Human-Assisted Continual Robot Learning with Foundation Models

Large Language Models (LLMs) have been shown to act like planners that can decompose high-level instructions into a sequence of executable instructions. However, current LLM-based planners are only able to operate with a fixed set of skills. We overcome this critical limitation and present a method for using LLM-based planners to query new skills and teach robots these skills in a data and time-efficient manner for rigid object manipulation. Our system can re-use newly acquired skills for future tasks, demonstrating the potential of open world and lifelong learning. We evaluate the proposed framework on multiple tasks in simulation and the real world. Videos are available at: https://sites.google.com/mit.edu/halp-robot-learning

MIRA: Mental Imagery for Robotic Affordances

Humans form mental images of 3D scenes to support counterfactual imagination, planning, and motor control. Our abilities to predict the appearance and affordance of the scene from previously unobserved viewpoints aid us in performing manipulation tasks (e.g., 6-DoF kitting) with a level of ease that is currently out of reach for existing robot learning frameworks. In this work, we aim to build artificial systems that can analogously plan actions on top of imagined images. To this end, we introduce Mental Imagery for Robotic Affordances (MIRA), an action reasoning framework that optimizes actions with novel-view synthesis and affordance prediction in the loop. Given a set of 2D RGB images, MIRA builds a consistent 3D scene representation, through which we synthesize novel orthographic views amenable to pixel-wise affordances prediction for action optimization. We illustrate how this optimization process enables us to generalize to unseen out-of-plane rotations for 6-DoF robotic manipulation tasks given a limited number of demonstrations, paving the way toward machines that autonomously learn to understand the world around them for planning actions.Comment: CoRL 2022, webpage: https://yenchenlin.me/mir

Kinetic and Structural Investigations of Novel Inhibitors of Human Epithelial 15-Lipoxygenase-2

Human epithelial 15-lipoxygenase-2 (h15-LOX-2, ALOX15B) is expressed in many tissues and has been implicated in atherosclerosis, cystic fibrosis and ferroptosis. However, there are few reported potent/selective inhibitors that are active ex vivo. In the current work, we report newly discovered molecules that are more potent and structurally distinct from our previous inhibitors, MLS000545091 and MLS000536924 (Jameson et al, PLoS One, 2014, 9, e104094), in that they contain a central imidazole ring, which is substituted at the 1-position with a phenyl moiety and with a benzylthio moiety at the 2-position. The initial three molecules were mixed-type, non-reductive inhibitors, with IC(50) values of 0.34 ± 0.05 μM for MLS000327069, 0.53 ± 0.04 μM for MLS000327186 and 0.87 ± 0.06 μM for MLS000327206 and greater than 50-fold selectivity versus h5-LOX, h12-LOX, h15-LOX-1, COX-1 and COX-2. A small set of focused analogs was synthesized to demonstrate the validity of the hits. In addition, a binding model was developed for the three imidazole inhibitors based on computational docking and a co-structure of h15-LOX-2 with MLS000536924. Hydrogen/deuterium exchange (HDX) results indicate a similar binding mode between MLS000536924 and MLS000327069, however, the latter restricts protein motion of helix-α2 more, consistent with its greater potency. Given these results, we designed, docked, and synthesized novel inhibitors of the imidazole scaffold and confirmed our binding mode hypothesis. Importantly, four of the five inhibitors mentioned above are active in an h15-LOX-2/HEK293 cell assay and thus they could be important tool compounds in gaining a better understanding of h15-LOX-2’s role in human biology. As such, a suite of similar pharmacophores that target h15-LOX-2 both in vitro and ex vivo are presented in the hope of developing them as therapeutic agents

Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions

Item does not contain fulltextMicroscale thermophoresis (MST) allows for quantitative analysis of protein interactions in free solution and with low sample consumption. The technique is based on thermophoresis, the directed motion of molecules in temperature gradients. Thermophoresis is highly sensitive to all types of binding-induced changes of molecular properties, be it in size, charge, hydration shell or conformation. In an all-optical approach, an infrared laser is used for local heating, and molecule mobility in the temperature gradient is analyzed via fluorescence. In standard MST one binding partner is fluorescently labeled. However, MST can also be performed label-free by exploiting intrinsic protein UV-fluorescence. Despite the high molecular weight ratio, the interaction of small molecules and peptides with proteins is readily accessible by MST. Furthermore, MST assays are highly adaptable to fit to the diverse requirements of different biomolecules, such as membrane proteins to be stabilized in solution. The type of buffer and additives can be chosen freely. Measuring is even possible in complex bioliquids like cell lysate allowing close to in vivo conditions without sample purification. Binding modes that are quantifiable via MST include dimerization, cooperativity and competition. Thus, its flexibility in assay design qualifies MST for analysis of biomolecular interactions in complex experimental settings, which we herein demonstrate by addressing typically challenging types of binding events from various fields of life science

Risks to Birds Traded for African Traditional Medicine: A Quantitative Assessment

Few regional or continent-wide assessments of bird use for traditional medicine have been attempted anywhere in the world. Africa has the highest known diversity of bird species used for this purpose. This study assesses the vulnerability of 354 bird species used for traditional medicine in 25 African countries, from 205 genera, 70 families, and 25 orders. The orders most represented were Passeriformes (107 species), Falconiformes (45 species), and Coraciiformes (24 species), and the families Accipitridae (37 species), Ardeidae (15 species), and Bucerotidae (12 species). The Barn owl (Tyto alba) was the most widely sold species (seven countries). The similarity of avifaunal orders traded is high (analogous to ‘‘morphospecies’’, and using Sørensen’s index), which suggests opportunities for a common understanding of cultural factors driving demand. The highest similarity was between bird orders sold in markets of Benin vs. Burkina Faso (90%), but even bird orders sold in two geographically separated countries (Benin vs. South Africa and Nigeria vs. South Africa) were 87% and 81% similar, respectively. Rabinowitz’s ‘‘7 forms of rarity’’ model, used to group species according to commonness or rarity, indicated that 24% of traded bird species are very common, locally abundant in several habitats, and occur over a large geographical area, but 10% are rare, occur in low numbers in specific habitats, and over a small geographical area. The order with the highest proportion of rare species was the Musophagiformes. An analysis of species mass (as a proxy for size) indicated that large and/or conspicuous species tend to be targeted by harvesters for the traditional medicine trade. Furthermore, based on cluster analyses for species groups of similar risk, vultures, hornbills, and other large avifauna, such as bustards, are most threatened by selective harvesting and should be prioritised for conservation action.University of the Witwatersrand SPARC Prestigious and URC Postdoctoral Fellowships; National Research Foundatio

Advancing Biological Understanding and Therapeutics Discovery with Small-Molecule Probes

Small-molecule probes can illuminate biological processes and aid in the assessment of emerging therapeutic targets by perturbing biological systems in a manner distinct from other experimental approaches. Despite the tremendous promise of chemical tools for investigating biology and disease, small-molecule probes were unavailable for most targets and pathways as recently as a decade ago. In 2005, the U.S. National Institutes of Health launched the decade-long Molecular Libraries Program with the intent of innovating in and broadening access to small-molecule science. This Perspective describes how novel small-molecule probes identified through the program are enabling the exploration of biological pathways and therapeutic hypotheses not otherwise testable. These experiences illustrate how small-molecule probes can help bridge the chasm between biological research and the development of medicines, but also highlight the need to innovate the science of therapeutic discovery.Chemistry and Chemical Biolog

A Long Horizon Planning Framework for Manipulating Rigid Pointcloud Objects

We present a framework for solving long-horizon planning problems involving manipulation of rigid objects that operates directly from a point-cloud observation, i.e. without prior object models. Our method plans in the space of object subgoals and frees the planner from reasoning about robot-object interaction dynamics by relying on a set of generalizable manipulation primitives. We show that for rigid bodies, this abstraction can be realized using low-level manipulation skills that maintain sticking contact with the object and represent subgoals as 3D transformations. To enable generalization to unseen objects and improve planning performance, we propose a novel way of representing subgoals for rigid-body manipulation and a graph-attention based neural network architecture for processing point-cloud inputs. We experimentally validate these choices using simulated and real-world experiments on the YuMi robot. Results demonstrate that our method can successfully manipulate new objects into target configurations requiring long-term planning. Overall, our framework realizes the best of the worlds of task-and-motion planning (TAMP) and learning-based approaches.S.M