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Oct 3

Beyond Vanilla Variational Autoencoders: Detecting Posterior Collapse in Conditional and Hierarchical Variational Autoencoders

The posterior collapse phenomenon in variational autoencoder (VAE), where the variational posterior distribution closely matches the prior distribution, can hinder the quality of the learned latent variables. As a consequence of posterior collapse, the latent variables extracted by the encoder in VAE preserve less information from the input data and thus fail to produce meaningful representations as input to the reconstruction process in the decoder. While this phenomenon has been an actively addressed topic related to VAE performance, the theory for posterior collapse remains underdeveloped, especially beyond the standard VAE. In this work, we advance the theoretical understanding of posterior collapse to two important and prevalent yet less studied classes of VAE: conditional VAE and hierarchical VAE. Specifically, via a non-trivial theoretical analysis of linear conditional VAE and hierarchical VAE with two levels of latent, we prove that the cause of posterior collapses in these models includes the correlation between the input and output of the conditional VAE and the effect of learnable encoder variance in the hierarchical VAE. We empirically validate our theoretical findings for linear conditional and hierarchical VAE and demonstrate that these results are also predictive for non-linear cases with extensive experiments.

Hi-VAE: Efficient Video Autoencoding with Global and Detailed Motion

Recent breakthroughs in video autoencoders (Video AEs) have advanced video generation, but existing methods fail to efficiently model spatio-temporal redundancies in dynamics, resulting in suboptimal compression factors. This shortfall leads to excessive training costs for downstream tasks. To address this, we introduce Hi-VAE, an efficient video autoencoding framework that hierarchically encode coarse-to-fine motion representations of video dynamics and formulate the decoding process as a conditional generation task. Specifically, Hi-VAE decomposes video dynamics into two latent spaces: Global Motion, capturing overarching motion patterns, and Detailed Motion, encoding high-frequency spatial details. Using separate self-supervised motion encoders, we compress video latents into compact motion representations to reduce redundancy significantly. A conditional diffusion decoder then reconstructs videos by combining hierarchical global and detailed motions, enabling high-fidelity video reconstructions. Extensive experiments demonstrate that Hi-VAE achieves a high compression factor of 1428times, almost 30times higher than baseline methods (e.g., Cosmos-VAE at 48times), validating the efficiency of our approach. Meanwhile, Hi-VAE maintains high reconstruction quality at such high compression rates and performs effectively in downstream generative tasks. Moreover, Hi-VAE exhibits interpretability and scalability, providing new perspectives for future exploration in video latent representation and generation.

Michelangelo: Conditional 3D Shape Generation based on Shape-Image-Text Aligned Latent Representation

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.

Generative Modeling of Regular and Irregular Time Series Data via Koopman VAEs

Generating realistic time series data is important for many engineering and scientific applications. Existing work tackles this problem using generative adversarial networks (GANs). However, GANs are often unstable during training, and they can suffer from mode collapse. While variational autoencoders (VAEs) are known to be more robust to these issues, they are (surprisingly) less often considered for time series generation. In this work, we introduce Koopman VAE (KVAE), a new generative framework that is based on a novel design for the model prior, and that can be optimized for either regular and irregular training data. Inspired by Koopman theory, we represent the latent conditional prior dynamics using a linear map. Our approach enhances generative modeling with two desired features: (i) incorporating domain knowledge can be achieved by leverageing spectral tools that prescribe constraints on the eigenvalues of the linear map; and (ii) studying the qualitative behavior and stablity of the system can be performed using tools from dynamical systems theory. Our results show that KVAE outperforms state-of-the-art GAN and VAE methods across several challenging synthetic and real-world time series generation benchmarks. Whether trained on regular or irregular data, KVAE generates time series that improve both discriminative and predictive metrics. We also present visual evidence suggesting that KVAE learns probability density functions that better approximate empirical ground truth distributions.

PaccMann$^{RL}$ on SARS-CoV-2: Designing antiviral candidates with conditional generative models

With the fast development of COVID-19 into a global pandemic, scientists around the globe are desperately searching for effective antiviral therapeutic agents. Bridging systems biology and drug discovery, we propose a deep learning framework for conditional de novo design of antiviral candidate drugs tailored against given protein targets. First, we train a multimodal ligand--protein binding affinity model on predicting affinities of antiviral compounds to target proteins and couple this model with pharmacological toxicity predictors. Exploiting this multi-objective as a reward function of a conditional molecular generator (consisting of two VAEs), we showcase a framework that navigates the chemical space toward regions with more antiviral molecules. Specifically, we explore a challenging setting of generating ligands against unseen protein targets by performing a leave-one-out-cross-validation on 41 SARS-CoV-2-related target proteins. Using deep RL, it is demonstrated that in 35 out of 41 cases, the generation is biased towards sampling more binding ligands, with an average increase of 83% comparing to an unbiased VAE. We present a case-study on a potential Envelope-protein inhibitor and perform a synthetic accessibility assessment of the best generated molecules is performed that resembles a viable roadmap towards a rapid in-vitro evaluation of potential SARS-CoV-2 inhibitors.

Vector Quantized Diffusion Model for Text-to-Image Synthesis

We present the vector quantized diffusion (VQ-Diffusion) model for text-to-image generation. This method is based on a vector quantized variational autoencoder (VQ-VAE) whose latent space is modeled by a conditional variant of the recently developed Denoising Diffusion Probabilistic Model (DDPM). We find that this latent-space method is well-suited for text-to-image generation tasks because it not only eliminates the unidirectional bias with existing methods but also allows us to incorporate a mask-and-replace diffusion strategy to avoid the accumulation of errors, which is a serious problem with existing methods. Our experiments show that the VQ-Diffusion produces significantly better text-to-image generation results when compared with conventional autoregressive (AR) models with similar numbers of parameters. Compared with previous GAN-based text-to-image methods, our VQ-Diffusion can handle more complex scenes and improve the synthesized image quality by a large margin. Finally, we show that the image generation computation in our method can be made highly efficient by reparameterization. With traditional AR methods, the text-to-image generation time increases linearly with the output image resolution and hence is quite time consuming even for normal size images. The VQ-Diffusion allows us to achieve a better trade-off between quality and speed. Our experiments indicate that the VQ-Diffusion model with the reparameterization is fifteen times faster than traditional AR methods while achieving a better image quality.

ECHOPulse: ECG controlled echocardio-grams video generation

Echocardiography (ECHO) is essential for cardiac assessments, but its video quality and interpretation heavily relies on manual expertise, leading to inconsistent results from clinical and portable devices. ECHO video generation offers a solution by improving automated monitoring through synthetic data and generating high-quality videos from routine health data. However, existing models often face high computational costs, slow inference, and rely on complex conditional prompts that require experts' annotations. To address these challenges, we propose ECHOPULSE, an ECG-conditioned ECHO video generation model. ECHOPULSE introduces two key advancements: (1) it accelerates ECHO video generation by leveraging VQ-VAE tokenization and masked visual token modeling for fast decoding, and (2) it conditions on readily accessible ECG signals, which are highly coherent with ECHO videos, bypassing complex conditional prompts. To the best of our knowledge, this is the first work to use time-series prompts like ECG signals for ECHO video generation. ECHOPULSE not only enables controllable synthetic ECHO data generation but also provides updated cardiac function information for disease monitoring and prediction beyond ECG alone. Evaluations on three public and private datasets demonstrate state-of-the-art performance in ECHO video generation across both qualitative and quantitative measures. Additionally, ECHOPULSE can be easily generalized to other modality generation tasks, such as cardiac MRI, fMRI, and 3D CT generation. Demo can seen from https://github.com/levyisthebest/ECHOPulse_Prelease.

DiffuseVAE: Efficient, Controllable and High-Fidelity Generation from Low-Dimensional Latents

Diffusion probabilistic models have been shown to generate state-of-the-art results on several competitive image synthesis benchmarks but lack a low-dimensional, interpretable latent space, and are slow at generation. On the other hand, standard Variational Autoencoders (VAEs) typically have access to a low-dimensional latent space but exhibit poor sample quality. We present DiffuseVAE, a novel generative framework that integrates VAE within a diffusion model framework, and leverage this to design novel conditional parameterizations for diffusion models. We show that the resulting model equips diffusion models with a low-dimensional VAE inferred latent code which can be used for downstream tasks like controllable synthesis. The proposed method also improves upon the speed vs quality tradeoff exhibited in standard unconditional DDPM/DDIM models (for instance, FID of 16.47 vs 34.36 using a standard DDIM on the CelebA-HQ-128 benchmark using T=10 reverse process steps) without having explicitly trained for such an objective. Furthermore, the proposed model exhibits synthesis quality comparable to state-of-the-art models on standard image synthesis benchmarks like CIFAR-10 and CelebA-64 while outperforming most existing VAE-based methods. Lastly, we show that the proposed method exhibits inherent generalization to different types of noise in the conditioning signal. For reproducibility, our source code is publicly available at https://github.com/kpandey008/DiffuseVAE.

PortaSpeech: Portable and High-Quality Generative Text-to-Speech

Non-autoregressive text-to-speech (NAR-TTS) models such as FastSpeech 2 and Glow-TTS can synthesize high-quality speech from the given text in parallel. After analyzing two kinds of generative NAR-TTS models (VAE and normalizing flow), we find that: VAE is good at capturing the long-range semantics features (e.g., prosody) even with small model size but suffers from blurry and unnatural results; and normalizing flow is good at reconstructing the frequency bin-wise details but performs poorly when the number of model parameters is limited. Inspired by these observations, to generate diverse speech with natural details and rich prosody using a lightweight architecture, we propose PortaSpeech, a portable and high-quality generative text-to-speech model. Specifically, 1) to model both the prosody and mel-spectrogram details accurately, we adopt a lightweight VAE with an enhanced prior followed by a flow-based post-net with strong conditional inputs as the main architecture. 2) To further compress the model size and memory footprint, we introduce the grouped parameter sharing mechanism to the affine coupling layers in the post-net. 3) To improve the expressiveness of synthesized speech and reduce the dependency on accurate fine-grained alignment between text and speech, we propose a linguistic encoder with mixture alignment combining hard inter-word alignment and soft intra-word alignment, which explicitly extracts word-level semantic information. Experimental results show that PortaSpeech outperforms other TTS models in both voice quality and prosody modeling in terms of subjective and objective evaluation metrics, and shows only a slight performance degradation when reducing the model parameters to 6.7M (about 4x model size and 3x runtime memory compression ratio compared with FastSpeech 2). Our extensive ablation studies demonstrate that each design in PortaSpeech is effective.