Understanding cellular responses to chemical interventions is critical to the discovery of effective therapeutics. Because individual biological techniques often measure only one axis of cellular response at a time, high-quality multimodal datasets are needed to unlock a holistic understanding of how cells respond to treatments and to advance computational methods that integrate modalities. However, many techniques destroy cells and thus preclude paired measurements, and attempts to match disparate unimodal datasets are often confounded by data being generated in incompatible experimental settings. Here we introduce scGeneScope, a multimodal single‑cell RNA sequencing (scRNA-seq) and Cell Painting microscopy image dataset conditionally paired by chemical treatment, designed to facilitate the development and benchmarking of unimodal, multimodal, and multiple profile machine learning methods for cellular profiling. 28 chemicals, each acting on distinct biological pathways or mechanisms of action (MoAs), were applied to U2-OS cells in two experimental data generation rounds, creating paired sets of replicates that were then profiled independently by scRNA‑seq or Cell Painting. Using scGeneScope, we derive a replicate- and experiment-split treatment identification benchmark simulating MoA discovery under realistic laboratory variability conditions and evaluate unimodal, multimodal, and multiprofile models ranging in complexity from linear approaches to recent foundation models. Multiprofile integration improved performance in both the unimodal and multimodal settings, with gains more consistent in the former. Evaluation of unimodal models for MoA identification demonstrated that recent scRNA-seq foundation models deployed zero-shot were consistently outperformed by classic fit-to-data methods, underscoring the need for careful, realistic benchmarking in machine learning for biology. We release the scGeneScope dataset and benchmarking code to support further research.

We focus on the problem of how we can enable a robot to collaborate seamlessly with a human partner, specifically in scenarios where preexisting data is sparse. Much prior work in human-robot collaboration uses observational models of humans (i.e. models that treat the robot purely as an observer) to choose the robot’s behavior, but such models do not account for the influence the robot has on the human’s actions, which may lead to inefficient interactions. We instead formulate the problem of optimally choosing a collaborative robot’s behavior based on a conditional model of the human that depends on the robot’s future behavior. First, we propose a novel model-based formulation of conditional behavior prediction that allows the robot to infer the human’s intentions based on its future plan in data-sparse environments. We then show how to utilize a conditional model for proactive goal selection and safe trajectory generation around human collaborators. Finally, we use our proposed proactive controller in a collaborative task with real users to show that it can improve users’ interactions with a robot collaborator quantitatively and qualitatively.

As robots are deployed in human spaces, it is important that they are able to coordinate their actions with the people around them. Part of such coordination involves ensuring that people have a good understanding of how a robot will act in the environment. This can be achieved through explanations of the robot’s policy. Much prior work in explainable AI and RL focuses on generating explanations for single-agent policies, but little has been explored in generating explanations for collaborative policies. In this work, we investigate how to generate multi-agent strategy explanations for human-robot collaboration. We formulate the problem using a generic multi-agent planner, show how to generate visual explanations through strategy-conditioned landmark states and generate textual explanations by giving the landmarks to an LLM. Through a user study, we find that when presented with explanations from our proposed framework, users are able to better explore the full space of strategies and collaborate more efficiently with new robot partners.

Many collaborative human-robot tasks require the robot to stay safe and work efficiently around humans. Since the robot can only stay safe with respect to its own model of the human, we want the robot to learn a good model of the human in order to act both safely and efficiently. This paper studies methods that enable a robot to safely explore the space of a human-robot system to improve the robot's model of the human, which will consequently allow the robot to access a larger state space and better work with the human. In particular, we introduce active exploration under the framework of energy-function based safe control, investigate the effect of different active exploration strategies, and finally analyze the effect of safe active exploration on both analytical and neural network human models.

MOTIVATION: Intra-tumor heterogeneity is one of the key confounding factors in deciphering tumor evolution. Malignant cells exhibit variations in their gene expression, copy numbers and mutation even when originating from a single progenitor cell. Single cell sequencing of tumor cells has recently emerged as a viable option for unmasking the underlying tumor heterogeneity. However, extracting features from single cell genomic data in order to infer their evolutionary trajectory remains computationally challenging due to the extremely noisy and sparse nature of the data. RESULTS: Here we describe 'Dhaka', a variational autoencoder method which transforms single cell genomic data to a reduced dimension feature space that is more efficient in differentiating between (hidden) tumor subpopulations. Our method is general and can be applied to several different types of genomic data including copy number variation from scDNA-Seq and gene expression from scRNA-Seq experiments. We tested the method on synthetic and six single cell cancer datasets where the number of cells ranges from 250 to 6000 for each sample. Analysis of the resulting feature space revealed subpopulations of cells and their marker genes. The features are also able to infer the lineage and/or differentiation trajectory between cells greatly improving upon prior methods suggested for feature extraction and dimensionality reduction of such data. AVAILABILITY AND IMPLEMENTATION: All the datasets used in the paper are publicly available and developed software package and supporting info is available on Github https://github.com/MicrosoftGenomics/Dhaka. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

People frequently face challenging decision-making problems in which outcomes are uncertain or unknown. Artificial intelligence (AI) algorithms exist that can outperform humans at learning such tasks. Thus, there is an opportunity for AI agents to assist people in learning these tasks more effectively. In this work, we use a multi-armed bandit as a controlled setting in which to explore this direction. We pair humans with a selection of agents and observe how well each human-agent team performs. We find that team performance can beat both human and agent performance in isolation. Interestingly, we also find that an agent's performance in isolation does not necessarily correlate with the human-agent team's performance. A drop in agent performance can lead to a disproportionately large drop in team performance, or in some settings can even improve team performance. Pairing a human with an agent that performs slightly better than them can make them perform much better, while pairing them with an agent that performs the same can make them them perform much worse. Further, our results suggest that people have different exploration strategies and might perform better with agents that match their strategy. Overall, optimizing human-agent team performance requires going beyond optimizing agent performance, to understanding how the agent's suggestions will influence human decision-making.

Our goal is for people to be physically comfortable when taking objects from robots. This puts a burden on the robot to hand over the object in such a way that a person can easily reach it, without needing to strain or twist their arm - a way that is conducive to ergonomic human grasping configurations. To achieve this, the robot needs to understand what makes a configuration more or less ergonomic to the person, i.e. their ergonomic cost function. In this work, we formulate learning a person's ergonomic cost as an online estimation problem. The robot can implicitly make queries to the person by handing them objects in different configurations, and gets observations in response about the way they choose to take the object. We compare the performance of both passive and active approaches for solving this problem in simulation, as well as in an in-person user study.

Millirobots are a promising robotic platform for many applications due to their small size and low manufacturing costs. Legged millirobots, in particular, can provide increased mobility in complex environments and improved scaling of obstacles. However, controlling these small, highly dynamic, and underactuated legged systems is difficult. Hand-engineered controllers can sometimes control these legged millirobots, but they have difficulties with dynamic maneuvers and complex terrains. We present an approach for controlling a real-world legged millirobot that is based on learned neural network models. Using less than 17 minutes of data, our method can learn a predictive model of the robot's dynamics that can enable effective gaits to be synthesized on the fly for following user-specified waypoints on a given terrain. Furthermore, by leveraging expressive, high-capacity neural network models, our approach allows for these predictions to be directly conditioned on camera images, endowing the robot with the ability to predict how different terrains might affect its dynamics. This enables sample-efficient and effective learning for locomotion of a dynamic legged millirobot on various terrains, including gravel, turf, carpet, and styrofoam. Videos and further details can be found at https://sites.google.com/view/imageconddyn.

Cloud computing is a new computing paradigm, combining diverse client devices -- PCs, smartphones, sensors, single-function, and embedded -- with computation and data storage in the cloud. As with every advance in computing, programming is a fundamental challenge, as the cloud is a concurrent, distributed system running on unreliable hardware and networks.