC 2018 Challenge dataset, a collection of dermoscopic images of skin lesions for the detection of skin cancer, and 2) the SD-198 dataset, a collection of clinical images capturing a wide variety of skin diseases. To estimate ITA, we first develop segmentation models to isolate non-diseased areas of skin. We find that the majority of the data in the the two datasets have ITA values between 34.5° and 48°, which are associated with lighter skin, and is consistent with under-representation of darker skinned populations in these datasets. We also find no measurable correlation between performance of machine learning model and ITA values, though more comprehensive data is needed for further validation.
Noel C. F. Codella, Michael Hind, Karthikeyan Natesan Ramamurthy, Murray Campbell, Amit Dhurandhar, Kush R. Varshney, Dennis Wei, Aleksandra Mojsilovic
The adoption of machine learning in high-stakes applications such as healthcare and law has lagged in part because predictions are not accompanied by explanations comprehensible to the domain user, who often holds the ultimate responsibility for decisions and outcomes. In this paper, we propose an approach to generate such explanations in which training data is augmented to include, in addition to features and labels, explanations elicited from domain users. A joint model is then learned to produce both labels and explanations from the input features. This simple idea ensures that explanations are tailored to the complexity expectations and domain knowledge of the consumer. Evaluation spans multiple modeling techniques on a game dataset, a (visual) aesthetics dataset, a chemical odor dataset and a Melanoma dataset showing that our approach is generalizable across domains and algorithms. Results demonstrate that meaningful explanations can be reliably taught to machine learning algorithms, and in some cases, also improve modeling accuracy.
Noel C. F. Codella, Chung-Ching Lin, Allan Halpern, Michael Hind, Rogerio Feris, John R. Smith
Automated dermoscopic image analysis has witnessed rapid growth in diagnostic performance. Yet adoption faces resistance, in part, because no evidence is provided to support decisions. In this work, an approach for evidence-based classification is presented. A feature embedding is learned with CNNs, triplet-loss, and global average pooling, and used to classify via kNN search. Evidence is provided as both the discovered neighbors, as well as localized image regions most relevant to measuring distance between query and neighbors. To ensure that results are relevant in terms of both label accuracy and human visual similarity for any skill level, a novel hierarchical triplet logic is implemented to jointly learn an embedding according to disease labels and non-expert similarity. Results are improved over baselines trained on disease labels alone, as well as standard multiclass loss. Quantitative relevance of results, according to non-expert similarity, as well as localized image regions, are also significantly improved.
David Gutman, Noel C. F. Codella, Emre Celebi, Brian Helba, Michael Marchetti, Nabin Mishra, Allan Halpern
In this article, we describe the design and implementation of a publicly accessible dermatology image analysis benchmark challenge. The goal of the challenge is to sup- port research and development of algorithms for automated diagnosis of melanoma, a lethal form of skin cancer, from dermoscopic images. The challenge was divided into sub-challenges for each task involved in image analysis, including lesion segmentation, dermoscopic feature detection within a lesion, and classification of melanoma. Training data included 900 images. A separate test dataset of 379 images was provided to measure resultant performance of systems developed with the training data. Ground truth for both training and test sets was generated by a panel of dermoscopic experts. In total, there were 79 submissions from a group of 38 participants, making this the largest standardized and comparative study for melanoma diagnosis in dermoscopic images to date. While the official challenge duration and ranking of participants has concluded, the datasets remain available for further research and development.
Noel C. F. Codella, Daren Anderson, Tyler Philips, Anthony Porto, Kevin Massey, Jane Snowdon, Rogerio Feris, John Smith
This work presents the first segmentation study of both diseased and healthy skin in standard camera photographs from a clinical environment. Challenges arise from varied lighting conditions, skin types, backgrounds, and pathological states. For study, 400 clinical photographs (with skin segmentation masks) representing various pathological states of skin are retrospectively collected from a primary care network. 100 images are used for training and fine-tuning, and 300 are used for evaluation. This distribution between training and test partitions is chosen to reflect the difficulty in amassing large quantities of labeled data in this domain. A deep learning approach is used, and 3 public segmentation datasets of healthy skin are collected to study the potential benefits of pre-training. Two variants of U-Net are evaluated: U-Net and Dense Residual U-Net. We find that Dense Residual U-Nets have a 7.8% improvement in Jaccard, compared to classical U-Net architectures (0.55 vs. 0.51 Jaccard), for direct transfer, where fine-tuning data is not utilized. However, U-Net outperforms Dense Residual U-Net for both direct training (0.83 vs. 0.80) and fine-tuning (0.89 vs. 0.88). The stark performance improvement with fine-tuning compared to direct transfer and direct training emphasizes both the need for adequate representative data of diseased skin, and the utility of other publicly available data sources for this task.
Tassilo Wald, Ibrahim Ethem Hamamci, Yuan Gao, Sam Bond-Taylor, Harshita Sharma, Maximilian Ilse, Cynthia Lo, Olesya Melnichenko, Anton Schwaighofer, Noel C. F. Codella, Maria Teodora Wetscherek, Klaus H. Maier-Hein, Panagiotis Korfiatis, Valentina Salvatelli, Javier Alvarez-Valle, Fernando Pérez-García
Vision-language pre-training, i.e., aligning images with paired text, is a powerful paradigm to create encoders that can be directly used for tasks such as classification, retrieval, and segmentation. In the 3D medical image domain, these capabilities allow vision-language encoders (VLEs) to support radiologists by retrieving patients with similar abnormalities, predicting likelihoods of abnormality, or, with downstream adaptation, generating radiological reports. While the methodology holds promise, data availability and domain-specific hurdles limit the capabilities of current 3D VLEs. In this paper, we overcome these challenges by injecting additional supervision via a report generation objective and combining vision-language with vision-only pre-training. This allows us to leverage both image-only and paired image-text 3D datasets, increasing the total amount of data to which our model is exposed. Through these additional objectives, paired with best practices of the 3D medical imaging domain, we develop the Comprehensive Language-Image Pre-training (COLIPRI) encoder family. Our COLIPRI encoders achieve state-of-the-art performance in report generation, semantic segmentation, classification probing, and zero-shot classification. The model is available at https://huggingface.co/microsoft/colipri.
Noel C. F. Codella, Ying Jin, Shrey Jain, Yu Gu, Ho Hin Lee, Asma Ben Abacha, Alberto Santamaria-Pang, Will Guyman, Naiteek Sangani, Sheng Zhang, Hoifung Poon, Stephanie Hyland, Shruthi Bannur, Javier Alvarez-Valle, Xue Li, John Garrett, Alan McMillan, Gaurav Rajguru, Madhu Maddi, Nilesh Vijayrania, Rehaan Bhimai, Nick Mecklenburg, Rupal Jain, Daniel Holstein, Naveen Gaur, Vijay Aski, Jenq-Neng Hwang, Thomas Lin, Ivan Tarapov, Matthew Lungren, Mu Wei
In this work, we present MedImageInsight, an open-source medical imaging embedding model. MedImageInsight is trained on medical images with associated text and labels across a diverse collection of domains, including X-Ray, CT, MRI, dermoscopy, OCT, fundus photography, ultrasound, histopathology, and mammography. Rigorous evaluations demonstrate MedImageInsight's ability to achieve state-of-the-art (SOTA) or human expert level performance across classification, image-image search, and fine-tuning tasks. Specifically, on public datasets, MedImageInsight achieves SOTA in CT 3D medical image retrieval, as well as SOTA in disease classification and search for chest X-ray, dermatology, and OCT imaging. Furthermore, MedImageInsight achieves human expert performance in bone age estimation (on both public and partner data), as well as AUC above 0.9 in most other domains. When paired with a text decoder, MedImageInsight achieves near SOTA level single image report findings generation with less than 10\% the parameters of other models. Compared to fine-tuning GPT-4o with only MIMIC-CXR data for the same task, MedImageInsight outperforms in clinical metrics, but underperforms on lexical metrics where GPT-4o sets a new SOTA. Importantly for regulatory purposes, MedImageInsight can generate ROC curves, adjust sensitivity and specificity based on clinical need, and provide evidence-based decision support through image-image search (which can also enable retrieval augmented generation). In an independent clinical evaluation of image-image search in chest X-ray, MedImageInsight outperformed every other publicly available foundation model evaluated by large margins (over 6 points AUC), and significantly outperformed other models in terms of AI fairness (across age and gender). We hope releasing MedImageInsight will help enhance collective progress in medical imaging AI research and development.
Zhecan Wang, Long Chen, Haoxuan You, Keyang Xu, Yicheng He, Wenhao Li, Noel Codella, Kai-Wei Chang, Shih-Fu Chang
Vision-language (VL) understanding tasks evaluate models' comprehension of complex visual scenes through multiple-choice questions. However, we have identified two dataset biases that models can exploit as shortcuts to resolve various VL tasks correctly without proper understanding. The first type of dataset bias is \emph{Unbalanced Matching} bias, where the correct answer overlaps the question and image more than the incorrect answers. The second type of dataset bias is \emph{Distractor Similarity} bias, where incorrect answers are overly dissimilar to the correct answer but significantly similar to other incorrect answers within the same sample. To address these dataset biases, we first propose Adversarial Data Synthesis (ADS) to generate synthetic training and debiased evaluation data. We then introduce Intra-sample Counterfactual Training (ICT) to assist models in utilizing the synthesized training data, particularly the counterfactual data, via focusing on intra-sample differentiation. Extensive experiments demonstrate the effectiveness of ADS and ICT in consistently improving model performance across different benchmarks, even in domain-shifted scenarios.