Nick Altieri

Nick Altieri, Briton Park, Mara Olson et al.

Precision medicine has the potential to revolutionize healthcare, but much of the data for patients is locked away in unstructured free-text, limiting research and delivery of effective personalized treatments. Generating large annotated datasets for information extraction from clinical notes is often challenging and expensive due to the high level of expertise needed for high quality annotations. To enable natural language processing for small dataset sizes, we develop a novel enriched hierarchical annotation scheme and algorithm, Supervised Line Attention (SLA), and apply this algorithm to predicting categorical tumor attributes from kidney and colon cancer pathology reports from the University of California San Francisco (UCSF). Whereas previous work only annotated document level labels, we in addition ask the annotators to enrich the traditional label by asking them to also highlight the relevant line or potentially lines for the final label, which leads to a 20% increase of annotation time required per document. With the enriched annotations, we develop a simple and interpretable machine learning algorithm that first predicts the relevant lines in the document and then predicts the tumor attribute. Our results show across the small dataset sizes of 32, 64, 128, and 186 labeled documents per cancer, SLA only requires half the number of labeled documents as state-of-the-art methods to achieve similar or better micro-f1 and macro-f1 scores for the vast majority of comparisons that we made. Accounting for the increased annotation time, this leads to a 40% reduction in total annotation time over the state of the art.

Nick Altieri, Rebecca L. Barter, James Duncan et al.

As the COVID-19 outbreak evolves, accurate forecasting continues to play an extremely important role in informing policy decisions. In this paper, we present our continuous curation of a large data repository containing COVID-19 information from a range of sources. We use this data to develop predictions and corresponding prediction intervals for the short-term trajectory of COVID-19 cumulative death counts at the county-level in the United States up to two weeks ahead. Using data from January 22 to June 20, 2020, we develop and combine multiple forecasts using ensembling techniques, resulting in an ensemble we refer to as Combined Linear and Exponential Predictors (CLEP). Our individual predictors include county-specific exponential and linear predictors, a shared exponential predictor that pools data together across counties, an expanded shared exponential predictor that uses data from neighboring counties, and a demographics-based shared exponential predictor. We use prediction errors from the past five days to assess the uncertainty of our death predictions, resulting in generally-applicable prediction intervals, Maximum (absolute) Error Prediction Intervals (MEPI). MEPI achieves a coverage rate of more than 94% when averaged across counties for predicting cumulative recorded death counts two weeks in the future. Our forecasts are currently being used by the non-profit organization, Response4Life, to determine the medical supply need for individual hospitals and have directly contributed to the distribution of medical supplies across the country. We hope that our forecasts and data repository at https://covidseverity.com can help guide necessary county-specific decision-making and help counties prepare for their continued fight against COVID-19.

John D. Co-Reyes, Abhishek Gupta, Suvansh Sanjeev et al.

Behavioral skills or policies for autonomous agents are conventionally learned from reward functions, via reinforcement learning, or from demonstrations, via imitation learning. However, both modes of task specification have their disadvantages: reward functions require manual engineering, while demonstrations require a human expert to be able to actually perform the task in order to generate the demonstration. Instruction following from natural language instructions provides an appealing alternative: in the same way that we can specify goals to other humans simply by speaking or writing, we would like to be able to specify tasks for our machines. However, a single instruction may be insufficient to fully communicate our intent or, even if it is, may be insufficient for an autonomous agent to actually understand how to perform the desired task. In this work, we propose an interactive formulation of the task specification problem, where iterative language corrections are provided to an autonomous agent, guiding it in acquiring the desired skill. Our proposed language-guided policy learning algorithm can integrate an instruction and a sequence of corrections to acquire new skills very quickly. In our experiments, we show that this method can enable a policy to follow instructions and corrections for simulated navigation and manipulation tasks, substantially outperforming direct, non-interactive instruction following.