Concentric tube robots (CTRs) offer dexterous motion at millimeter scales, enabling minimally invasive procedures through natural orifices. This work presents a coordinated model-based resection planner and learning-based retraction network that work together to enable semi-autonomous tissue resection using a dual-arm transurethral concentric tube robot (the Virtuoso). The resection planner operates directly on segmented CT volumes of prostate phantoms, automatically generating tool trajectories for a three-phase median lobe resection workflow: left/median trough resection, right/median trough resection, and median blunt dissection. The retraction network, PushCVAE, trained on surgeon demonstrations, generates retractions according to the procedural phase. The procedure is executed under Level-3 (supervised) autonomy on a prostate phantom composed of hydrogel materials that replicate the mechanical and cutting properties of tissue. As a feasibility study, we demonstrate that our combined autonomous system achieves a 97.1% resection of the targeted volume of the median lobe. Our study establishes a foundation for image-guided autonomy in transurethral robotic surgery and represents a first step toward fully automated minimally-invasive prostate enucleation.

Drug discovery is fundamentally a process of inferring the effects of treatments on patients, and would therefore benefit immensely from computational models that can reliably simulate patient responses, enabling researchers to generate and test large numbers of therapeutic hypotheses safely and economically before initiating costly clinical trials. Even a more specific model that predicts the functional response of cells to a wide range of perturbations would be tremendously valuable for discovering safe and effective treatments that successfully translate to the clinic. Creating such virtual cells has long been a goal of the computational research community that unfortunately remains unachieved given the daunting complexity and scale of cellular biology. Nevertheless, recent advances in AI, computing power, lab automation, and high-throughput cellular profiling provide new opportunities for reaching this goal. In this perspective, we present a vision for developing and evaluating virtual cells that builds on our experience at Recursion. We argue that in order to be a useful tool to discover novel biology, virtual cells must accurately predict the functional response of a cell to perturbations and explain how the predicted response is a consequence of modifications to key biomolecular interactions. We then introduce key principles for designing therapeutically-relevant virtual cells, describe a lab-in-the-loop approach for generating novel insights with them, and advocate for biologically-grounded benchmarks to guide virtual cell development. Finally, we make the case that our approach to virtual cells provides a useful framework for building other models at higher levels of organization, including virtual patients. We hope that these directions prove useful to the research community in developing virtual models optimized for positive impact on drug discovery outcomes.

This work leverages the recent advancements of deep learning in image processing to find optimal locations that present the important characteristics of a field. The data for training are collected at different fields in local farms with five features: aspect, flow accumulation, slope, NDVI (normalized difference vegetation index), and yield. The soil sampling dataset is challenging because the ground truth is highly imbalanced binary images. Therefore, we approached the problem with two methods, the first approach involves utilizing a state-of-the-art model with the convolutional neural network (CNN) backbone, while the second is to innovate a deep-learning design grounded in the concepts of transformer and self-attention. Our framework is constructed with an encoder-decoder architecture with the self-attention mechanism as the backbone. In the encoder, the self-attention mechanism is the key feature extractor, which produces feature maps. In the decoder, we introduce atrous convolution networks to concatenate, fuse the extracted features, and then export the optimal locations for soil sampling. Currently, the model has achieved impressive results on the testing dataset, with a mean accuracy of 99.52%, a mean Intersection over Union (IoU) of 57.35%, and a mean Dice Coefficient of 71.47%, while the performance metrics of the state-of-the-art CNN-based model are 66.08%, 3.85%, and 1.98%, respectively. This indicates that our proposed model outperforms the CNN-based method on the soil-sampling dataset. To the best of our knowledge, our work is the first to provide a soil-sampling dataset with multiple attributes and leverage deep learning techniques to enable the automatic selection of soil-sampling sites. This work lays a foundation for novel applications of data science and machine-learning technologies to solve other emerging agricultural problems.

There has been great progress in unifying various table-to-text tasks using a single encoder-decoder model trained via multi-task learning (Xie et al., 2022). However, existing methods typically encode task information with a simple dataset name as a prefix to the encoder. This not only limits the effectiveness of multi-task learning, but also hinders the model's ability to generalize to new domains or tasks that were not seen during training, which is crucial for real-world applications. In this paper, we propose compositional task configurations, a set of prompts prepended to the encoder to improve cross-task generalization of unified models. We design the task configurations to explicitly specify the task type, as well as its input and output types. We show that this not only allows the model to better learn shared knowledge across different tasks at training, but also allows us to control the model by composing new configurations that apply novel input-output combinations in a zero-shot manner. We demonstrate via experiments over ten table-to-text tasks that our method outperforms the UnifiedSKG baseline by noticeable margins in both in-domain and zero-shot settings, with average improvements of +0.5 and +12.6 from using a T5-large backbone, respectively.

Inhomogeneities in the aortic wall can lead to localized stress accumulations, possibly initiating dissection. In many cases, a dissection results from pathological changes such as fragmentation or loss of elastic fibers. But it has been shown that even the healthy aortic wall has an inherent heterogeneous microstructure. Some parts of the aorta are particularly susceptible to the development of inhomogeneities due to pathological changes, however, the distribution in the aortic wall and the spatial extent, such as size, shape, and type, are difficult to predict. Motivated by this observation, we describe the heterogeneous distribution of elastic fiber degradation in the dissected aortic wall using a stochastic constitutive model. For this purpose, random field realizations, which model the stochastic distribution of degraded elastic fibers, are generated over a non-equidistant grid. The random field then serves as input for a uni-axial extension test of the pathological aortic wall, solved with the finite-element (FE) method. To include the microstructure of the dissected aortic wall, a constitutive model developed in a previous study is applied, which also includes an approach to model the degradation of inter-lamellar elastic fibers. Then to assess the uncertainty in the output stress distribution due to this stochastic constitutive model, a convolutional neural network, specifically a Bayesian encoder-decoder, was used as a surrogate model that maps the random input fields to the output stress distribution obtained from the FE analysis. The results show that the neural network is able to predict the stress distribution of the FE analysis while significantly reducing the computational time. In addition, it provides the probability for exceeding critical stresses within the aortic wall, which could allow for the prediction of delamination or fatal rupture.

We present a novel algorithm that predicts the probability that time derivative of the horizontal component of the ground magnetic field $dB/dt$ exceeds a specified threshold at a given location. This quantity provides important information that is physically relevant to Geomagnetically Induced Currents (GIC), which are electric currents induced by sudden changes of the Earth's magnetic field due to Space Weather events. The model follows a 'gray-box' approach by combining the output of a physics-based model with a machine learning approach. Specifically, we use the University of Michigan's Geospace model, that is operational at the NOAA Space Weather Prediction Center, with a boosted ensemble of classification trees. We discuss in detail the issue of combining a large dataset of ground-based measurements ($\sim$ 20 years) with a limited set of simulation runs ($\sim$ 2 years) by developing a surrogate model for the years in which simulation runs are not available. We also discuss the problem of re-calibrating the output of the decision tree to obtain reliable probabilities. The performance of the model is assessed by typical metrics for probabilistic forecasts: Probability of Detection and False Detection, True Skill Score, Heidke Skill Score, and Receiver Operating Characteristic curve.

This paper proposes a model for an artificial autonomous moral agent (AAMA), which is parsimonious in its ontology and minimal in its ethical assumptions. Starting from a set of moral data, this AAMA is able to learn and develop a form of moral competency. It resembles an “optimizing predictive mind,” which uses moral data (describing typical behavior of humans) and a set of dispositional traits to learn how to classify different actions (given a given background knowledge) as morally right, wrong, or neutral. When confronted with a new situation, this AAMA is supposedly able to predict a behavior consistent with the training set. This paper argues that a promising computational tool that fits our model is “neuroevolution,” i.e. evolving artificial neural networks.