Elena Sizikova

Andrea Kim, Niloufar Saharkhiz, Elena Sizikova et al.

Development of artificial intelligence (AI) techniques in medical imaging requires access to large-scale and diverse datasets for training and evaluation. In dermatology, obtaining such datasets remains challenging due to significant variations in patient populations, illumination conditions, and acquisition system characteristics. In this work, we propose S-SYNTH, the first knowledge-based, adaptable open-source skin simulation framework to rapidly generate synthetic skin, 3D models and digitally rendered images, using an anatomically inspired multi-layer, multi-component skin and growing lesion model. The skin model allows for controlled variation in skin appearance, such as skin color, presence of hair, lesion shape, and blood fraction among other parameters. We use this framework to study the effect of possible variations on the development and evaluation of AI models for skin lesion segmentation, and show that results obtained using synthetic data follow similar comparative trends as real dermatologic images, while mitigating biases and limitations from existing datasets including small dataset size, lack of diversity, and underrepresentation.

Xu Cao, Wenqian Ye, Elena Sizikova et al.

Autism spectrum disorder (ASD) is a lifelong neurodevelopmental disorder with very high prevalence around the world. Research progress in the field of ASD facial analysis in pediatric patients has been hindered due to a lack of well-established baselines. In this paper, we propose the use of the Vision Transformer (ViT) for the computational analysis of pediatric ASD. The presented model, known as ViTASD, distills knowledge from large facial expression datasets and offers model structure transferability. Specifically, ViTASD employs a vanilla ViT to extract features from patients' face images and adopts a lightweight decoder with a Gaussian Process layer to enhance the robustness for ASD analysis. Extensive experiments conducted on standard ASD facial analysis benchmarks show that our method outperforms all of the representative approaches in ASD facial analysis, while the ViTASD-L achieves a new state-of-the-art. Our code and pretrained models are available at https://github.com/IrohXu/ViTASD.

Ajay Subramanian, Elena Sizikova, Najib J. Majaj et al.

What spatial frequency information do humans and neural networks use to recognize objects? In neuroscience, critical band masking is an established tool that can reveal the frequency-selective filters used for object recognition. Critical band masking measures the sensitivity of recognition performance to noise added at each spatial frequency. Existing critical band masking studies show that humans recognize periodic patterns (gratings) and letters by means of a spatial-frequency filter (or "channel") that has a frequency bandwidth of one octave (doubling of frequency). Here, we introduce critical band masking as a task for network-human comparison and test 14 humans and 76 neural networks on 16-way ImageNet categorization in the presence of narrowband noise. We find that humans recognize objects in natural images using the same one-octave-wide channel that they use for letters and gratings, making it a canonical feature of human object recognition. Unlike humans, the neural network channel is very broad, 2-4 times wider than the human channel. Thus, noise at certain high and low frequencies will impair network performance and spare human performance. Adversarial and augmented-image training are commonly used to increase network robustness and shape bias. Does this training align network and human object recognition channels? Three network channel properties (bandwidth, center frequency, peak noise sensitivity) correlate strongly with shape bias (51% variance explained) and robustness of adversarially-trained networks (66% variance explained). Adversarial training increases robustness but expands the channel bandwidth even further beyond the human bandwidth. Thus, critical band masking reveals that the network channel is more than twice as wide as the human channel, and that adversarial training only makes it worse. Networks with narrower channels might be more robust.

Elena Sizikova, Niloufar Saharkhiz, Diksha Sharma et al.

To generate evidence regarding the safety and efficacy of artificial intelligence (AI) enabled medical devices, AI models need to be evaluated on a diverse population of patient cases, some of which may not be readily available. We propose an evaluation approach for testing medical imaging AI models that relies on in silico imaging pipelines in which stochastic digital models of human anatomy (in object space) with and without pathology are imaged using a digital replica imaging acquisition system to generate realistic synthetic image datasets. Here, we release M-SYNTH, a dataset of cohorts with four breast fibroglandular density distributions imaged at different exposure levels using Monte Carlo x-ray simulations with the publicly available Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) toolkit. We utilize the synthetic dataset to analyze AI model performance and find that model performance decreases with increasing breast density and increases with higher mass density, as expected. As exposure levels decrease, AI model performance drops with the highest performance achieved at exposure levels lower than the nominal recommended dose for the breast type.

Pranav Singh, Elena Sizikova, Jacopo Cirrone

Recent advances in deep learning and computer vision have reduced many barriers to automated medical image analysis, allowing algorithms to process label-free images and improve performance. However, existing techniques have extreme computational requirements and drop a lot of performance with a reduction in batch size or training epochs. This paper presents Cross Architectural - Self Supervision (CASS), a novel self-supervised learning approach that leverages Transformer and CNN simultaneously. Compared to the existing state of the art self-supervised learning approaches, we empirically show that CASS-trained CNNs and Transformers across four diverse datasets gained an average of 3.8% with 1% labeled data, 5.9% with 10% labeled data, and 10.13% with 100% labeled data while taking 69% less time. We also show that CASS is much more robust to changes in batch size and training epochs. Notably, one of the test datasets comprised histopathology slides of an autoimmune disease, a condition with minimal data that has been underrepresented in medical imaging. The code is open source and is available on GitHub.

Elena Sizikova, Joshua Vendrow, Xu Cao et al.

Automatic infectious disease classification from images can facilitate needed medical diagnoses. Such an approach can identify diseases, like tuberculosis, which remain under-diagnosed due to resource constraints and also novel and emerging diseases, like monkeypox, which clinicians have little experience or acumen in diagnosing. Avoiding missed or delayed diagnoses would prevent further transmission and improve clinical outcomes. In order to understand and trust neural network predictions, analysis of learned representations is necessary. In this work, we argue that automatic discovery of concepts, i.e., human interpretable attributes, allows for a deep understanding of learned information in medical image analysis tasks, generalizing beyond the training labels or protocols. We provide an overview of existing concept discovery approaches in medical image and computer vision communities, and evaluate representative methods on tuberculosis (TB) prediction and monkeypox prediction tasks. Finally, we propose NMFx, a general NMF formulation of interpretability by concept discovery that works in a unified way in unsupervised, weakly supervised, and supervised scenarios.

Ajay Subramanian, Sara Price, Omkar Kumbhar et al.

The core of everyday tasks like reading and driving is active object recognition. Attempts to model such tasks are currently stymied by the inability to incorporate time. People show a flexible tradeoff between speed and accuracy and this tradeoff is a crucial human skill. Deep neural networks have emerged as promising candidates for predicting peak human object recognition performance and neural activity. However, modeling the temporal dimension i.e., the speed-accuracy tradeoff (SAT), is essential for them to serve as useful computational models for how humans recognize objects. To this end, we here present the first large-scale (148 observers, 4 neural networks, 8 tasks) dataset of the speed-accuracy tradeoff (SAT) in recognizing ImageNet images. In each human trial, a beep, indicating the desired reaction time, sounds at a fixed delay after the image is presented, and observer's response counts only if it occurs near the time of the beep. In a series of blocks, we test many beep latencies, i.e., reaction times. We observe that human accuracy increases with reaction time and proceed to compare its characteristics with the behavior of several dynamic neural networks that are capable of inference-time adaptive computation. Using FLOPs as an analog for reaction time, we compare networks with humans on curve-fit error, category-wise correlation, and curve steepness, and conclude that cascaded dynamic neural networks are a promising model of human reaction time in object recognition tasks.

Elena Sizikova, Xu Cao, Ashia Lewis et al.

Chest computed tomography (CT) imaging adds valuable insight in the diagnosis and management of pulmonary infectious diseases, like tuberculosis (TB). However, due to the cost and resource limitations, only X-ray images may be available for initial diagnosis or follow up comparison imaging during treatment. Due to their projective nature, X-rays images may be more difficult to interpret by clinicians. The lack of publicly available paired X-ray and CT image datasets makes it challenging to train a 3D reconstruction model. In addition, Chest X-ray radiology may rely on different device modalities with varying image quality and there may be variation in underlying population disease spectrum that creates diversity in inputs. We propose shape induction, that is, learning the shape of 3D CT from X-ray without CT supervision, as a novel technique to incorporate realistic X-ray distributions during training of a reconstruction model. Our experiments demonstrate that this process improves both the perceptual quality of generated CT and the accuracy of down-stream classification of pulmonary infectious diseases.

Kun Tang, Xu Cao, Zhipeng Cao et al.

Nowadays, autonomous vehicle technology is becoming more and more mature. Critical to progress and safety, high-definition (HD) maps, a type of centimeter-level map collected using a laser sensor, provide accurate descriptions of the surrounding environment. The key challenge of HD map production is efficient, high-quality collection and annotation of large-volume datasets. Due to the demand for high quality, HD map production requires significant manual human effort to create annotations, a very time-consuming and costly process for the map industry. In order to reduce manual annotation burdens, many artificial intelligence (AI) algorithms have been developed to pre-label the HD maps. However, there still exists a large gap between AI algorithms and the traditional manual HD map production pipelines in accuracy and robustness. Furthermore, it is also very resource-costly to build large-scale annotated datasets and advanced machine learning algorithms for AI-based HD map automatic labeling systems. In this paper, we introduce the Tencent HD Map AI (THMA) system, an innovative end-to-end, AI-based, active learning HD map labeling system capable of producing and labeling HD maps with a scale of hundreds of thousands of kilometers. In THMA, we train AI models directly from massive HD map datasets via supervised, self-supervised, and weakly supervised learning to achieve high accuracy and efficiency required by downstream users. THMA has been deployed by the Tencent Map team to provide services to downstream companies and users, serving over 1,000 labeling workers and producing more than 30,000 kilometers of HD map data per day at most. More than 90 percent of the HD map data in Tencent Map is labeled automatically by THMA, accelerating the traditional HD map labeling process by more than ten times.

Christopher Wiedeman, Anastasiia Sarmakeeva, Elena Sizikova et al.

One of the key impediments for developing and assessing robust medical imaging algorithms is limited access to large-scale datasets with suitable annotations. Synthetic data generated with plausible physical and biological constraints may address some of these data limitations. We propose the use of physics simulations to generate synthetic images with pixel-level segmentation annotations, which are notoriously difficult to obtain. Specifically, we apply this approach to breast imaging analysis and release T-SYNTH, a large-scale open-source dataset of paired 2D digital mammography (DM) and 3D digital breast tomosynthesis (DBT) images. Our initial experimental results indicate that T-SYNTH images show promise for augmenting limited real patient datasets for detection tasks in DM and DBT. Our data and code are publicly available at https://github.com/DIDSR/tsynth-release.

Huy V. Vo, Elena Sizikova, Cordelia Schmid et al.

Existing approaches to unsupervised object discovery (UOD) do not scale up to large datasets without approximations that compromise their performance. We propose a novel formulation of UOD as a ranking problem, amenable to the arsenal of distributed methods available for eigenvalue problems and link analysis. Through the use of self-supervised features, we also demonstrate the first effective fully unsupervised pipeline for UOD. Extensive experiments on COCO and OpenImages show that, in the single-object discovery setting where a single prominent object is sought in each image, the proposed LOD (Large-scale Object Discovery) approach is on par with, or better than the state of the art for medium-scale datasets (up to 120K images), and over 37% better than the only other algorithms capable of scaling up to 1.7M images. In the multi-object discovery setting where multiple objects are sought in each image, the proposed LOD is over 14% better in average precision (AP) than all other methods for datasets ranging from 20K to 1.7M images. Using self-supervised features, we also show that the proposed method obtains state-of-the-art UOD performance on OpenImages. Our code is publicly available at https://github.com/huyvvo/LOD.

Elena Sizikova, Andreu Badal, Jana G. Delfino et al.

A key challenge for the development and deployment of artificial intelligence (AI) solutions in radiology is solving the associated data limitations. Obtaining sufficient and representative patient datasets with appropriate annotations may be burdensome due to high acquisition cost, safety limitations, patient privacy restrictions or low disease prevalence rates. In silico data offers a number of potential advantages to patient data, such as diminished patient harm, reduced cost, simplified data acquisition, scalability, improved quality assurance testing, and a mitigation approach to data imbalances. We summarize key research trends and practical uses for synthetically generated data for radiological applications of AI. Specifically, we discuss different types of techniques for generating synthetic examples, their main application areas, and related quality control assessment issues. We also discuss current approaches for evaluating synthetic imaging data. Overall, synthetic data holds great promise in addressing current data availability gaps, but additional work is needed before its full potential is realized.

Ghada Zamzmi, Adarsh Subbaswamy, Elena Sizikova et al.

Although interest in synthetic medical data (SMD) for training and testing AI methods is growing, the absence of a standardized framework to evaluate its quality and applicability hinders its wider adoption. Here, we outline an evaluation framework designed to meet the unique requirements of medical applications, and introduce SMD Card, which can serve as comprehensive reports that accompany artificially generated datasets. This card provides a transparent and standardized framework for evaluating and reporting the quality of synthetic data, which can benefit SMD developers, users, and regulators, particularly for AI models using SMD in regulatory submissions.

Jamie Haddock, Lara Kassab, Sixian Li et al.

We propose new semi-supervised nonnegative matrix factorization (SSNMF) models for document classification and provide motivation for these models as maximum likelihood estimators. The proposed SSNMF models simultaneously provide both a topic model and a model for classification, thereby offering highly interpretable classification results. We derive training methods using multiplicative updates for each new model, and demonstrate the application of these models to single-label and multi-label document classification, although the models are flexible to other supervised learning tasks such as regression. We illustrate the promise of these models and training methods on document classification datasets (e.g., 20 Newsgroups, Reuters).

Ashia Lewis, Evanjelin Mahmoodi, Yuyue Zhou et al.

The evaluation of infectious disease processes on radiologic images is an important and challenging task in medical image analysis. Pulmonary infections can often be best imaged and evaluated through computed tomography (CT) scans, which are often not available in low-resource environments and difficult to obtain for critically ill patients. On the other hand, X-ray, a different type of imaging procedure, is inexpensive, often available at the bedside and more widely available, but offers a simpler, two dimensional image. We show that by relying on a model that learns to generate CT images from X-rays synthetically, we can improve the automatic disease classification accuracy and provide clinicians with a different look at the pulmonary disease process. Specifically, we investigate Tuberculosis (TB), a deadly bacterial infectious disease that predominantly affects the lungs, but also other organ systems. We show that relying on synthetically generated CT improves TB identification by 7.50% and distinguishes TB properties up to 12.16% better than the X-ray baseline.

Omkar Kumbhar, Elena Sizikova, Najib Majaj et al.

Neural networks today often recognize objects as well as people do, and thus might serve as models of the human recognition process. However, most such networks provide their answer after a fixed computational effort, whereas human reaction time varies, e.g. from 0.2 to 10 s, depending on the properties of stimulus and task. To model the effect of difficulty on human reaction time, we considered a classification network that uses early-exit classifiers to make anytime predictions. Comparing human and MSDNet accuracy in classifying CIFAR-10 images in added Gaussian noise, we find that the network equivalent input noise SD is 15 times higher than human, and that human efficiency is only 0.6\% that of the network. When appropriate amounts of noise are present to bring the two observers (human and network) into the same accuracy range, they show very similar dependence on duration or FLOPS, i.e. very similar speed-accuracy tradeoff. We conclude that Anytime classification (i.e. early exits) is a promising model for human reaction time in recognition tasks.

Fangyin Wei, Elena Sizikova, Avneesh Sud et al.

Many applications in 3D shape design and augmentation require the ability to make specific edits to an object's semantic parameters (e.g., the pose of a person's arm or the length of an airplane's wing) while preserving as much existing details as possible. We propose to learn a deep network that infers the semantic parameters of an input shape and then allows the user to manipulate those parameters. The network is trained jointly on shapes from an auxiliary synthetic template and unlabeled realistic models, ensuring robustness to shape variability while relieving the need to label realistic exemplars. At testing time, edits within the parameter space drive deformations to be applied to the original shape, which provides semantically-meaningful manipulation while preserving the details. This is in contrast to prior methods that either use autoencoders with a limited latent-space dimensionality, failing to preserve arbitrary detail, or drive deformations with purely-geometric controls, such as cages, losing the ability to update local part regions. Experiments with datasets of chairs, airplanes, and human bodies demonstrate that our method produces more natural edits than prior work.

Jamie Haddock, Lara Kassab, Sixian Li et al.

We propose several new models for semi-supervised nonnegative matrix factorization (SSNMF) and provide motivation for SSNMF models as maximum likelihood estimators given specific distributions of uncertainty. We present multiplicative updates training methods for each new model, and demonstrate the application of these models to classification, although they are flexible to other supervised learning tasks. We illustrate the promise of these models and training methods on both synthetic and real data, and achieve high classification accuracy on the 20 Newsgroups dataset.

Sahar Siddiqui, Elena Sizikova, Gemma Roig et al.

Scene text recognition models have advanced greatly in recent years. Inspired by human reading we characterize two important scene text recognition models by measuring their domains i.e. the range of stimulus images that they can read. The domain specifies the ability of readers to generalize to different word lengths, fonts, and amounts of occlusion. These metrics identify strengths and weaknesses of existing models. Relative to the attention-based (Attn) model, we discover that the connectionist temporal classification (CTC) model is more robust to noise and occlusion, and better at generalizing to different word lengths. Further, we show that in both models, adding noise to training images yields better generalization to occlusion. These results demonstrate the value of testing models till they break, complementing the traditional data science focus on optimizing performance.

Miju Ahn, Nicole Eikmeier, Jamie Haddock et al.

There is currently an unprecedented demand for large-scale temporal data analysis due to the explosive growth of data. Dynamic topic modeling has been widely used in social and data sciences with the goal of learning latent topics that emerge, evolve, and fade over time. Previous work on dynamic topic modeling primarily employ the method of nonnegative matrix factorization (NMF), where slices of the data tensor are each factorized into the product of lower-dimensional nonnegative matrices. With this approach, however, information contained in the temporal dimension of the data is often neglected or underutilized. To overcome this issue, we propose instead adopting the method of nonnegative CANDECOMP/PARAPAC (CP) tensor decomposition (NNCPD), where the data tensor is directly decomposed into a minimal sum of outer products of nonnegative vectors, thereby preserving the temporal information. The viability of NNCPD is demonstrated through application to both synthetic and real data, where significantly improved results are obtained compared to those of typical NMF-based methods. The advantages of NNCPD over such approaches are studied and discussed. To the best of our knowledge, this is the first time that NNCPD has been utilized for the purpose of dynamic topic modeling, and our findings will be transformative for both applications and further developments.