Babenko, Boris
An Operational Deep Learning System for Satellite-Based High-Resolution Global Nowcasting
Agrawal, Shreya, Hassen, Mohammed Alewi, Brempong, Emmanuel Asiedu, Babenko, Boris, Zyda, Fred, Graham, Olivia, Li, Di, Merchant, Samier, Potes, Santiago Hincapie, Russell, Tyler, Cheresnick, Danny, Kakkirala, Aditya Prakash, Rasp, Stephan, Hassidim, Avinatan, Matias, Yossi, Kalchbrenner, Nal, Gupta, Pramod, Hickey, Jason, Bell, Aaron
Precipitation nowcasting, which predicts rainfall up to a few hours ahead, is a critical tool for vulnerable communities in the Global South frequently exposed to intense, rapidly developing storms. Timely forecasts provide a crucial window to protect lives and livelihoods. Traditional numerical weather prediction (NWP) methods suffer from high latency, low spatial and temporal resolution, and significant gaps in accuracy across the world. Recent machine learning-based nowcasting methods, common in the Global North, cannot be extended to the Global South due to extremely sparse radar coverage. We present Global MetNet, an operational global machine learning nowcasting model. It leverages the Global Precipitation Mission's CORRA dataset, geostationary satellite data, and global NWP data to predict precipitation for the next 12 hours. The model operates at a high resolution of approximately 0.05° (~5km) spatially and 15 minutes temporally. Global MetNet significantly outperforms industry-standard hourly forecasts and achieves significantly higher skill, making forecasts useful over a much larger area of the world than previously available. Our model demonstrates better skill in data-sparse regions than even the best high-resolution NWP models achieve in the US. Validated using ground radar and satellite data, it shows significant improvements across key metrics like the critical success index and fractions skill score for all precipitation rates and lead times. Crucially, our model generates forecasts in under a minute, making it readily deployable for real-time applications. It is already deployed for millions of users on Google Search. This work represents a key step in reducing global disparities in forecast quality and integrating sparse, high-resolution satellite observations into weather forecasting.
- North America > United States (1.00)
- Asia > Japan (0.05)
- Asia > East Asia (0.04)
- (16 more...)
PathAlign: A vision-language model for whole slide images in histopathology
Ahmed, Faruk, Sellergren, Andrew, Yang, Lin, Xu, Shawn, Babenko, Boris, Ward, Abbi, Olson, Niels, Mohtashamian, Arash, Matias, Yossi, Corrado, Greg S., Duong, Quang, Webster, Dale R., Shetty, Shravya, Golden, Daniel, Liu, Yun, Steiner, David F., Wulczyn, Ellery
Microscopic interpretation of histopathology images underlies many important diagnostic and treatment decisions. While advances in vision-language modeling raise new opportunities for analysis of such images, the gigapixel-scale size of whole slide images (WSIs) introduces unique challenges. Additionally, pathology reports simultaneously highlight key findings from small regions while also aggregating interpretation across multiple slides, often making it difficult to create robust image-text pairs. As such, pathology reports remain a largely untapped source of supervision in computational pathology, with most efforts relying on region-of-interest annotations or self-supervision at the patch-level. In this work, we develop a vision-language model based on the BLIP-2 framework using WSIs paired with curated text from pathology reports. This enables applications utilizing a shared image-text embedding space, such as text or image retrieval for finding cases of interest, as well as integration of the WSI encoder with a frozen large language model (LLM) for WSI-based generative text capabilities such as report generation or AI-in-the-loop interactions. We utilize a de-identified dataset of over 350,000 WSIs and diagnostic text pairs, spanning a wide range of diagnoses, procedure types, and tissue types. We present pathologist evaluation of text generation and text retrieval using WSI embeddings, as well as results for WSI classification and workflow prioritization (slide-level triaging). Model-generated text for WSIs was rated by pathologists as accurate, without clinically significant error or omission, for 78% of WSIs on average. This work demonstrates exciting potential capabilities for language-aligned WSI embeddings.
- North America > United States > California > San Diego County > San Diego (0.04)
- North America > United States > Maryland > Howard County > Columbia (0.04)
- Research Report > Experimental Study (1.00)
- Research Report > New Finding (0.67)
- Health & Medicine > Therapeutic Area > Dermatology (0.93)
- Health & Medicine > Therapeutic Area > Obstetrics/Gynecology (0.93)
- Health & Medicine > Diagnostic Medicine > Biopsy (0.74)
- Health & Medicine > Therapeutic Area > Oncology > Carcinoma (0.68)
Interdisciplinary Expertise to Advance Equitable Explainable AI
Bennett, Chloe R., Cole-Lewis, Heather, Farquhar, Stephanie, Haamel, Naama, Babenko, Boris, Lang, Oran, Fleck, Mat, Traynis, Ilana, Lau, Charles, Horn, Ivor, Lyles, Courtney
The field of artificial intelligence (AI) is rapidly influencing health and healthcare, but bias and poor performance persists for populations who face widespread structural oppression. Previous work has clearly outlined the need for more rigorous attention to data representativeness and model performance to advance equity and reduce bias. However, there is an opportunity to also improve the explainability of AI by leveraging best practices of social epidemiology and health equity to help us develop hypotheses for associations found. In this paper, we focus on explainable AI (XAI) and describe a framework for interdisciplinary expert panel review to discuss and critically assess AI model explanations from multiple perspectives and identify areas of bias and directions for future research. We emphasize the importance of the interdisciplinary expert panel to produce more accurate, equitable interpretations which are historically and contextually informed. Interdisciplinary panel discussions can help reduce bias, identify potential confounders, and identify opportunities for additional research where there are gaps in the literature. In turn, these insights can suggest opportunities for AI model improvement.
- North America > United States > California > San Francisco County > San Francisco (0.28)
- North America > United States > Massachusetts > Suffolk County > Boston (0.04)
- North America > United States > Illinois > Lake County > Deerfield (0.04)
- (8 more...)
- Research Report > New Finding (0.68)
- Research Report > Experimental Study (0.46)
Using generative AI to investigate medical imagery models and datasets
Lang, Oran, Yaya-Stupp, Doron, Traynis, Ilana, Cole-Lewis, Heather, Bennett, Chloe R., Lyles, Courtney, Lau, Charles, Semturs, Christopher, Webster, Dale R., Corrado, Greg S., Hassidim, Avinatan, Matias, Yossi, Liu, Yun, Hammel, Naama, Babenko, Boris
AI models have shown promise in many medical imaging tasks. However, our ability to explain what signals these models have learned is severely lacking. Explanations are needed in order to increase the trust in AI-based models, and could enable novel scientific discovery by uncovering signals in the data that are not yet known to experts. In this paper, we present a method for automatic visual explanations leveraging team-based expertise by generating hypotheses of what visual signals in the images are correlated with the task. We propose the following 4 steps: (i) Train a classifier to perform a given task (ii) Train a classifier guided StyleGAN-based image generator (StylEx) (iii) Automatically detect and visualize the top visual attributes that the classifier is sensitive towards (iv) Formulate hypotheses for the underlying mechanisms, to stimulate future research. Specifically, we present the discovered attributes to an interdisciplinary panel of experts so that hypotheses can account for social and structural determinants of health. We demonstrate results on eight prediction tasks across three medical imaging modalities: retinal fundus photographs, external eye photographs, and chest radiographs. We showcase examples of attributes that capture clinically known features, confounders that arise from factors beyond physiological mechanisms, and reveal a number of physiologically plausible novel attributes. Our approach has the potential to enable researchers to better understand, improve their assessment, and extract new knowledge from AI-based models. Importantly, we highlight that attributes generated by our framework can capture phenomena beyond physiology or pathophysiology, reflecting the real world nature of healthcare delivery and socio-cultural factors. Finally, we intend to release code to enable researchers to train their own StylEx models and analyze their predictive tasks.
- North America > United States > California > San Francisco County > San Francisco (0.28)
- Europe > United Kingdom (0.28)
- North America > United States > Washington > King County > Seattle (0.14)
- (10 more...)
- Research Report > New Finding (1.00)
- Research Report > Experimental Study (1.00)
- Health & Medicine > Nuclear Medicine (1.00)
- Health & Medicine > Diagnostic Medicine > Imaging (1.00)
- Health & Medicine > Therapeutic Area > Endocrinology > Diabetes (0.69)
Discovering novel systemic biomarkers in photos of the external eye
Babenko, Boris, Traynis, Ilana, Chen, Christina, Singh, Preeti, Uddin, Akib, Cuadros, Jorge, Daskivich, Lauren P., Maa, April Y., Kim, Ramasamy, Kang, Eugene Yu-Chuan, Matias, Yossi, Corrado, Greg S., Peng, Lily, Webster, Dale R., Semturs, Christopher, Krause, Jonathan, Varadarajan, Avinash V., Hammel, Naama, Liu, Yun
External eye photos were recently shown to reveal signs of diabetic retinal disease and elevated HbA1c. In this paper, we evaluate if external eye photos contain information about additional systemic medical conditions. We developed a deep learning system (DLS) that takes external eye photos as input and predicts multiple systemic parameters, such as those related to the liver (albumin, AST); kidney (eGFR estimated using the race-free 2021 CKD-EPI creatinine equation, the urine ACR); bone & mineral (calcium); thyroid (TSH); and blood count (Hgb, WBC, platelets). Development leveraged 151,237 images from 49,015 patients with diabetes undergoing diabetic eye screening in 11 sites across Los Angeles county, CA. Evaluation focused on 9 pre-specified systemic parameters and leveraged 3 validation sets (A, B, C) spanning 28,869 patients with and without diabetes undergoing eye screening in 3 independent sites in Los Angeles County, CA, and the greater Atlanta area, GA. We compared against baseline models incorporating available clinicodemographic variables (e.g. age, sex, race/ethnicity, years with diabetes). Relative to the baseline, the DLS achieved statistically significant superior performance at detecting AST>36, calcium<8.6, eGFR<60, Hgb<11, platelets<150, ACR>=300, and WBC<4 on validation set A (a patient population similar to the development sets), where the AUC of DLS exceeded that of the baseline by 5.2-19.4%. On validation sets B and C, with substantial patient population differences compared to the development sets, the DLS outperformed the baseline for ACR>=300 and Hgb<11 by 7.3-13.2%. Our findings provide further evidence that external eye photos contain important biomarkers of systemic health spanning multiple organ systems. Further work is needed to investigate whether and how these biomarkers can be translated into clinical impact.
- North America > United States > California > Los Angeles County > Los Angeles (0.14)
- North America > United States > Pennsylvania > Philadelphia County > Philadelphia (0.04)
- North America > United States > Illinois > Lake County > Deerfield (0.04)
- (6 more...)
- Research Report > New Finding (1.00)
- Research Report > Experimental Study (1.00)
Poverty Mapping Using Convolutional Neural Networks Trained on High and Medium Resolution Satellite Images, With an Application in Mexico
Babenko, Boris, Hersh, Jonathan, Newhouse, David, Ramakrishnan, Anusha, Swartz, Tom
Mapping the spatial distribution of poverty in developing countries remains an important and costly challenge. These "poverty maps" are key inputs for poverty targeting, public goods provision, political accountability, and impact evaluation, that are all the more important given the geographic dispersion of the remaining bottom billion severely poor individuals. In this paper we train Convolutional Neural Networks (CNNs) to estimate poverty directly from high and medium resolution satellite images. We use both Planet and Digital Globe imagery with spatial resolutions of 3-5 sq. m. and 50 sq. cm. respectively, covering all 2 million sq. km. of Mexico. Benchmark poverty estimates come from the 2014 MCS-ENIGH combined with the 2015 Intercensus and are used to estimate poverty rates for 2,456 Mexican municipalities. CNNs are trained using the 896 municipalities in the 2014 MCS-ENIGH. We experiment with several architectures (GoogleNet, VGG) and use GoogleNet as a final architecture where weights are fine-tuned from ImageNet. We find that 1) the best models, which incorporate satellite-estimated land use as a predictor, explain approximately 57% of the variation in poverty in a validation sample of 10 percent of MCS-ENIGH municipalities; 2) Across all MCS-ENIGH municipalities explanatory power reduces to 44% in a CNN prediction and landcover model; 3) Predicted poverty from the CNN predictions alone explains 47% of the variation in poverty in the validation sample, and 37% over all MCS-ENIGH municipalities; 4) In urban areas we see slight improvements from using Digital Globe versus Planet imagery, which explain 61% and 54% of poverty variation respectively. We conclude that CNNs can be trained end-to-end on satellite imagery to estimate poverty, although there is much work to be done to understand how the training process influences out of sample validation.
- North America > United States > District of Columbia > Washington (0.05)
- North America > United States > California > Santa Clara County > Mountain View (0.05)
- South America (0.05)
- (8 more...)