arXiv subjects

Anima Anandkumar

Publications and source records attributed to Anima Anandkumar.

At least 163 records · Page 9Linked to original sources

arXiv2023

I$^2$SB: Image-to-Image Schrödinger Bridge

We propose Image-to-Image Schrödinger Bridge (I$^2$SB), a new class of conditional diffusion models that directly learn the nonlinear diffusion processes between two given distributions. These diffusion bridges are particularly useful for image restoration, as the degraded images are structurally informative priors for reconstructing the clean images. I$^2$SB belongs to a tractable class of Schrödinger bridge, the nonlinear extension to score-based models, whose marginal distributions can be computed analytically given boundary pairs. This results in a simulation-free framework for nonlinear diffusions, where the I$^2$SB training becomes scalable by adopting practical techniques used in standard diffusion models. We validate I$^2$SB in solving various image restoration tasks, including inpainting, super-resolution, deblurring, and JPEG restoration on ImageNet 256x256 and show that I$^2$SB surpasses standard conditional diffusion models with more interpretable generative processes. Moreover, I$^2$SB matches the performance of inverse methods that additionally require the knowledge of the corruption operators. Our work opens up new algorithmic opportunities for developing efficient nonlinear diffusion models on a large scale. scale. Project page and codes: https://i2sb.github.io/

cs.CV↗

arXiv2023

Fast Monocular Scene Reconstruction with Global-Sparse Local-Dense Grids

Indoor scene reconstruction from monocular images has long been sought after by augmented reality and robotics developers. Recent advances in neural field representations and monocular priors have led to remarkable results in scene-level surface reconstructions. The reliance on Multilayer Perceptrons (MLP), however, significantly limits speed in training and rendering. In this work, we propose to directly use signed distance function (SDF) in sparse voxel block grids for fast and accurate scene reconstruction without MLPs. Our globally sparse and locally dense data structure exploits surfaces' spatial sparsity, enables cache-friendly queries, and allows direct extensions to multi-modal data such as color and semantic labels. To apply this representation to monocular scene reconstruction, we develop a scale calibration algorithm for fast geometric initialization from monocular depth priors. We apply differentiable volume rendering from this initialization to refine details with fast convergence. We also introduce efficient high-dimensional Continuous Random Fields (CRFs) to further exploit the semantic-geometry consistency between scene objects. Experiments show that our approach is 10x faster in training and 100x faster in rendering while achieving comparable accuracy to state-of-the-art neural implicit methods.

cs.CV↗

arXiv2023

Context Generation Improves Open Domain Question Answering

Closed-book question answering (QA) requires a model to directly answer an open-domain question without access to any external knowledge. Prior work on closed-book QA either directly finetunes or prompts a pretrained language model (LM) to leverage the stored knowledge. However, they do not fully exploit the parameterized knowledge. To address this issue, we propose a two-stage, closed-book QA framework which employs a coarse-to-fine approach to extract relevant knowledge and answer a question. Our approach first generates a related context for a given question by prompting a pretrained LM. We then prompt the same LM for answer prediction using the generated context and the question. Additionally, to eliminate failure caused by context uncertainty, we marginalize over generated contexts. Experimental results on three QA benchmarks show that our method significantly outperforms previous closed-book QA methods (e.g. exact matching 68.6% vs. 55.3%), and is on par with open-book methods that exploit external knowledge sources (e.g. 68.6% vs. 68.0%). Our method is able to better exploit the stored knowledge in pretrained LMs without adding extra learnable parameters or needing finetuning, and paves the way for hybrid models that integrate pretrained LMs with external knowledge.

cs.CL↗

arXiv2023

AI-aided Geometric Design of Anti-infection Catheters

Bacteria can swim upstream due to hydrodynamic interactions with the fluid flow in a narrow tube, and pose a clinical threat of urinary tract infection to patients implanted with catheters. Coatings and structured surfaces have been proposed as a way to suppress bacterial contamination in catheters. However, there is no surface structuring or coating approach to date that thoroughly addresses the contamination problem. Here, based on the physical mechanism of upstream swimming, we propose a novel geometric design, optimized by an AI model predicting in-flow bacterial dynamics. The AI method, based on Fourier neural operator, offers significant speedups over traditional simulation methods. Using Escherichia coli, we demonstrate the anti-infection mechanism in quasi-2D micro-fluidic experiments and evaluate the effectiveness of the design in 3Dprinted prototype catheters under clinical flow rates. Our catheter design shows 1-2 orders of magnitude improved suppression of bacterial contamination at the upstream end of the catheter, potentially prolonging the in-dwelling time for catheter use and reducing the overall risk of catheter-associated urinary tract infections.

physics.med-ph↗

arXiv2023

Retrieval-based Controllable Molecule Generation

Generating new molecules with specified chemical and biological properties via generative models has emerged as a promising direction for drug discovery. However, existing methods require extensive training/fine-tuning with a large dataset, often unavailable in real-world generation tasks. In this work, we propose a new retrieval-based framework for controllable molecule generation. We use a small set of exemplar molecules, i.e., those that (partially) satisfy the design criteria, to steer the pre-trained generative model towards synthesizing molecules that satisfy the given design criteria. We design a retrieval mechanism that retrieves and fuses the exemplar molecules with the input molecule, which is trained by a new self-supervised objective that predicts the nearest neighbor of the input molecule. We also propose an iterative refinement process to dynamically update the generated molecules and retrieval database for better generalization. Our approach is agnostic to the choice of generative models and requires no task-specific fine-tuning. On various tasks ranging from simple design criteria to a challenging real-world scenario for designing lead compounds that bind to the SARS-CoV-2 main protease, we demonstrate our approach extrapolates well beyond the retrieval database, and achieves better performance and wider applicability than previous methods. Code is available at https://github.com/NVlabs/RetMol.

q-bio.QM↗

arXiv2023

State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life. Despite recent advancements in protein structure prediction, existing algorithms are so far unable to systematically predict the binding ligand structures along with their regulatory effects on protein folding. To address this discrepancy, we present NeuralPLexer, a computational approach that can directly predict protein-ligand complex structures solely using protein sequence and ligand molecular graph inputs. NeuralPLexer adopts a deep generative model to sample the 3D structures of the binding complex and their conformational changes at an atomistic resolution. The model is based on a diffusion process that incorporates essential biophysical constraints and a multi-scale geometric deep learning system to iteratively sample residue-level contact maps and all heavy-atom coordinates in a hierarchical manner. NeuralPLexer achieves state-of-the-art performance compared to all existing methods on benchmarks for both protein-ligand blind docking and flexible binding site structure recovery. Moreover, owing to its specificity in sampling both ligand-free-state and ligand-bound-state ensembles, NeuralPLexer consistently outperforms AlphaFold2 in terms of global protein structure accuracy on both representative structure pairs with large conformational changes (average TM-score=0.93) and recently determined ligand-binding proteins (average TM-score=0.89). Case studies reveal that the predicted conformational variations are consistent with structure determination experiments for important targets, including human KRAS$^\textrm{G12C}$, ketol-acid reductoisomerase, and purine GPCRs. Our study suggests that a data-driven approach can capture the structural cooperativity between proteins and small molecules, showing promise in accelerating the design of enzymes, drug molecules, and beyond.

q-bio.QM↗

arXiv2023

Bongard-HOI: Benchmarking Few-Shot Visual Reasoning for Human-Object Interactions

A significant gap remains between today's visual pattern recognition models and human-level visual cognition especially when it comes to few-shot learning and compositional reasoning of novel concepts. We introduce Bongard-HOI, a new visual reasoning benchmark that focuses on compositional learning of human-object interactions (HOIs) from natural images. It is inspired by two desirable characteristics from the classical Bongard problems (BPs): 1) few-shot concept learning, and 2) context-dependent reasoning. We carefully curate the few-shot instances with hard negatives, where positive and negative images only disagree on action labels, making mere recognition of object categories insufficient to complete our benchmarks. We also design multiple test sets to systematically study the generalization of visual learning models, where we vary the overlap of the HOI concepts between the training and test sets of few-shot instances, from partial to no overlaps. Bongard-HOI presents a substantial challenge to today's visual recognition models. The state-of-the-art HOI detection model achieves only 62% accuracy on few-shot binary prediction while even amateur human testers on MTurk have 91% accuracy. With the Bongard-HOI benchmark, we hope to further advance research efforts in visual reasoning, especially in holistic perception-reasoning systems and better representation learning.

cs.CV↗

arXiv2023

VoxFormer: Sparse Voxel Transformer for Camera-based 3D Semantic Scene Completion

Humans can easily imagine the complete 3D geometry of occluded objects and scenes. This appealing ability is vital for recognition and understanding. To enable such capability in AI systems, we propose VoxFormer, a Transformer-based semantic scene completion framework that can output complete 3D volumetric semantics from only 2D images. Our framework adopts a two-stage design where we start from a sparse set of visible and occupied voxel queries from depth estimation, followed by a densification stage that generates dense 3D voxels from the sparse ones. A key idea of this design is that the visual features on 2D images correspond only to the visible scene structures rather than the occluded or empty spaces. Therefore, starting with the featurization and prediction of the visible structures is more reliable. Once we obtain the set of sparse queries, we apply a masked autoencoder design to propagate the information to all the voxels by self-attention. Experiments on SemanticKITTI show that VoxFormer outperforms the state of the art with a relative improvement of 20.0% in geometry and 18.1% in semantics and reduces GPU memory during training to less than 16GB. Our code is available on https://github.com/NVlabs/VoxFormer.

cs.CV↗

arXiv2023

Fourier Neural Operator for Plasma Modelling

Predicting plasma evolution within a Tokamak is crucial to building a sustainable fusion reactor. Whether in the simulation space or within the experimental domain, the capability to forecast the spatio-temporal evolution of plasma field variables rapidly and accurately could improve active control methods on current tokamak devices and future fusion reactors. In this work, we demonstrate the utility of using Fourier Neural Operator (FNO) to model the plasma evolution in simulations and experiments. Our work shows that the FNO is capable of predicting magnetohydrodynamic models governing the plasma dynamics, 6 orders of magnitude faster than the traditional numerical solver, while maintaining considerable accuracy (NMSE $\sim 10^{-5})$. Our work also benchmarks the performance of the FNO against other standard surrogate models such as Conv-LSTM and U-Net and demonstrate that the FNO takes significantly less time to train, requires less parameters and outperforms other models. We extend the FNO approach to model the plasma evolution observed by the cameras positioned within the MAST spherical tokamak. We illustrate its capability in forecasting the formation of filaments within the plasma as well as the heat deposits. The FNO deployed to model the camera is capable of forecasting the full length of the plasma shot within half the time of the shot duration.

physics.plasm-ph↗

arXiv2023

Forecasting subcritical cylinder wakes with Fourier Neural Operators

We apply Fourier neural operators (FNOs), a state-of-the-art operator learning technique, to forecast the temporal evolution of experimentally measured velocity fields. FNOs are a recently developed machine learning method capable of approximating solution operators to systems of partial differential equations through data alone. The learned FNO solution operator can be evaluated in milliseconds, potentially enabling faster-than-real-time modeling for predictive flow control in physical systems. Here we use FNOs to predict how physical fluid flows evolve in time, training with particle image velocimetry measurements depicting cylinder wakes in the subcritical vortex shedding regime. We train separate FNOs at Reynolds numbers ranging from Re = 240 to Re = 3060 and study how increasingly turbulent flow phenomena impact prediction accuracy. We focus here on a short prediction horizon of ten non-dimensionalized time-steps, as would be relevant for problems of predictive flow control. We find that FNOs are capable of accurately predicting the evolution of experimental velocity fields throughout the range of Reynolds numbers tested (L2 norm error < 0.1) despite being provided with limited and imperfect flow observations. Given these results, we conclude that this method holds significant potential for real-time predictive flow control of physical systems.

physics.flu-dyn↗

arXiv2023

Vision Transformers Are Good Mask Auto-Labelers

We propose Mask Auto-Labeler (MAL), a high-quality Transformer-based mask auto-labeling framework for instance segmentation using only box annotations. MAL takes box-cropped images as inputs and conditionally generates their mask pseudo-labels.We show that Vision Transformers are good mask auto-labelers. Our method significantly reduces the gap between auto-labeling and human annotation regarding mask quality. Instance segmentation models trained using the MAL-generated masks can nearly match the performance of their fully-supervised counterparts, retaining up to 97.4\% performance of fully supervised models. The best model achieves 44.1\% mAP on COCO instance segmentation (test-dev 2017), outperforming state-of-the-art box-supervised methods by significant margins. Qualitative results indicate that masks produced by MAL are, in some cases, even better than human annotations.

cs.CV↗

arXiv2022

Towards Neural Variational Monte Carlo That Scales Linearly with System Size

Quantum many-body problems are some of the most challenging problems in science and are central to demystifying some exotic quantum phenomena, e.g., high-temperature superconductors. The combination of neural networks (NN) for representing quantum states, coupled with the Variational Monte Carlo (VMC) algorithm, has been shown to be a promising method for solving such problems. However, the run-time of this approach scales quadratically with the number of simulated particles, constraining the practically usable NN to - in machine learning terms - minuscule sizes (<10M parameters). Considering the many breakthroughs brought by extreme NN in the +1B parameters scale to other domains, lifting this constraint could significantly expand the set of quantum systems we can accurately simulate on classical computers, both in size and complexity. We propose a NN architecture called Vector-Quantized Neural Quantum States (VQ-NQS) that utilizes vector-quantization techniques to leverage redundancies in the local-energy calculations of the VMC algorithm - the source of the quadratic scaling. In our preliminary experiments, we demonstrate VQ-NQS ability to reproduce the ground state of the 2D Heisenberg model across various system sizes, while reporting a significant reduction of about ${\times}10$ in the number of FLOPs in the local-energy calculation.

quant-ph↗

arXiv2022

HEAT: Hardware-Efficient Automatic Tensor Decomposition for Transformer Compression

Transformers have attained superior performance in natural language processing and computer vision. Their self-attention and feedforward layers are overparameterized, limiting inference speed and energy efficiency. Tensor decomposition is a promising technique to reduce parameter redundancy by leveraging tensor algebraic properties to express the parameters in a factorized form. Prior efforts used manual or heuristic factorization settings without hardware-aware customization, resulting in poor hardware efficiencies and large performance degradation. In this work, we propose a hardware-aware tensor decomposition framework, dubbed HEAT, that enables efficient exploration of the exponential space of possible decompositions and automates the choice of tensorization shape and decomposition rank with hardware-aware co-optimization. We jointly investigate tensor contraction path optimizations and a fused Einsum mapping strategy to bridge the gap between theoretical benefits and real hardware efficiency improvement. Our two-stage knowledge distillation flow resolves the trainability bottleneck and thus significantly boosts the final accuracy of factorized Transformers. Overall, we experimentally show that our hardware-aware factorized BERT variants reduce the energy-delay product by 5.7x with less than 1.1% accuracy loss and achieve a better efficiency-accuracy Pareto frontier than hand-tuned and heuristic baselines.

cs.LG↗

arXiv2022

Machine Learning Accelerated PDE Backstepping Observers

State estimation is important for a variety of tasks, from forecasting to substituting for unmeasured states in feedback controllers. Performing real-time state estimation for PDEs using provably and rapidly converging observers, such as those based on PDE backstepping, is computationally expensive and in many cases prohibitive. We propose a framework for accelerating PDE observer computations using learning-based approaches that are much faster while maintaining accuracy. In particular, we employ the recently-developed Fourier Neural Operator (FNO) to learn the functional mapping from the initial observer state and boundary measurements to the state estimate. By employing backstepping observer gains for previously-designed observers with particular convergence rate guarantees, we provide numerical experiments that evaluate the increased computational efficiency gained with FNO. We consider the state estimation for three benchmark PDE examples motivated by applications: first, for a reaction-diffusion (parabolic) PDE whose state is estimated with an exponential rate of convergence; second, for a parabolic PDE with exact prescribed-time estimation; and, third, for a pair of coupled first-order hyperbolic PDEs that modeling traffic flow density and velocity. The ML-accelerated observers trained on simulation data sets for these PDEs achieves up to three orders of magnitude improvement in computational speed compared to classical methods. This demonstrates the attractiveness of the ML-accelerated observers for real-time state estimation and control.

eess.SY↗

arXiv2022

Simulation Intelligence: Towards a New Generation of Scientific Methods

The original "Seven Motifs" set forth a roadmap of essential methods for the field of scientific computing, where a motif is an algorithmic method that captures a pattern of computation and data movement. We present the "Nine Motifs of Simulation Intelligence", a roadmap for the development and integration of the essential algorithms necessary for a merger of scientific computing, scientific simulation, and artificial intelligence. We call this merger simulation intelligence (SI), for short. We argue the motifs of simulation intelligence are interconnected and interdependent, much like the components within the layers of an operating system. Using this metaphor, we explore the nature of each layer of the simulation intelligence operating system stack (SI-stack) and the motifs therein: (1) Multi-physics and multi-scale modeling; (2) Surrogate modeling and emulation; (3) Simulation-based inference; (4) Causal modeling and inference; (5) Agent-based modeling; (6) Probabilistic programming; (7) Differentiable programming; (8) Open-ended optimization; (9) Machine programming. We believe coordinated efforts between motifs offers immense opportunity to accelerate scientific discovery, from solving inverse problems in synthetic biology and climate science, to directing nuclear energy experiments and predicting emergent behavior in socioeconomic settings. We elaborate on each layer of the SI-stack, detailing the state-of-art methods, presenting examples to highlight challenges and opportunities, and advocating for specific ways to advance the motifs and the synergies from their combinations. Advancing and integrating these technologies can enable a robust and efficient hypothesis-simulation-analysis type of scientific method, which we introduce with several use-cases for human-machine teaming and automated science.

cs.AI↗

arXiv2022

MineDojo: Building Open-Ended Embodied Agents with Internet-Scale Knowledge

Autonomous agents have made great strides in specialist domains like Atari games and Go. However, they typically learn tabula rasa in isolated environments with limited and manually conceived objectives, thus failing to generalize across a wide spectrum of tasks and capabilities. Inspired by how humans continually learn and adapt in the open world, we advocate a trinity of ingredients for building generalist agents: 1) an environment that supports a multitude of tasks and goals, 2) a large-scale database of multimodal knowledge, and 3) a flexible and scalable agent architecture. We introduce MineDojo, a new framework built on the popular Minecraft game that features a simulation suite with thousands of diverse open-ended tasks and an internet-scale knowledge base with Minecraft videos, tutorials, wiki pages, and forum discussions. Using MineDojo's data, we propose a novel agent learning algorithm that leverages large pre-trained video-language models as a learned reward function. Our agent is able to solve a variety of open-ended tasks specified in free-form language without any manually designed dense shaping reward. We open-source the simulation suite, knowledge bases, algorithm implementation, and pretrained models (https://minedojo.org) to promote research towards the goal of generally capable embodied agents.

cs.LG↗

arXiv2022

Can You Label Less by Using Out-of-Domain Data? Active & Transfer Learning with Few-shot Instructions

Labeling social-media data for custom dimensions of toxicity and social bias is challenging and labor-intensive. Existing transfer and active learning approaches meant to reduce annotation effort require fine-tuning, which suffers from over-fitting to noise and can cause domain shift with small sample sizes. In this work, we propose a novel Active Transfer Few-shot Instructions (ATF) approach which requires no fine-tuning. ATF leverages the internal linguistic knowledge of pre-trained language models (PLMs) to facilitate the transfer of information from existing pre-labeled datasets (source-domain task) with minimum labeling effort on unlabeled target data (target-domain task). Our strategy can yield positive transfer achieving a mean AUC gain of 10.5% compared to no transfer with a large 22b parameter PLM. We further show that annotation of just a few target-domain samples via active learning can be beneficial for transfer, but the impact diminishes with more annotation effort (26% drop in gain between 100 and 2000 annotated examples). Finally, we find that not all transfer scenarios yield a positive gain, which seems related to the PLMs initial performance on the target-domain task.

cs.CL↗

arXiv2022

Understanding The Robustness in Vision Transformers

Recent studies show that Vision Transformers(ViTs) exhibit strong robustness against various corruptions. Although this property is partly attributed to the self-attention mechanism, there is still a lack of systematic understanding. In this paper, we examine the role of self-attention in learning robust representations. Our study is motivated by the intriguing properties of the emerging visual grouping in Vision Transformers, which indicates that self-attention may promote robustness through improved mid-level representations. We further propose a family of fully attentional networks (FANs) that strengthen this capability by incorporating an attentional channel processing design. We validate the design comprehensively on various hierarchical backbones. Our model achieves a state-of-the-art 87.1% accuracy and 35.8% mCE on ImageNet-1k and ImageNet-C with 76.8M parameters. We also demonstrate state-of-the-art accuracy and robustness in two downstream tasks: semantic segmentation and object detection. Code is available at: https://github.com/NVlabs/FAN.

cs.CV↗