A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of improving the efficiency of MD simulations through better numerical methods and, more recently, by utilizing machine learning (ML) methods. Yet, challenges remain, such as accurate modeling of extended-timescale simulations. To address this issue, we propose NeuralMD, the first ML surrogate that can facilitate numerical MD and provide accurate simulations in protein-ligand binding. We propose a principled approach that incorporates a novel physics-informed multi-grained group symmetric framework. Specifically, we propose (1) a BindingNet model that satisfies group symmetry using vector frames and captures the multi-level protein-ligand interactions, and (2) an augmented neural differential equation solver that learns the trajectory under Newtonian mechanics. For the experiment, we design ten single-trajectory and three multi-trajectory binding simulation tasks. We show the efficiency and effectiveness of NeuralMD, with a 2000$\times$ speedup over standard numerical MD simulation and outperforming all other ML approaches by up to 80% under the stability metric. We further qualitatively show that NeuralMD reaches more stable binding predictions compared to other machine learning methods.

SySMOL: A Hardware-software Co-design Framework for Ultra-Low and Fine-Grained Mixed-Precision Neural Networks

Recent advancements in quantization and mixed-precision techniques offer significant promise for improving the run-time and energy efficiency of neural networks. In this work, we further showed that neural networks, wherein individual parameters or activations can take on different precisions ranging between 1 and 4 bits, can achieve accuracies comparable to or exceeding the full-precision counterparts. However, the deployment of such networks poses numerous challenges, stemming from the necessity to manage and control the compute/communication/storage requirements associated with these extremely fine-grained mixed precisions for each piece of data. There is a lack of existing efficient hardware and system-level support tailored to these unique and challenging requirements. Our research introduces the first novel holistic hardware-software co-design approach for these networks, which enables a continuous feedback loop between hardware design, training, and inference to facilitate systematic design exploration. As a proof-of-concept, we illustrate this co-design approach by designing new, configurable CPU SIMD architectures tailored for these networks, tightly integrating the architecture with new system-aware training and inference techniques. We perform systematic design space exploration using this framework to analyze various tradeoffs. The design for mixed-precision networks that achieves optimized tradeoffs corresponds to an architecture that supports 1, 2, and 4-bit fixed-point operations with four configurable precision patterns, when coupled with system-aware training and inference optimization -- networks trained for this design achieve accuracies that closely match full-precision accuracies, while compressing and improving run-time efficiency of the neural networks drastically by 10-20x, compared to full-precision networks.

SIMD Dataflow Co-optimization for Efficient Neural Networks Inferences on CPUs

We address the challenges associated with deploying neural networks on CPUs, with a particular focus on minimizing inference time while maintaining accuracy. Our novel approach is to use the dataflow (i.e., computation order) of a neural network to explore data reuse opportunities using heuristic-guided analysis and a code generation framework, which enables exploration of various Single Instruction, Multiple Data (SIMD) implementations to achieve optimized neural network execution. Our results demonstrate that the dataflow that keeps outputs in SIMD registers while also maximizing both input and weight reuse consistently yields the best performance for a wide variety of inference workloads, achieving up to 3x speedup for 8-bit neural networks, and up to 4.8x speedup for binary neural networks, respectively, over the optimized implementations of neural networks today.

Representation Disparity-aware Distillation for 3D Object Detection

In this paper, we focus on developing knowledge distillation (KD) for compact 3D detectors. We observe that off-the-shelf KD methods manifest their efficacy only when the teacher model and student counterpart share similar intermediate feature representations. This might explain why they are less effective in building extreme-compact 3D detectors where significant representation disparity arises due primarily to the intrinsic sparsity and irregularity in 3D point clouds. This paper presents a novel representation disparity-aware distillation (RDD) method to address the representation disparity issue and reduce performance gap between compact students and over-parameterized teachers. This is accomplished by building our RDD from an innovative perspective of information bottleneck (IB), which can effectively minimize the disparity of proposal region pairs from student and teacher in features and logits. Extensive experiments are performed to demonstrate the superiority of our RDD over existing KD methods. For example, our RDD increases mAP of CP-Voxel-S to 57.1% on nuScenes dataset, which even surpasses teacher performance while taking up only 42% FLOPs.

DCP-NAS: Discrepant Child-Parent Neural Architecture Search for 1-bit CNNs

Neural architecture search (NAS) proves to be among the effective approaches for many tasks by generating an application-adaptive neural architecture, which is still challenged by high computational cost and memory consumption. At the same time, 1-bit convolutional neural networks (CNNs) with binary weights and activations show their potential for resource-limited embedded devices. One natural approach is to use 1-bit CNNs to reduce the computation and memory cost of NAS by taking advantage of the strengths of each in a unified framework, while searching the 1-bit CNNs is more challenging due to the more complicated processes involved. In this paper, we introduce Discrepant Child-Parent Neural Architecture Search (DCP-NAS) to efficiently search 1-bit CNNs, based on a new framework of searching the 1-bit model (Child) under the supervision of a real-valued model (Parent). Particularly, we first utilize a Parent model to calculate a tangent direction, based on which the tangent propagation method is introduced to search the optimized 1-bit Child. We further observe a coupling relationship between the weights and architecture parameters existing in such differentiable frameworks. To address the issue, we propose a decoupled optimization method to search an optimized architecture. Extensive experiments demonstrate that our DCP-NAS achieves much better results than prior arts on both CIFAR-10 and ImageNet datasets. In particular, the backbones achieved by our DCP-NAS achieve strong generalization performance on person re-identification and object detection.

Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials

Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these scientific problems, molecules serve as the fundamental building blocks, and machine learning has emerged as a highly effective and powerful tool for modeling their geometric structures. Nevertheless, due to the rapidly evolving process of the field and the knowledge gap between science (e.g., physics, chemistry, & biology) and machine learning communities, a benchmarking study on geometrical representation for such data has not been conducted. To address such an issue, in this paper, we first provide a unified view of the current symmetry-informed geometric methods, classifying them into three main categories: invariance, equivariance with spherical frame basis, and equivariance with vector frame basis. Then we propose a platform, coined Geom3D, which enables benchmarking the effectiveness of geometric strategies. Geom3D contains 16 advanced symmetry-informed geometric representation models and 14 geometric pretraining methods over 46 diverse datasets, including small molecules, proteins, and crystalline materials. We hope that Geom3D can, on the one hand, eliminate barriers for machine learning researchers interested in exploring scientific problems; and, on the other hand, provide valuable guidance for researchers in computational chemistry, structural biology, and materials science, aiding in the informed selection of representation techniques for specific applications.

Bi-ViT: Pushing the Limit of Vision Transformer Quantization

Vision transformers (ViTs) quantization offers a promising prospect to facilitate deploying large pre-trained networks on resource-limited devices. Fully-binarized ViTs (Bi-ViT) that pushes the quantization of ViTs to its limit remain largely unexplored and a very challenging task yet, due to their unacceptable performance. Through extensive empirical analyses, we identify the severe drop in ViT binarization is caused by attention distortion in self-attention, which technically stems from the gradient vanishing and ranking disorder. To address these issues, we first introduce a learnable scaling factor to reactivate the vanished gradients and illustrate its effectiveness through theoretical and experimental analyses. We then propose a ranking-aware distillation method to rectify the disordered ranking in a teacher-student framework. Bi-ViT achieves significant improvements over popular DeiT and Swin backbones in terms of Top-1 accuracy and FLOPs. For example, with DeiT-Tiny and Swin-Tiny, our method significantly outperforms baselines by 22.1% and 21.4% respectively, while 61.5x and 56.1x theoretical acceleration in terms of FLOPs compared with real-valued counterparts on ImageNet.

Q-DETR: An Efficient Low-Bit Quantized Detection Transformer

The recent detection transformer (DETR) has advanced object detection, but its application on resource-constrained devices requires massive computation and memory resources. Quantization stands out as a solution by representing the network in low-bit parameters and operations. However, there is a significant performance drop when performing low-bit quantized DETR (Q-DETR) with existing quantization methods. We find that the bottlenecks of Q-DETR come from the query information distortion through our empirical analyses. This paper addresses this problem based on a distribution rectification distillation (DRD). We formulate our DRD as a bi-level optimization problem, which can be derived by generalizing the information bottleneck (IB) principle to the learning of Q-DETR. At the inner level, we conduct a distribution alignment for the queries to maximize the self-information entropy. At the upper level, we introduce a new foreground-aware query matching scheme to effectively transfer the teacher information to distillation-desired features to minimize the conditional information entropy. Extensive experimental results show that our method performs much better than prior arts. For example, the 4-bit Q-DETR can theoretically accelerate DETR with ResNet-50 backbone by 6.6x and achieve 39.4% AP, with only 2.6% performance gaps than its real-valued counterpart on the COCO dataset.

Implicit Diffusion Models for Continuous Super-Resolution

Image super-resolution (SR) has attracted increasing attention due to its wide applications. However, current SR methods generally suffer from over-smoothing and artifacts, and most work only with fixed magnifications. This paper introduces an Implicit Diffusion Model (IDM) for high-fidelity continuous image super-resolution. IDM integrates an implicit neural representation and a denoising diffusion model in a unified end-to-end framework, where the implicit neural representation is adopted in the decoding process to learn continuous-resolution representation. Furthermore, we design a scale-controllable conditioning mechanism that consists of a low-resolution (LR) conditioning network and a scaling factor. The scaling factor regulates the resolution and accordingly modulates the proportion of the LR information and generated features in the final output, which enables the model to accommodate the continuous-resolution requirement. Extensive experiments validate the effectiveness of our IDM and demonstrate its superior performance over prior arts.

Confidence-driven Bounding Box Localization for Small Object Detection

Despite advancements in generic object detection, there remains a performance gap in detecting small objects compared to normal-scale objects. We for the first time observe that existing bounding box regression methods tend to produce distorted gradients for small objects and result in less accurate localization. To address this issue, we present a novel Confidence-driven Bounding Box Localization (C-BBL) method to rectify the gradients. C-BBL quantizes continuous labels into grids and formulates two-hot ground truth labels. In prediction, the bounding box head generates a confidence distribution over the grids. Unlike the bounding box regression paradigms in conventional detectors, we introduce a classification-based localization objective through cross entropy between ground truth and predicted confidence distribution, generating confidence-driven gradients. Additionally, C-BBL describes a uncertainty loss based on distribution entropy in labels and predictions to further reduce the uncertainty in small object localization. The method is evaluated on multiple detectors using three object detection benchmarks and consistently improves baseline detectors, achieving state-of-the-art performance. We also demonstrate the generalizability of C-BBL to different label systems and effectiveness for high resolution detection, which validates its prospect as a general solution.