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Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research., Comment: 98 pages

Reinforcement Learning (RL) for control has become increasingly popular due to its ability to learn rich feedback policies that take into account uncertainty and complex representations of the environment. When considering safety constraints, constrained optimization approaches, where agents are penalized for constraint violations, are commonly used. In such methods, if agents are initialized in, or must visit, states where constraint violation might be inevitable, it is unclear how much they should be penalized. We address this challenge by formulating a constraint on the counterfactual harm of the learned policy compared to a default, safe policy. In a philosophical sense this formulation only penalizes the learner for constraint violations that it caused; in a practical sense it maintains feasibility of the optimal control problem. We present simulation studies on a rover with uncertain road friction and a tractor-trailer parking environment that demonstrate our constraint formulation enables agents to learn safer policies than contemporary constrained RL methods.

Recent reinforcement learning approaches have shown surprisingly strong capabilities of bang-bang policies for solving continuous control benchmarks. The underlying coarse action space discretizations often yield favourable exploration characteristics while final performance does not visibly suffer in the absence of action penalization in line with optimal control theory. In robotics applications, smooth control signals are commonly preferred to reduce system wear and energy efficiency, but action costs can be detrimental to exploration during early training. In this work, we aim to bridge this performance gap by growing discrete action spaces from coarse to fine control resolution, taking advantage of recent results in decoupled Q-learning to scale our approach to high-dimensional action spaces up to dim(A) = 38. Our work indicates that an adaptive control resolution in combination with value decomposition yields simple critic-only algorithms that yield surprisingly strong performance on continuous control tasks.

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique "fingerprint" of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy makes the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. We demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.

Rupture of intracranial aneurysms results in severe subarachnoidal hemorrhage, which is associated with high morbidity and mortality. Neurointerventional occlusion of the aneurysm through coiling has evolved to a therapeutical standard. The choice of the specific coil has an important influence on secondary regrowth requiring retreatment. Aneurysm occlusion was simulated either through virtual implantation of a preshaped 3D coil or with a porous media approach. In this study, we used a recently developed numerical approach to simulate aneurysm shapes in specific challenging aneurysm anatomies and correlated these with aneurysm recurrence 6 months after treatment. The simulation showed a great variety of coil shapes depending on the variability in possible microcatheter positions. Aneurysms with a later recurrence showed a tendency for more successful coiling attempts. Results revealed further trends suggesting lower simulated packing densities in aneurysms with reoccurrence. Simulated packing densities did not correlate with those calculated by conventional software, indicating the potential for our approach to offer additional predictive value. Our study, therefore, pioneers a comprehensive numerical model for simulating aneurysm coiling, providing insights into individualized treatment strategies and outcome prediction. Future directions involve expanding the model's capabilities to simulate intraprocedural outcomes and long-term predictions, aiming to refine occlusion quality criteria and validate prediction parameters in larger patient cohorts. This simulation framework holds promise for enhancing clinical decision-making and optimizing patient outcomes in endovascular aneurysm treatment., Comment: 13 pages, 4 figures

Predicting the long-term success of endovascular interventions in the clinical management of cerebral aneurysms requires detailed insight into the patient-specific physiological conditions. In this work, we not only propose numerical representations of endovascular medical devices such as coils, flow diverters or Woven EndoBridge but also outline numerical models for the prediction of blood flow patterns in the aneurysm cavity right after a surgical intervention. Detailed knowledge about the post-surgical state then lays the basis to assess the chances of a stable occlusion of the aneurysm required for a long-term treatment success. To this end, we propose mathematical and mechanical models of endovascular medical devices made out of thin metal wires. These can then be used for fully resolved flow simulations of the post-surgical blood flow, which in this work will be performed by means of a Lattice Boltzmann method applied to the incompressible Navier-Stokes equations and patient-specific geometries. To probe the suitability of homogenized models, we also investigate poro-elastic models to represent such medical devices. In particular, we examine the validity of this modeling approach for flow diverter placement across the opening of the aneurysm cavity. For both approaches, physiologically meaningful boundary conditions are provided from reduced-order models of the vascular system. The present study demonstrates our capabilities to predict the post-surgical state and lays a solid foundation to tackle the prediction of thrombus formation and, thus, the aneurysm occlusion in a next step.

Scene flow estimation is a crucial component in the development of autonomous driving and 3D robotics, providing valuable information for environment perception and navigation. Despite the advantages of learning-based scene flow estimation techniques, their domain specificity and limited generalizability across varied scenarios pose challenges. In contrast, non-learning optimization-based methods, incorporating robust priors or regularization, offer competitive scene flow estimation performance, require no training, and show extensive applicability across datasets, but suffer from lengthy inference times. In this paper, we present OptFlow, a fast optimization-based scene flow estimation method. Without relying on learning or any labeled datasets, OptFlow achieves state-of-the-art performance for scene flow estimation on popular autonomous driving benchmarks. It integrates a local correlation weight matrix for correspondence matching, an adaptive correspondence threshold limit for nearest-neighbor search, and graph prior rigidity constraints, resulting in expedited convergence and improved point correspondence identification. Moreover, we demonstrate how integrating a point cloud registration function within our objective function bolsters accuracy and differentiates between static and dynamic points without relying on external odometry data. Consequently, OptFlow outperforms the baseline graph-prior method by approximately 20% and the Neural Scene Flow Prior method by 5%-7% in accuracy, all while offering the fastest inference time among all non-learning scene flow estimation methods., Comment: Accepted at the proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2024

Accurate image registration is pivotal in biomedical image analysis, where selecting suitable registration algorithms demands careful consideration. While numerous algorithms are available, the evaluation metrics to assess their performance have remained relatively static. This study addresses this challenge by introducing a novel evaluation metric termed Landmark Hit Rate (HitR), which focuses on the clinical relevance of image registration accuracy. Unlike traditional metrics such as Target Registration Error, which emphasize subresolution differences, HitR considers whether registration algorithms successfully position landmarks within defined confidence zones. This paradigm shift acknowledges the inherent annotation noise in medical images, allowing for more meaningful assessments. To equip HitR with label-noise-awareness, we propose defining these confidence zones based on an Inter-rater Variance analysis. Consequently, hit rate curves are computed for varying landmark zone sizes, enabling performance measurement for a task-specific level of accuracy. Our approach offers a more realistic and meaningful assessment of image registration algorithms, reflecting their suitability for clinical and biomedical applications.

Efficiently and accurately translating a corpus into a low-resource language remains a challenge, regardless of the strategies employed, whether manual, automated, or a combination of the two. Many Christian organizations are dedicated to the task of translating the Holy Bible into languages that lack a modern translation. Bible translation (BT) work is currently underway for over 3000 extremely low resource languages. We introduce the eBible corpus: a dataset containing 1009 translations of portions of the Bible with data in 833 different languages across 75 language families. In addition to a BT benchmarking dataset, we introduce model performance benchmarks built on the No Language Left Behind (NLLB) neural machine translation (NMT) models. Finally, we describe several problems specific to the domain of BT and consider how the established data and model benchmarks might be used for future translation efforts. For a BT task trained with NLLB, Austronesian and Trans-New Guinea language families achieve 35.1 and 31.6 BLEU scores respectively, which spurs future innovations for NMT for low-resource languages in Papua New Guinea.

Even though simultaneous optimization of similarity metrics is a standard procedure in the field of semantic segmentation, surprisingly, this is much less established for image registration. To help closing this gap in the literature, we investigate in a complex multi-modal 3D setting whether simultaneous optimization of registration metrics, here implemented by means of primitive summation, can benefit image registration. We evaluate two challenging datasets containing collections of pre- to post-operative and pre- to intra-operative MR images of glioma. Employing the proposed optimization, we demonstrate improved registration accuracy in terms of TRE on expert neuroradiologists' landmark annotations.

While there has been substantial success for solving continuous control with actor-critic methods, simpler critic-only methods such as Q-learning find limited application in the associated high-dimensional action spaces. However, most actor-critic methods come at the cost of added complexity: heuristics for stabilisation, compute requirements and wider hyperparameter search spaces. We show that a simple modification of deep Q-learning largely alleviates these issues. By combining bang-bang action discretization with value decomposition, framing single-agent control as cooperative multi-agent reinforcement learning (MARL), this simple critic-only approach matches performance of state-of-the-art continuous actor-critic methods when learning from features or pixels. We extend classical bandit examples from cooperative MARL to provide intuition for how decoupled critics leverage state information to coordinate joint optimization, and demonstrate surprisingly strong performance across a variety of continuous control tasks.

Experience replay plays a crucial role in improving the sample efficiency of deep reinforcement learning agents. Recent advances in experience replay propose using Mixup (Zhang et al., 2018) to further improve sample efficiency via synthetic sample generation. We build upon this technique with Neighborhood Mixup Experience Replay (NMER), a geometrically-grounded replay buffer that interpolates transitions with their closest neighbors in state-action space. NMER preserves a locally linear approximation of the transition manifold by only applying Mixup between transitions with vicinal state-action features. Under NMER, a given transition's set of state action neighbors is dynamic and episode agnostic, in turn encouraging greater policy generalizability via inter-episode interpolation. We combine our approach with recent off-policy deep reinforcement learning algorithms and evaluate on continuous control environments. We observe that NMER improves sample efficiency by an average 94% (TD3) and 29% (SAC) over baseline replay buffers, enabling agents to effectively recombine previous experiences and learn from limited data., Comment: Accepted to L4DC 2022

Dendritic microstructures are ubiquitous in nature and are the primary solidification morphologies in metallic materials. Techniques such as x-ray computed tomography (XCT) have provided new insights into dendritic phase transformation phenomena. However, manual identification of dendritic morphologies in microscopy data can be both labor intensive and potentially ambiguous. The analysis of 3D datasets is particularly challenging due to their large sizes (terabytes) and the presence of artifacts scattered within the imaged volumes. In this study, we trained 3D convolutional neural networks (CNNs) to segment 3D datasets. Three CNN architectures were investigated, including a new 3D version of FCDense. We show that using hyperparameter optimization (HPO) and fine-tuning techniques, both 2D and 3D CNN architectures can be trained to outperform the previous state of the art. The 3D U-Net architecture trained in this study produced the best segmentations according to quantitative metrics (pixel-wise accuracy of 99.84% and a boundary displacement error of 0.58 pixels), while 3D FCDense produced the smoothest boundaries and best segmentations according to visual inspection. The trained 3D CNNs are able to segment entire 852 x 852 x 250 voxel 3D volumes in only ~60 seconds, thus hastening the progress towards a deeper understanding of phase transformation phenomena such as dendritic solidification.

In most classical Autonomous Vehicle (AV) stacks, the prediction and planning layers are separated, limiting the planner to react to predictions that are not informed by the planned trajectory of the AV. This work presents a module that tightly couples these layers via a game-theoretic Model Predictive Controller (MPC) that uses a novel interactive multi-agent neural network policy as part of its predictive model. In our setting, the MPC planner considers all the surrounding agents by informing the multi-agent policy with the planned state sequence. Fundamental to the success of our method is the design of a novel multi-agent policy network that can steer a vehicle given the state of the surrounding agents and the map information. The policy network is trained implicitly with ground-truth observation data using backpropagation through time and a differentiable dynamics model to roll out the trajectory forward in time. Finally, we show that our multi-agent policy network learns to drive while interacting with the environment, and, when combined with the game-theoretic MPC planner, can successfully generate interactive behaviors., Comment: accepted to L4DC

Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. Quantitative evaluation and ranking were based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency analysis, and test-time instance optimization per-case basis as a post-processing step. The top-ranked method attained the MEE at or below that of the inter-rater variability for approximately 60% of the evaluated landmarks, underscoring the scope for further accuracy and robustness improvements, especially relative to human experts. The aim of BraTS-Reg is to continue to serve as an active resource for research, with the data and online evaluation tools accessible at https://bratsreg.github.io/.

Data-driven simulators promise high data-efficiency for driving policy learning. When used for modelling interactions, this data-efficiency becomes a bottleneck: Small underlying datasets often lack interesting and challenging edge cases for learning interactive driving. We address this challenge by proposing a simulation method that uses in-painted ado vehicles for learning robust driving policies. Thus, our approach can be used to learn policies that involve multi-agent interactions and allows for training via state-of-the-art policy learning methods. We evaluate the approach for learning standard interaction scenarios in driving. In extensive experiments, our work demonstrates that the resulting policies can be directly transferred to a full-scale autonomous vehicle without making use of any traditional sim-to-real transfer techniques such as domain randomization., Comment: The first two authors contributed equally to this this work. Code is available here: http://vista.csail.mit.edu/

Simulation has the potential to transform the development of robust algorithms for mobile agents deployed in safety-critical scenarios. However, the poor photorealism and lack of diverse sensor modalities of existing simulation engines remain key hurdles towards realizing this potential. Here, we present VISTA, an open source, data-driven simulator that integrates multiple types of sensors for autonomous vehicles. Using high fidelity, real-world datasets, VISTA represents and simulates RGB cameras, 3D LiDAR, and event-based cameras, enabling the rapid generation of novel viewpoints in simulation and thereby enriching the data available for policy learning with corner cases that are difficult to capture in the physical world. Using VISTA, we demonstrate the ability to train and test perception-to-control policies across each of the sensor types and showcase the power of this approach via deployment on a full scale autonomous vehicle. The policies learned in VISTA exhibit sim-to-real transfer without modification and greater robustness than those trained exclusively on real-world data., Comment: First two authors contributed equally. Code and project website is available here: https://vista.csail.mit.edu

Reinforcement learning (RL) for continuous control typically employs distributions whose support covers the entire action space. In this work, we investigate the colloquially known phenomenon that trained agents often prefer actions at the boundaries of that space. We draw theoretical connections to the emergence of bang-bang behavior in optimal control, and provide extensive empirical evaluation across a variety of recent RL algorithms. We replace the normal Gaussian by a Bernoulli distribution that solely considers the extremes along each action dimension - a bang-bang controller. Surprisingly, this achieves state-of-the-art performance on several continuous control benchmarks - in contrast to robotic hardware, where energy and maintenance cost affect controller choices. Since exploration, learning,and the final solution are entangled in RL, we provide additional imitation learning experiments to reduce the impact of exploration on our analysis. Finally, we show that our observations generalize to environments that aim to model real-world challenges and evaluate factors to mitigate the emergence of bang-bang solutions. Our findings emphasize challenges for benchmarking continuous control algorithms, particularly in light of potential real-world applications.

The High-Throughput Experimental Materials Database (HTEM-DB) is the endpoint repository for inorganic thin-film materials data collected during combinatorial experiments at the National Renewable Energy Laboratory (NREL). This unique data asset is enabled by the Research Data Infrastructure (RDI) - a set of custom data tools that collect, process, and store experimental data and metadata. Here, we describe the experimental data-tool workflow from the RDI to the HTEM-DB to illustrate the strategies and best practices currently used for materials data at NREL. Integration of these data tools with the experimental processes establishes a data communication pipeline between experimental and data science communities. In doing so, this work motivates the creation of similar data workflows at other institutions to aggregate valuable data and increase its usefulness for future data studies. These types of investments can greatly accelerate the pace of learning and discovery in the materials science field, by making data accessible to new and rapidly evolving data methods.

Learning competitive behaviors in multi-agent settings such as racing requires long-term reasoning about potential adversarial interactions. This paper presents Deep Latent Competition (DLC), a novel reinforcement learning algorithm that learns competitive visual control policies through self-play in imagination. The DLC agent imagines multi-agent interaction sequences in the compact latent space of a learned world model that combines a joint transition function with opponent viewpoint prediction. Imagined self-play reduces costly sample generation in the real world, while the latent representation enables planning to scale gracefully with observation dimensionality. We demonstrate the effectiveness of our algorithm in learning competitive behaviors on a novel multi-agent racing benchmark that requires planning from image observations. Code and videos available at https://sites.google.com/view/deep-latent-competition., Comment: Wilko, Tim, and Igor contributed equally to this work; published in Conference on Robot Learning 2020