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Applications/Chemistry and Drug Discovery

Zuobai Zhang, Minghao Xu, Aurelie Lozano, Vijil Chenthamarakshan, Payel Das, Jian Tang

Self-supervised pre-training methods on proteins have recently gained attention, with most approaches focusing on either protein sequences or structures, neglecting the exploration of their joint distribution, which is crucial for a comprehensive understanding of protein functions by integrating co-evolutionary information and structural characteristics. In this work, inspired by the success of denoising diffusion models in generative tasks, we propose the DiffPreT approach to pre-train a protein encoder by sequence-structure joint diffusion modeling. DiffPreT guides the encoder to recover the native protein sequences and structures from the perturbed ones along the joint diffusion trajectory, which acquires the joint distribution of sequences and structures. Considering the essential protein conformational variations, we enhance DiffPreT by a method called Siamese Diffusion Trajectory Prediction (SiamDiff) to capture the correlation between different conformers of a protein. SiamDiff attains this goal by maximizing the mutual information between representations of diffusion trajectories of structurally-correlated conformers. We study the effectiveness of DiffPreT and SiamDiff on both atom- and residue-level structure-based protein understanding tasks. Experimental results show that the performance of DiffPreT is consistently competitive on all tasks, and SiamDiff achieves new state-of-the-art performance, considering the mean ranks on all tasks. Code will be released upon acceptance.

Applications/Computer Vision

Zibo Zhao, Wen Liu, Xin Chen, Xianfang Zeng, Rui Wang, Pei Cheng, BIN FU, Tao Chen, Gang Yu, Shenghua Gao

We present a novel alignment-before-generation approach to tackle the challenging task of generating general 3D shapes based on 2D images or texts. Directly learning a conditional generative model from images or texts to 3D shapes is prone to producing inconsistent results with the conditions because 3D shapes have an additional dimension whose distribution significantly differs from that of 2D images and texts. To bridge the domain gap among the three modalities and facilitate multi-modal-conditioned 3D shape generation, we explore representing 3D shapes in a shape-image-text-aligned space. Our framework comprises two models: a Shape-Image-Text-Aligned Variational Auto-Encoder (SITA-VAE) and a conditional Aligned Shape Latent Diffusion Model (ASLDM). The former model encodes the 3D shapes into the shape latent space aligned to the image and text and reconstructs the fine-grained 3D neural fields corresponding to given shape embeddings via the transformer-based decoder. The latter model learns a probabilistic mapping function from the image or text space to the latent shape space. Our extensive experiments demonstrate that our proposed approach can generate higher-quality and more diverse 3D shapes that better semantically conform to the visual or textural conditional inputs, validating the effectiveness of the shape-image-text-aligned space for cross-modality 3D shape generation.

Xiangning Chen, Chen Liang, Da Huang, Esteban Real, Kaiyuan Wang, Hieu Pham, Xuanyi Dong, Thang Luong, Cho-Jui Hsieh, Yifeng Lu 等

We present a method to formulate algorithm discovery as program search, and apply it to discover optimization algorithms for deep neural network training. We leverage efficient search techniques to explore an infinite and sparse program space. To bridge the large generalization gap between proxy and target tasks, we also introduce program selection and simplification strategies.Our method discovers a simple and effective optimization algorithm, $\textbf{Lion}$ ($\textit{Evo$\textbf{L}$ved S$\textbf{i}$gn M$\textbf{o}$me$\textbf{n}$tum}$). It is more memory-efficient than Adam as it only keeps track of the momentum. Different from adaptive optimizers, its update has the same magnitude for each parameter calculated through the sign operation.We compare Lion with widely used optimizers, such as Adam and Adafactor, for training a variety of models on different tasks. On image classification, Lion boosts the accuracy of ViT by up to 2\% on ImageNet and saves up to 5x the pre-training compute on JFT. On vision-language contrastive learning, we achieve 88.3\% $\textit{zero-shot}$ and 91.1\% $\textit{fine-tuning}$ accuracy on ImageNet, surpassing the previous best results by 2\% and 0.1\%, respectively. On diffusion models, Lion outperforms Adam by achieving a better FID score and reducing the training compute by up to 2.3x. For autoregressive, masked language modeling, and fine-tuning, Lion exhibits a similar or better performance compared to Adam. Our analysis of Lion reveals that its performance gain grows with the training batch size. It also requires a smaller learning rate than Adam due to the larger norm of the update produced by the sign function. Additionally, we examine the limitations of Lion and identify scenarios where its improvements are small or not statistically significant.

Reinforcement Learning/Deep RL

Cong Lu, Philip Ball, Yee Whye Teh, Jack Parker-Holder

A key theme in the past decade has been that when large neural networks and large datasets combine they can produce remarkable results. In deep reinforcement learning (RL), this paradigm is commonly made possible through experience replay, whereby a dataset of past experiences is used to train a policy or value function. However, unlike in supervised or self-supervised learning, an RL agent has to collect its own data, which is often limited. Thus, it is challenging to reap the benefits of deep learning, and even small neural networks can overfit at the start of training. In this work, we leverage the tremendous recent progress in generative modeling and propose Synthetic Experience Replay (SynthER), a diffusion-based approach to flexibly upsample an agent's collected experience. We show that SynthER is an effective method for training RL agents across offline and online settings, in both proprioceptive and pixel-based environments. In offline settings, we observe drastic improvements when upsampling small offline datasets and see that additional synthetic data also allows us to effectively train larger networks. Furthermore, SynthER enables online agents to train with a much higher update-to-data ratio than before, leading to a significant increase in sample efficiency, without any algorithmic changes. We believe that synthetic training data could open the door to realizing the full potential of deep learning for replay-based RL algorithms from limited data. Finally, we open-source our code at https://github.com/conglu1997/SynthER.

Deep Learning/Generative Models and Autoencoders

Ling Yang, Jingwei Liu, Shenda Hong, Zhilong Zhang, Zhilin Huang, Zheming Cai, Wentao Zhang, Bin CUI

Diffusion models are a new class of generative models, and have dramatically promoted image generation with unprecedented quality and diversity. Existing diffusion models mainly try to reconstruct input image from a corrupted one with a pixel-wise or feature-wise constraint along spatial axes. However, such point-based reconstruction may fail to make each predicted pixel/feature fully preserve its neighborhood context, impairing diffusion-based image synthesis. As a powerful source of automatic supervisory signal, context has been well studied for learning representations. Inspired by this, we for the first time propose ConPreDiff to improve diffusion-based image synthesis with context prediction. We explicitly reinforce each point to predict its neighborhood context (i.e., multi-stride pixels/features) with a context decoder at the end of diffusion denoising blocks in training stage, and remove the decoder for inference. In this way, each point can better reconstruct itself by preserving its semantic connections with neighborhood context. This new paradigm of ConPreDiff can generalize to arbitrary discrete and continuous diffusion backbones without introducing extra parameters in sampling procedure. Extensive experiments are conducted on unconditional image generation, text-to-image generation and image inpainting tasks. Our ConPreDiff consistently outperforms previous methods and achieves new SOTA text-to-image generation results on MS-COCO, with a zero-shot FID score of 6.21.

Applications/Computer Vision

Peng Jin, Yang Wu, Yanbo Fan, Zhongqian Sun, Wei Yang, Li Yuan

Most text-driven human motion generation methods employ sequential modeling approaches, e.g., transformer, to extract sentence-level text representations automatically and implicitly for human motion synthesis. However, these compact text representations may overemphasize the action names at the expense of other important properties and lack fine-grained details to guide the synthesis of subtly distinct motion. In this paper, we propose hierarchical semantic graphs for fine-grained control over motion generation. Specifically, we disentangle motion descriptions into hierarchical semantic graphs including three levels of motions, actions, and specifics. Such global-to-local structures facilitate a comprehensive understanding of motion description and fine-grained control of motion generation. Correspondingly, to leverage the coarse-to-fine topology of hierarchical semantic graphs, we decompose the text-to-motion diffusion process into three semantic levels, which correspond to capturing the overall motion, local actions, and action specifics. Extensive experiments on two benchmark human motion datasets, including HumanML3D and KIT, with superior performances, justify the efficacy of our method. More encouragingly, by modifying the edge weights of hierarchical semantic graphs, our method can continuously refine the generated motion, which may have a far-reaching impact on the community. Code and pre-trained weights are available at https://github.com/jpthu17/GraphMotion.

Applications/Health

Shenghuan Sun, Greg Goldgof, Atul Butte, Ahmed Alaa

Generative models capable of precisely capturing nuanced clinical features in medical images hold great promise for facilitating clinical data sharing, enhancing rare disease datasets, and efficiently synthesizing (annotated) medical images at scale. Despite their potential, assessing the quality of synthetic medical images remains a challenge. While modern generative models can synthesize visually-realistic medical images, the clinical plausibility of these images may be called into question. Domain-agnostic scores, such as FID score, precision, and recall, cannot incorporate clinical knowledge and are, therefore, not suitable for assessing clinical sensibility. Additionally, there are numerous unpredictable ways in which generative models may fail to synthesize clinically plausible images, making it challenging to anticipate potential failures and design automated scores for their detection. To address these challenges, this paper introduces a pathologist-in-the-loop framework for generating clinically-plausible synthetic medical images. Our framework comprises three steps: (1) pretraining a conditional diffusion model to generate medical images conditioned on a clinical concept, (2) expert pathologist evaluation of the generated images to assess whether they satisfy clinical desiderata, and (3) training a reward model that predicts human feedback on new samples, which we use to incorporate expert knowledge into the finetuning objective of the diffusion model. Our results show that human feedback significantly improves the quality of synthetic images in terms of fidelity, diversity, utility in downstream applications, and plausibility as evaluated by experts. We also demonstrate that human feedback can teach the model new clinical concepts not annotated in the original training data. Our results demonstrate the value of incorporating human feedback in clinical applications where generative models may struggle to capture extensive domain knowledge from raw data alone.

Deep Learning/Other Representation Learning

Yuhan Ding, Fukun Yin, Jiayuan Fan, Hui Li, Xin Chen, Wen Liu, Chongshan Lu, Gang Yu, Tao Chen

Recent advances in implicit neural representations have achieved impressive results by sampling and fusing individual points along sampling rays in the sampling space. However, due to the explosively growing sampling space, finely representing and synthesizing detailed textures remains a challenge for unbounded large-scale outdoor scenes. To alleviate the dilemma of using individual points to perceive the entire colossal space, we explore learning the surface distribution of the scene to provide structural priors and reduce the samplable space and propose a Point Diffusion implicit Function, PDF, for large-scale scene neural representation. The core of our method is a large-scale point cloud super-resolution diffusion module that enhances the sparse point cloud reconstructed from several training images into a dense point cloud as an explicit prior. Then in the rendering stage, only sampling points with prior points within the sampling radius are retained. That is, the sampling space is reduced from the unbounded space to the scene surface. Meanwhile, to fill in the background of the scene that cannot be provided by point clouds, the region sampling based on Mip-NeRF 360 is employed to model the background representation. Expensive experiments have demonstrated the effectiveness of our method for large-scale scene novel view synthesis, which outperforms relevant state-of-the-art baselines.

Deep Learning/Generative Models and Autoencoders

Wenliang Zhao, Lujia Bai, Yongming Rao, Jie Zhou, Jiwen Lu

Diffusion probabilistic models (DPMs) have demonstrated a very promising ability in high-resolution image synthesis. However, sampling from a pre-trained DPM is time-consuming due to the multiple evaluations of the denoising network, making it more and more important to accelerate the sampling of DPMs. Despite recent progress in designing fast samplers, existing methods still cannot generate satisfying images in many applications where fewer steps (e.g., $<$10) are favored. In this paper, we develop a unified corrector (UniC) that can be applied after any existing DPM sampler to increase the order of accuracy without extra model evaluations, and derive a unified predictor (UniP) that supports arbitrary order as a byproduct. Combining UniP and UniC, we propose a unified predictor-corrector framework called UniPC for the fast sampling of DPMs, which has a unified analytical form for any order and can significantly improve the sampling quality over previous methods, especially in extremely few steps. We evaluate our methods through extensive experiments including both unconditional and conditional sampling using pixel-space and latent-space DPMs. Our UniPC can achieve 3.87 FID on CIFAR10 (unconditional) and 7.51 FID on ImageNet 256$\times$256 (conditional) with only 10 function evaluations. Code is available at https://github.com/wl-zhao/UniPC.

Applications/Physics

Laurence Midgley, Vincent Stimper, Javier Antorán, Emile Mathieu, Bernhard Schölkopf, José Miguel Hernández-Lobato

Coupling normalizing flows allow for fast sampling and density evaluation, making them the tool of choice for probabilistic modeling of physical systems. However, the standard coupling architecture precludes endowing flows that operate on the Cartesian coordinates of atoms with the SE(3) and permutation invariances of physical systems. This work proposes a coupling flow that preserves SE(3) and permutation equivariance by performing coordinate splits along additional augmented dimensions. At each layer, the flow maps atoms' positions into learned SE(3) invariant bases, where we apply standard flow transformations, such as monotonic rational-quadratic splines, before returning to the original basis.Crucially, our flow preserves fast sampling and density evaluation, and may be used to produce unbiased estimates of expectations with respect to the target distribution via importance sampling.When trained on the DW4, LJ13, and QM9-positional datasets, our flow is competitive with equivariant continuous normalizing flows and diffusion models, while allowing sampling more than an order of magnitude faster.Moreover, to the best of our knowledge, we are the first to learn the full Boltzmann distribution of alanine dipeptide by only modeling the Cartesian positions of its atoms.Lastly, we demonstrate that our flow can be trained to approximately sample from the Boltzmann distribution of the DW4 and LJ13 particle systems using only their energy functions.

Applications/Computer Vision

Mihir Prabhudesai, Tsung-Wei Ke, Alex Li, Deepak Pathak, Katerina Fragkiadaki

The advancements in generative modeling, particularly the advent of diffusion models, have sparked a fundamental question: how can these models be effectively used for discriminative tasks? In this work, we find that generative models can be great test-time adapters for discriminative models. Our method, Diffusion-TTA, adapts pre-trained discriminative models such as image classifiers, segmenters and depth predictors, to each unlabelled example in the test set using generative feedback from a diffusion model. We achieve this by modulating the conditioning of the diffusion model using the output of the discriminative model. We then maximize the image likelihood objective by backpropagating the gradients to discriminative model’s parameters. We show Diffusion-TTA significantly enhances the accuracy of various large-scale pre-trained discriminative models, such as, ImageNet classifiers, CLIP models, image pixel labellers and image depth predictors. Diffusion-TTA outperforms existing test-time adaptation methods, including TTT-MAE and TENT, and particularly shines in online adaptation setups, where the discriminative model is continually adapted to each example in the test set. We provide access to code, results, and visualizations on our website: diffusion-tta.github.io/

Deep Learning/Generative Models and Autoencoders

Benno Krojer, Elinor Poole-Dayan, Vikram Voleti, Chris Pal, Siva Reddy

Text-conditioned image generation models have recently shown immense qualitative success using denoising diffusion processes. However, unlike discriminative vision-and-language models, it is a non-trivial task to subject these diffusion-based generative models to automatic fine-grained quantitative evaluation of high-level phenomena such as compositionality.Towards this goal, we perform two innovations. First, we transform diffusion-based models (in our case, Stable Diffusion) for any image-text matching (ITM) task using a novel method called DiffusionITM.Second, we introduce the Generative-Discriminative Evaluation Benchmark (GDBench) benchmark with 7 complex vision-and-language tasks, bias evaluation and detailed analysis.We find that Stable Diffusion + DiffusionITM is competitive on many tasks and outperforms CLIP on compositional tasks like like CLEVR and Winoground.We further boost its compositional performance with a transfer setup by fine-tuning on MS-COCO while retaining generative capabilities. We also measure the stereotypical bias in diffusion models, and find that Stable Diffusion 2.1 is, for the most part, less biased than Stable Diffusion 1.5.Overall, our results point in an exciting direction bringing discriminative and generative model evaluation closer. We will release code and benchmark setup soon.

Social Aspects/Privacy-preserving Statistics and Machine Learning

Wenxuan Bao, Francesco Pittaluga, Vijay Kumar B G, Vincent Bindschaedler

Data augmentation techniques, such as image transformations and combinations, are highly effective at improving the generalization of computer vision models, especially when training data is limited. However, such techniques are fundamentally incompatible with differentially private learning approaches, due to the latter’s built-in assumption that each training image’s contribution to the learned model is bounded. In this paper, we investigate why naive applications of multi-sample data augmentation techniques, such as mixup, fail to achieve good performance and propose two novel data augmentation techniques specifically designed for the constraints of differentially private learning. Our first technique, DP-Mix_Self, achieves SoTA classification performance across a range of datasets and settings by performing mixup on self-augmented data. Our second technique, DP-Mix_Diff, further improves performance by incorporating synthetic data from a pre-trained diffusion model into the mixup process. We open-source the code at https://github.com/wenxuan-Bao/DP-Mix.

Deep Learning/Generative Models and Autoencoders

Jian Chen, Ruiyi Zhang, Tong Yu, Rohan Sharma, Zhiqiang Xu, Tong Sun, Changyou Chen

Learning from noisy labels is an important and long-standing problem in machine learning for real applications. One of the main research lines focuses on learning a label corrector to purify potential noisy labels. However, these methods typically rely on strict assumptions and are limited to certain types of label noise. In this paper, we reformulate the label-noise problem from a generative-model perspective, *i.e.*, labels are generated by gradually refining an initial random guess. This new perspective immediately enables existing powerful diffusion models to seamlessly learn the stochastic generative process. Once the generative uncertainty is modeled, we can perform classification inference using maximum likelihood estimation of labels. To mitigate the impact of noisy labels, we propose the **L**abel-**R**etrieval-**A**ugmented (LRA) diffusion model, which leverages neighbor consistency to effectively construct pseudo-clean labels for diffusion training. Our model is flexible and general, allowing easy incorporation of different types of conditional information, *e.g.*, use of pre-trained models, to further boost model performance. Extensive experiments are conducted for evaluation. Our model achieves new state-of-the-art (SOTA) results on all the standard real-world benchmark datasets. Remarkably, by incorporating conditional information from the powerful CLIP model, our method can boost the current SOTA accuracy by 10-20 absolute points in many cases. Code is available: https://anonymous.4open.science/r/LRA-diffusion-5F2F

Deep Learning/Generative Models and Autoencoders

Ethan Pronovost, Meghana Reddy Ganesina, Noureldin Hendy, Zeyu Wang, Andres Morales, Kai Wang, Nick Roy

Automated creation of synthetic traffic scenarios is a key part of scaling the safety validation of autonomous vehicles (AVs). In this paper, we propose Scenario Diffusion, a novel diffusion-based architecture for generating traffic scenarios that enables controllable scenario generation. We combine latent diffusion, object detection and trajectory regression to generate distributions of synthetic agent poses, orientations and trajectories simultaneously. This distribution is conditioned on the map and sets of tokens describing the desired scenario to provide additional control over the generated scenario. We show that our approach has sufficient expressive capacity to model diverse traffic patterns and generalizes to different geographical regions.

Miscellaneous Aspects of Machine Learning/General Machine Learning Techniques

Litu Rout, Negin Raoof, Giannis Daras, Constantine Caramanis, Alex Dimakis, Sanjay Shakkottai

We present the first framework to solve linear inverse problems leveraging pre-trained \textit{latent} diffusion models. Previously proposed algorithms (such as DPS and DDRM) only apply to \textit{pixel-space} diffusion models. We theoretically analyze our algorithm showing provable sample recovery in a linear model setting. The algorithmic insight obtained from our analysis extends to more general settings often considered in practice. Experimentally, we outperform previously proposed posterior sampling algorithms in a wide variety of problems including random inpainting, block inpainting, denoising, deblurring, destriping, and super-resolution.

Deep Learning/Generative Models and Autoencoders

Alexander Shmakov, Kevin Greif, Michael Fenton, Aishik Ghosh, Pierre Baldi, Daniel Whiteson

High-energy collisions at the Large Hadron Collider (LHC) provide valuable insights into open questions in particle physics. However, detector effects must be corrected before measurements can be compared to certain theoretical predictions or measurements from other detectors. Methods to solve this inverse problem of mapping detector observations to theoretical quantities of the underlying collision are essential parts of many physics analyses at the LHC. We investigate and compare various generative deep learning methods to approximate this inverse mapping. We introduce a novel unified architecture, termed latent variational diffusion models, which combines the latent learning of cutting-edge generative art approaches with an end-to-end variational framework. We demonstrate the effectiveness of this approach for reconstructing global distributions of theoretical kinematic quantities, as well as for ensuring the adherence of the learned posterior distributions to known physics constraints. Our unified approach achieves a distribution-free distance to the truth of over 20 times smaller than non-latent state-of-the-art baseline and 3 times smaller than traditional latent diffusion models.

Zineng Tang, Ziyi Yang, Chenguang Zhu, Michael Zeng, Mohit Bansal

We present Composable Diffusion (CoDi), a novel generative model capable of generating any combination of output modalities, such as language, image, video, or audio, from any combination of input modalities. Unlike existing generative AI systems, CoDi can generate multiple modalities in parallel and its input is not limited to a subset of modalities like text or image. Despite the absence of training datasets for many combinations of modalities, we propose to align modalities in both the input and output space. This allows CoDi to freely condition on any input combination and generate any group of modalities, even if they are not present in the training data. CoDi employs a novel composable generation strategy which involves building a shared multimodal space by bridging alignment in the diffusion process, enabling the synchronized generation of intertwined modalities, such as temporally aligned video and audio. Highly customizable and flexible, CoDi achieves strong joint-modality generation quality, and outperforms or is on par with the unimodal state-of-the-art for single-modality synthesis.

Deep Learning/Generative Models and Autoencoders

Sungik Choi, Hankook Lee, Honglak Lee, Moontae Lee

Novelty detection is a fundamental task of machine learning which aims to detect abnormal (*i.e.* out-of-distribution (OOD)) samples. Since diffusion models have recently emerged as the de facto standard generative framework with surprising generation results, novelty detection via diffusion models has also gained much attention. Recent methods have mainly utilized the reconstruction property of in-distribution samples. However, they often suffer from detecting OOD samples that share similar background information to the in-distribution data. Based on our observation that diffusion models can *project* any sample to an in-distribution sample with similar background information, we propose *Projection Regret (PR)*, an efficient novelty detection method that mitigates the bias of non-semantic information. To be specific, PR computes the perceptual distance between the test image and its diffusion-based projection to detect abnormality. Since the perceptual distance often fails to capture semantic changes when the background information is dominant, we cancel out the background bias by comparing it against recursive projections. Extensive experiments demonstrate that PR outperforms the prior art of generative-model-based novelty detection methods by a significant margin.

Probabilistic Methods/Monte Carlo and Sampling Methods

Luhuan Wu, Brian Trippe, Christian Naesseth, David Blei, John Cunningham

Diffusion models have been successful on a range of conditional generation tasks including molecular design and text-to-image generation. However, these achievements have primarily depended on task-specific conditional training or error-prone heuristic approximations. Ideally, a conditional generation method should provide exact samples for a broad range of conditional distributions without requiring task-specific training. To this end, we introduce the Twisted Diffusion Sampler, or TDS. TDS is a sequential Monte Carlo (SMC) algorithm that targets the conditional distributions of diffusion models through simulating a set of weighted particles. The main idea is to use twisting, an SMC technique that enjoys good computational efficiency, to incorporate heuristic approximations without compromising asymptotic exactness. We first find in simulation and in conditional image generation tasks that TDS provides a computational statistical trade-off, yielding more accurate approximations with many particles but with empirical improvements over heuristics with as few as two particles. We then turn to motif-scaffolding, a core task in protein design, using a TDS extension to Riemannian diffusion models; on benchmark tasks, TDS allows flexible conditioning criteria and often outperforms the state-of-the-art, conditionally trained model. Code can be found in https://github.com/blt2114/twisted_diffusion_sampler