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Mark Yatskar

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5 published item(s)

preprint2026arXiv

Self-Driving Datasets: From 20 Million Papers to Nuanced Biomedical Knowledge at Scale

Manually curated biomedical repositories -- spanning bioactivity, genomics, and chemistry -- are expensive to maintain, lag behind primary literature, and discard experimental context, obscuring nuances needed to assess data correctness and coverage. We show that PubMed itself can be autonomously and cost-effectively turned into structured datasets that are larger, more nuanced, and more accurate than the curated databases they replace. We present three coupled contributions: (1) an LLM-based entity-tagging pipeline, grounded in nine biomedical ontologies, that tags 4.5B entities across 19 categories in a 22.5M-paper, 2.5T-token PubMed corpus; (2) hybrid sparse-dense retrieval supporting entity-filtered semantic queries over the tagged corpus; and (3) Starling, a multi-agent deep research system that, given only a natural-language task description, designs precision- and recall-targeted retrieval filters, induces an extraction schema, and emits structured records with nuance-rich fields and supporting passages. Across six tasks -- blood-brain barrier permeability, oral bioavailability, acute toxicity (LD50), gene-disease associations, protein subcellular localization, and chemical reactions -- Starling produces ~6.3M records (91K-3M per task); several are, to our knowledge, the largest public datasets for their property. Frontier-model rejection of our extractions is 0.6-7.7% across tasks, far below error rates we measure on widely used curated counterparts (e.g., 16.5% on BBB_Martins, 7.3% on Bioavailability_Ma). Beyond scale and accuracy, the supporting passages carry nuance tabular databases discard -- e.g., oral bioavailability may depend on fed vs. fasted state. Together, the corpus, retrieval, and agent establish a foundation for AI-driven therapeutic design. Code and datasets: https://github.com/starling-labs/starling.

preprint2020arXiv

Grounded Situation Recognition

We introduce Grounded Situation Recognition (GSR), a task that requires producing structured semantic summaries of images describing: the primary activity, entities engaged in the activity with their roles (e.g. agent, tool), and bounding-box groundings of entities. GSR presents important technical challenges: identifying semantic saliency, categorizing and localizing a large and diverse set of entities, overcoming semantic sparsity, and disambiguating roles. Moreover, unlike in captioning, GSR is straightforward to evaluate. To study this new task we create the Situations With Groundings (SWiG) dataset which adds 278,336 bounding-box groundings to the 11,538 entity classes in the imsitu dataset. We propose a Joint Situation Localizer and find that jointly predicting situations and groundings with end-to-end training handily outperforms independent training on the entire grounding metric suite with relative gains between 8% and 32%. Finally, we show initial findings on three exciting future directions enabled by our models: conditional querying, visual chaining, and grounded semantic aware image retrieval. Code and data available at https://prior.allenai.org/projects/gsr.

preprint2020arXiv

RoboTHOR: An Open Simulation-to-Real Embodied AI Platform

Visual recognition ecosystems (e.g. ImageNet, Pascal, COCO) have undeniably played a prevailing role in the evolution of modern computer vision. We argue that interactive and embodied visual AI has reached a stage of development similar to visual recognition prior to the advent of these ecosystems. Recently, various synthetic environments have been introduced to facilitate research in embodied AI. Notwithstanding this progress, the crucial question of how well models trained in simulation generalize to reality has remained largely unanswered. The creation of a comparable ecosystem for simulation-to-real embodied AI presents many challenges: (1) the inherently interactive nature of the problem, (2) the need for tight alignments between real and simulated worlds, (3) the difficulty of replicating physical conditions for repeatable experiments, (4) and the associated cost. In this paper, we introduce RoboTHOR to democratize research in interactive and embodied visual AI. RoboTHOR offers a framework of simulated environments paired with physical counterparts to systematically explore and overcome the challenges of simulation-to-real transfer, and a platform where researchers across the globe can remotely test their embodied models in the physical world. As a first benchmark, our experiments show there exists a significant gap between the performance of models trained in simulation when they are tested in both simulations and their carefully constructed physical analogs. We hope that RoboTHOR will spur the next stage of evolution in embodied computer vision. RoboTHOR can be accessed at the following link: https://ai2thor.allenai.org/robothor

preprint2016arXiv

Commonly Uncommon: Semantic Sparsity in Situation Recognition

Semantic sparsity is a common challenge in structured visual classification problems; when the output space is complex, the vast majority of the possible predictions are rarely, if ever, seen in the training set. This paper studies semantic sparsity in situation recognition, the task of producing structured summaries of what is happening in images, including activities, objects and the roles objects play within the activity. For this problem, we find empirically that most object-role combinations are rare, and current state-of-the-art models significantly underperform in this sparse data regime. We avoid many such errors by (1) introducing a novel tensor composition function that learns to share examples across role-noun combinations and (2) semantically augmenting our training data with automatically gathered examples of rarely observed outputs using web data. When integrated within a complete CRF-based structured prediction model, the tensor-based approach outperforms existing state of the art by a relative improvement of 2.11% and 4.40% on top-5 verb and noun-role accuracy, respectively. Adding 5 million images with our semantic augmentation techniques gives further relative improvements of 6.23% and 9.57% on top-5 verb and noun-role accuracy.

preprint2010arXiv

For the sake of simplicity: Unsupervised extraction of lexical simplifications from Wikipedia

We report on work in progress on extracting lexical simplifications (e.g., "collaborate" -> "work together"), focusing on utilizing edit histories in Simple English Wikipedia for this task. We consider two main approaches: (1) deriving simplification probabilities via an edit model that accounts for a mixture of different operations, and (2) using metadata to focus on edits that are more likely to be simplification operations. We find our methods to outperform a reasonable baseline and yield many high-quality lexical simplifications not included in an independently-created manually prepared list.