A Text-guided Protein Design Framework

Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level properties. Yet, whether the incorporation of such text data can help protein design tasks has not been explored. To bridge this gap, we propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP that aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that generates the protein sequences from the representation. To train ProteinDT, we construct a large dataset, SwissProtCLAP, with 441K text and protein pairs. We empirically verify the effectiveness of ProteinDT from three aspects: (1) consistently superior performance on four out of six protein property prediction benchmarks; (2) over 90% accuracy for text-guided protein generation; and (3) promising results for zero-shot text-guided protein editing.

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.

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.

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.

Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing

There is increasing adoption of artificial intelligence in drug discovery. However, existing works use machine learning to mainly utilize the chemical structures of molecules yet ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions, and predict complex biological activities. We present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecule's chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct the largest multi-modal dataset to date, namely PubChemSTM, with over 280K chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM possesses two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.

Incremental Fourier Neural Operator

Recently, neural networks have proven their impressive ability to solve partial differential equations (PDEs). Among them, Fourier neural operator (FNO) has shown success in learning solution operators for highly non-linear problems such as turbulence flow. FNO is discretization-invariant, where it can be trained on low-resolution data and generalizes to problems with high-resolution. This property is related to the low-pass filters in FNO, where only a limited number of frequency modes are selected to propagate information. However, it is still a challenge to select an appropriate number of frequency modes and training resolution for different PDEs. Too few frequency modes and low-resolution data hurt generalization, while too many frequency modes and high-resolution data are computationally expensive and lead to over-fitting. To this end, we propose Incremental Fourier Neural Operator (IFNO), which augments both the frequency modes and data resolution incrementally during training. We show that IFNO achieves better generalization (around 15% reduction on testing L2 loss) while reducing the computational cost by 35%, compared to the standard FNO. In addition, we observe that IFNO follows the behavior of implicit regularization in FNO, which explains its excellent generalization ability.

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.

Fourier Continuation for Exact Derivative Computation in Physics-Informed Neural Operators

The physics-informed neural operator (PINO) is a machine learning architecture that has shown promising empirical results for learning partial differential equations. PINO uses the Fourier neural operator (FNO) architecture to overcome the optimization challenges often faced by physics-informed neural networks. Since the convolution operator in PINO uses the Fourier series representation, its gradient can be computed exactly on the Fourier space. While Fourier series cannot represent nonperiodic functions, PINO and FNO still have the expressivity to learn nonperiodic problems with Fourier extension via padding. However, computing the Fourier extension in the physics-informed optimization requires solving an ill-conditioned system, resulting in inaccurate derivatives which prevent effective optimization. In this work, we present an architecture that leverages Fourier continuation (FC) to apply the exact gradient method to PINO for nonperiodic problems. This paper investigates three different ways that FC can be incorporated into PINO by testing their performance on a 1D blowup problem. Experiments show that FC-PINO outperforms padded PINO, improving equation loss by several orders of magnitude, and it can accurately capture the third order derivatives of nonsmooth solution functions.

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.

Fast Sampling of Diffusion Models via Operator Learning

Diffusion models have found widespread adoption in various areas. However, sampling from them is slow because it involves emulating a reverse process with hundreds-to-thousands of network evaluations. Inspired by the success of neural operators in accelerating differential equations solving, we approach this problem by solving the underlying neural differential equation from an operator learning perspective. We examine probability flow ODE trajectories in diffusion models and observe a compact energy spectrum that can be learned efficiently in Fourier space. With this insight, we propose diffusion Fourier neural operator (DFNO) with temporal convolution in Fourier space to parameterize the operator that maps initial condition to the solution trajectory, which is a continuous function in time. DFNO can be applied to any diffusion model and generate high-quality samples in one model forward call. Our method achieves the state-of-the-art FID of 4.72 on CIFAR-10 using only one model evaluation.