Contrastive learning of cell state dynamics in response to perturbations

We introduce DynaCLR, a self-supervised framework for modeling cell dynamics via contrastive learning of representations of time-lapse datasets. Live cell imaging of cells and organelles is widely used to analyze cellular responses to perturbations. Human annotation of dynamic cell states captured by time-lapse perturbation datasets is laborious and prone to bias. DynaCLR integrates single-cell tracking with time-aware contrastive learning to map images of cells at neighboring time points to neighboring embeddings. Mapping the morphological dynamics of cells to a temporally regularized embedding space makes the annotation, classification, clustering, or interpretation of the cell states more quantitative and efficient. We illustrate the features and applications of DynaCLR with the following experiments: analyzing the kinetics of viral infection in human cells, detecting transient changes in cell morphology due to cell division, and mapping the dynamics of organelles due to viral infection. Models trained with DynaCLR consistently achieve $>95\%$ accuracy for infection state classification, enable the detection of transient cell states and reliably embed unseen experiments. DynaCLR provides a flexible framework for comparative analysis of cell state dynamics due to perturbations, such as infection, gene knockouts, and drugs. We provide PyTorch-based implementations of the model training and inference pipeline (https://github.com/mehta-lab/viscy) and a user interface (https://github.com/czbiohub-sf/napari-iohub) for the visualization and annotation of trajectories of cells in the real space and the embedding space.

14 Examples of How LLMs Can Transform Materials Science and Chemistry: A Reflection on a Large Language Model Hackathon

Chemistry and materials science are complex. Recently, there have been great successes in addressing this complexity using data-driven or computational techniques. Yet, the necessity of input structured in very specific forms and the fact that there is an ever-growing number of tools creates usability and accessibility challenges. Coupled with the reality that much data in these disciplines is unstructured, the effectiveness of these tools is limited. Motivated by recent works that indicated that large language models (LLMs) might help address some of these issues, we organized a hackathon event on the applications of LLMs in chemistry, materials science, and beyond. This article chronicles the projects built as part of this hackathon. Participants employed LLMs for various applications, including predicting properties of molecules and materials, designing novel interfaces for tools, extracting knowledge from unstructured data, and developing new educational applications. The diverse topics and the fact that working prototypes could be generated in less than two days highlight that LLMs will profoundly impact the future of our fields. The rich collection of ideas and projects also indicates that the applications of LLMs are not limited to materials science and chemistry but offer potential benefits to a wide range of scientific disciplines.

From Occlusion to Insight: Object Search in Semantic Shelves using Large Language Models

How can a robot efficiently extract a desired object from a shelf when it is fully occluded by other objects? Prior works propose geometric approaches for this problem but do not consider object semantics. Shelves in pharmacies, restaurant kitchens, and grocery stores are often organized such that semantically similar objects are placed close to one another. Can large language models (LLMs) serve as semantic knowledge sources to accelerate robotic mechanical search in semantically arranged environments? With Semantic Spatial Search on Shelves (S^4), we use LLMs to generate affinity matrices, where entries correspond to semantic likelihood of physical proximity between objects. We derive semantic spatial distributions by synthesizing semantics with learned geometric constraints. S^4 incorporates Optical Character Recognition (OCR) and semantic refinement with predictions from ViLD, an open-vocabulary object detection model. Simulation experiments suggest that semantic spatial search reduces the search time relative to pure spatial search by an average of 24% across three domains: pharmacy, kitchen, and office shelves. A manually collected dataset of 100 semantic scenes suggests that OCR and semantic refinement improve object detection accuracy by 35%. Lastly, physical experiments in a pharmacy shelf suggest 47.1% improvement over pure spatial search. Supplementary material can be found at https://sites.google.com/view/s4-rss/home.

Open Arms: Open-Source Arms, Hands & Control

Open Arms is a novel open-source platform of realistic human-like robotic hands and arms hardware with 28 Degree-of-Freedom (DoF), designed to extend the capabilities and accessibility of humanoid robotic grasping and manipulation. The Open Arms framework includes an open SDK and development environment, simulation tools, and application development tools to build and operate Open Arms. This paper describes these hands controls, sensing, mechanisms, aesthetic design, and manufacturing and their real-world applications with a teleoperated nursing robot. From 2015 to 2022, we have designed and established the manufacturing of Open Arms as a low-cost, high functionality robotic arms hardware and software framework to serve both humanoid robot applications and the urgent demand for low-cost prosthetics. Using the techniques of consumer product manufacturing, we set out to define modular, low-cost techniques for approximating the dexterity and sensitivity of human hands. To demonstrate the dexterity and control of our hands, we present a novel Generative Grasping Residual CNN (GGR-CNN) model that can generate robust antipodal grasps from input images of various objects at real-time speeds (22ms). We achieved state-of-the-art accuracy of 92.4% using our model architecture on a standard Cornell Grasping Dataset, which contains a diverse set of household objects.

Design of an Affordable Prosthetic Arm Equipped with Deep Learning Vision-Based Manipulation

Many amputees throughout the world are left with limited options to personally own a prosthetic arm due to the expensive cost, mechanical system complexity, and lack of availability. The three main control methods of prosthetic hands are: (1) body-powered control, (2) extrinsic mechanical control, and (3) myoelectric control. These methods can perform well under a controlled situation but will often break down in clinical and everyday use due to poor robustness, weak adaptability, long-term training, and heavy mental burden during use. This paper lays the complete outline of the design process of an affordable and easily accessible novel prosthetic arm that reduces the cost of prosthetics from $10,000 to $700 on average. The 3D printed prosthetic arm is equipped with a depth camera and closed-loop off-policy deep learning algorithm to help form grasps to the object in view. Current work in reinforcement learning masters only individual skills and is heavily focused on parallel jaw grippers for in-hand manipulation. In order to create generalization, which better performs real-world manipulation, the focus is specifically on using the general framework of Markov Decision Process (MDP) through scalable learning with off-policy algorithms such as deep deterministic policy gradient (DDPG) and to study this question in the context of grasping a prosthetic arm. We were able to achieve a 78% grasp success rate on previously unseen objects and generalize across multiple objects for manipulation tasks. This work will make prosthetics cheaper, easier to use and accessible globally for amputees. Future work includes applying similar approaches to other medical assistive devices where a human is interacting with a machine to complete a task.

A Neuro-Symbolic Humanlike Arm Controller for Sophia the Robot

We outline the design and construction of novel robotic arms using machine perception, convolutional neural networks, and symbolic AI for logical control and affordance indexing. We describe our robotic arms built with a humanlike mechanical configuration and aesthetic, with 28 degrees of freedom, touch sensors, and series elastic actuators. The arms were modelled in Roodle and Gazebo with URDF models, as well as Unity, and implement motion control solutions for solving live games of Baccarat (the casino card game), rock paper scissors, handshaking, and drawing. This includes live interactions with people, incorporating both social control of the hands and facial gestures, and physical inverse kinematics (IK) for grasping and manipulation tasks. The resulting framework is an integral part of the Sophia 2020 alpha platform, which is being used with ongoing research in the authors work with team AHAM, an ANA Avatar Xprize effort towards human-AI hybrid telepresence. These results are available to test on the broadly released Hanson Robotics Sophia 2020 robot platform, for users to try and extend.