A Library for Learning Neural Operators

We present NeuralOperator, an open-source Python library for operator learning. Neural operators generalize neural networks to maps between function spaces instead of finite-dimensional Euclidean spaces. They can be trained and inferenced on input and output functions given at various discretizations, satisfying a discretization convergence properties. Built on top of PyTorch, NeuralOperator provides all the tools for training and deploying neural operator models, as well as developing new ones, in a high-quality, tested, open-source package. It combines cutting-edge models and customizability with a gentle learning curve and simple user interface for newcomers.

Sequential Controlled Langevin Diffusions

An effective approach for sampling from unnormalized densities is based on the idea of gradually transporting samples from an easy prior to the complicated target distribution. Two popular methods are (1) Sequential Monte Carlo (SMC), where the transport is performed through successive annealed densities via prescribed Markov chains and resampling steps, and (2) recently developed diffusion-based sampling methods, where a learned dynamical transport is used. Despite the common goal, both approaches have different, often complementary, advantages and drawbacks. The resampling steps in SMC allow focusing on promising regions of the space, often leading to robust performance. While the algorithm enjoys asymptotic guarantees, the lack of flexible, learnable transitions can lead to slow convergence. On the other hand, diffusion-based samplers are learned and can potentially better adapt themselves to the target at hand, yet often suffer from training instabilities. In this work, we present a principled framework for combining SMC with diffusion-based samplers by viewing both methods in continuous time and considering measures on path space. This culminates in the new Sequential Controlled Langevin Diffusion (SCLD) sampling method, which is able to utilize the benefits of both methods and reaches improved performance on multiple benchmark problems, in many cases using only 10% of the training budget of previous diffusion-based samplers.

Automating Feedback Analysis in Surgical Training: Detection, Categorization, and Assessment

This work introduces the first framework for reconstructing surgical dialogue from unstructured real-world recordings, which is crucial for characterizing teaching tasks. In surgical training, the formative verbal feedback that trainers provide to trainees during live surgeries is crucial for ensuring safety, correcting behavior immediately, and facilitating long-term skill acquisition. However, analyzing and quantifying this feedback is challenging due to its unstructured and specialized nature. Automated systems are essential to manage these complexities at scale, allowing for the creation of structured datasets that enhance feedback analysis and improve surgical education. Our framework integrates voice activity detection, speaker diarization, and automated speech recaognition, with a novel enhancement that 1) removes hallucinations (non-existent utterances generated during speech recognition fueled by noise in the operating room) and 2) separates speech from trainers and trainees using few-shot voice samples. These aspects are vital for reconstructing accurate surgical dialogues and understanding the roles of operating room participants. Using data from 33 real-world surgeries, we demonstrated the system's capability to reconstruct surgical teaching dialogues and detect feedback instances effectively (F1 score of 0.79+/-0.07). Moreover, our hallucination removal step improves feedback detection performance by ~14%. Evaluation on downstream clinically relevant tasks of predicting Behavioral Adjustment of trainees and classifying Technical feedback, showed performances comparable to manual annotations with F1 scores of 0.82+/0.03 and 0.81+/0.03 respectively. These results highlight the effectiveness of our framework in supporting clinically relevant tasks and improving over manual methods.

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein language models (pLM) training on hundreds of graphical processing units (GPUs). We introduce the BioNeMo Framework to facilitate the training of computational biology and chemistry AI models across hundreds of GPUs. Its modular design allows the integration of individual components, such as data loaders, into existing workflows and is open to community contributions. We detail technical features of the BioNeMo Framework through use cases such as pLM pre-training and fine-tuning. On 256 NVIDIA A100s, BioNeMo Framework trains a three billion parameter BERT-based pLM on over one trillion tokens in 4.2 days. The BioNeMo Framework is open-source and free for everyone to use.

LeanAgent: Lifelong Learning for Formal Theorem Proving

Large Language Models (LLMs) have been successful in mathematical reasoning tasks such as formal theorem proving when integrated with interactive proof assistants like Lean. Existing approaches involve training or fine-tuning an LLM on a specific dataset to perform well on particular domains, such as undergraduate-level mathematics. These methods struggle with generalizability to advanced mathematics. A fundamental limitation is that these approaches operate on static domains, failing to capture how mathematicians often work across multiple domains and projects simultaneously or cyclically. We present LeanAgent, a novel lifelong learning framework for theorem proving that continuously generalizes to and improves on ever-expanding mathematical knowledge without forgetting previously learned knowledge. LeanAgent introduces several key innovations, including a curriculum learning strategy that optimizes the learning trajectory in terms of mathematical difficulty, a dynamic database for efficient management of evolving mathematical knowledge, and progressive training to balance stability and plasticity. LeanAgent successfully proves 162 theorems previously unproved by humans across 23 diverse Lean repositories, many from advanced mathematics. It performs up to 11$\times$ better than the static LLM baseline, proving challenging theorems in domains like abstract algebra and algebraic topology while showcasing a clear progression of learning from basic concepts to advanced topics. In addition, we analyze LeanAgent's superior performance on key lifelong learning metrics. LeanAgent achieves exceptional scores in stability and backward transfer, where learning new tasks improves performance on previously learned tasks. This emphasizes LeanAgent's continuous generalizability and improvement, explaining its superior theorem proving performance.

Diffusion State-Guided Projected Gradient for Inverse Problems

Recent advancements in diffusion models have been effective in learning data priors for solving inverse problems. They leverage diffusion sampling steps for inducing a data prior while using a measurement guidance gradient at each step to impose data consistency. For general inverse problems, approximations are needed when an unconditionally trained diffusion model is used since the measurement likelihood is intractable, leading to inaccurate posterior sampling. In other words, due to their approximations, these methods fail to preserve the generation process on the data manifold defined by the diffusion prior, leading to artifacts in applications such as image restoration. To enhance the performance and robustness of diffusion models in solving inverse problems, we propose Diffusion State-Guided Projected Gradient (DiffStateGrad), which projects the measurement gradient onto a subspace that is a low-rank approximation of an intermediate state of the diffusion process. DiffStateGrad, as a module, can be added to a wide range of diffusion-based inverse solvers to improve the preservation of the diffusion process on the prior manifold and filter out artifact-inducing components. We highlight that DiffStateGrad improves the robustness of diffusion models in terms of the choice of measurement guidance step size and noise while improving the worst-case performance. Finally, we demonstrate that DiffStateGrad improves upon the state-of-the-art on linear and nonlinear image restoration inverse problems.

Easy2Hard-Bench: Standardized Difficulty Labels for Profiling LLM Performance and Generalization

While generalization over tasks from easy to hard is crucial to profile language models (LLMs), the datasets with fine-grained difficulty annotations for each problem across a broad range of complexity are still blank. Aiming to address this limitation, we present Easy2Hard-Bench, a consistently formatted collection of 6 benchmark datasets spanning various domains, such as mathematics and programming problems, chess puzzles, and reasoning questions. Each problem within these datasets is annotated with numerical difficulty scores. To systematically estimate problem difficulties, we collect abundant performance data on attempts to each problem by humans in the real world or LLMs on the prominent leaderboard. Leveraging the rich performance data, we apply well-established difficulty ranking systems, such as Item Response Theory (IRT) and Glicko-2 models, to uniformly assign numerical difficulty scores to problems. Moreover, datasets in Easy2Hard-Bench distinguish themselves from previous collections by a higher proportion of challenging problems. Through extensive experiments with six state-of-the-art LLMs, we provide a comprehensive analysis of their performance and generalization capabilities across varying levels of difficulty, with the aim of inspiring future research in LLM generalization. The datasets are available at https://huggingface.co/datasets/furonghuang-lab/Easy2Hard-Bench.

Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design

Artificial intelligence models have shown great potential in structure-based drug design, generating ligands with high binding affinities. However, existing models have often overlooked a crucial physical constraint: atoms must maintain a minimum pairwise distance to avoid separation violation, a phenomenon governed by the balance of attractive and repulsive forces. To mitigate such separation violations, we propose NucleusDiff. It models the interactions between atomic nuclei and their surrounding electron clouds by enforcing the distance constraint between the nuclei and manifolds. We quantitatively evaluate NucleusDiff using the CrossDocked2020 dataset and a COVID-19 therapeutic target, demonstrating that NucleusDiff reduces violation rate by up to 100.00% and enhances binding affinity by up to 22.16%, surpassing state-of-the-art models for structure-based drug design. We also provide qualitative analysis through manifold sampling, visually confirming the effectiveness of NucleusDiff in reducing separation violations and improving binding affinities.

Fourier Neural Operators for Learning Dynamics in Quantum Spin Systems

Fourier Neural Operators (FNOs) excel on tasks using functional data, such as those originating from partial differential equations. Such characteristics render them an effective approach for simulating the time evolution of quantum wavefunctions, which is a computationally challenging, yet coveted task for understanding quantum systems. In this manuscript, we use FNOs to model the evolution of random quantum spin systems, so chosen due to their representative quantum dynamics and minimal symmetry. We explore two distinct FNO architectures and examine their performance for learning and predicting time evolution using both random and low-energy input states. Additionally, we apply FNOs to a compact set of Hamiltonian observables ($\sim\text{poly}(n)$) instead of the entire $2^n$ quantum wavefunction, which greatly reduces the size of our inputs and outputs and, consequently, the requisite dimensions of the resulting FNOs. Moreover, this Hamiltonian observable-based method demonstrates that FNOs can effectively distill information from high-dimensional spaces into lower-dimensional spaces. The extrapolation of Hamiltonian observables to times later than those used in training is of particular interest, as this stands to fundamentally increase the simulatability of quantum systems past both the coherence times of contemporary quantum architectures and the circuit-depths of tractable tensor networks.

Beyond Closure Models: Learning Chaotic-Systems via Physics-Informed Neural Operators

Accurately predicting the long-term behavior of chaotic systems is crucial for various applications such as climate modeling. However, achieving such predictions typically requires iterative computations over a dense spatiotemporal grid to account for the unstable nature of chaotic systems, which is expensive and impractical in many real-world situations. An alternative approach to such a full-resolved simulation is using a coarse grid and then correcting its errors through a \textit{closure model}, which approximates the overall information from fine scales not captured in the coarse-grid simulation. Recently, ML approaches have been used for closure modeling, but they typically require a large number of training samples from expensive fully-resolved simulations (FRS). In this work, we prove an even more fundamental limitation, i.e., the standard approach to learning closure models suffers from a large approximation error for generic problems, no matter how large the model is, and it stems from the non-uniqueness of the mapping. We propose an alternative end-to-end learning approach using a physics-informed neural operator (PINO) that overcomes this limitation by not using a closure model or a coarse-grid solver. We first train the PINO model on data from a coarse-grid solver and then fine-tune it with (a small amount of) FRS and physics-based losses on a fine grid. The discretization-free nature of neural operators means that they do not suffer from the restriction of a coarse grid that closure models face, and they can provably approximate the long-term statistics of chaotic systems. In our experiments, our PINO model achieves a 120x speedup compared to FRS with a relative error $\sim 5\%$. In contrast, the closure model coupled with a coarse-grid solver is $58$x slower than PINO while having a much higher error $\sim205\%$ when the closure model is trained on the same FRS dataset.