Daily Papers

We introduce MAGNeT, a masked generative sequence modeling method that operates directly over several streams of audio tokens. Unlike prior work, MAGNeT is comprised of a single-stage, non-autoregressive transformer. During training, we predict spans of masked tokens obtained from a masking scheduler, while during inference we gradually construct the output sequence using several decoding steps. To further enhance the quality of the generated audio, we introduce a novel rescoring method in which, we leverage an external pre-trained model to rescore and rank predictions from MAGNeT, which will be then used for later decoding steps. Lastly, we explore a hybrid version of MAGNeT, in which we fuse between autoregressive and non-autoregressive models to generate the first few seconds in an autoregressive manner while the rest of the sequence is being decoded in parallel. We demonstrate the efficiency of MAGNeT for the task of text-to-music and text-to-audio generation and conduct an extensive empirical evaluation, considering both objective metrics and human studies. The proposed approach is comparable to the evaluated baselines, while being significantly faster (x7 faster than the autoregressive baseline). Through ablation studies and analysis, we shed light on the importance of each of the components comprising MAGNeT, together with pointing to the trade-offs between autoregressive and non-autoregressive modeling, considering latency, throughput, and generation quality. Samples are available on our demo page https://pages.cs.huji.ac.il/adiyoss-lab/MAGNeT.

We introduce MoMask, a novel masked modeling framework for text-driven 3D human motion generation. In MoMask, a hierarchical quantization scheme is employed to represent human motion as multi-layer discrete motion tokens with high-fidelity details. Starting at the base layer, with a sequence of motion tokens obtained by vector quantization, the residual tokens of increasing orders are derived and stored at the subsequent layers of the hierarchy. This is consequently followed by two distinct bidirectional transformers. For the base-layer motion tokens, a Masked Transformer is designated to predict randomly masked motion tokens conditioned on text input at training stage. During generation (i.e. inference) stage, starting from an empty sequence, our Masked Transformer iteratively fills up the missing tokens; Subsequently, a Residual Transformer learns to progressively predict the next-layer tokens based on the results from current layer. Extensive experiments demonstrate that MoMask outperforms the state-of-art methods on the text-to-motion generation task, with an FID of 0.045 (vs e.g. 0.141 of T2M-GPT) on the HumanML3D dataset, and 0.228 (vs 0.514) on KIT-ML, respectively. MoMask can also be seamlessly applied in related tasks without further model fine-tuning, such as text-guided temporal inpainting.

Generating human motion from text has been dominated by denoising motion models either through diffusion or generative masking process. However, these models face great limitations in usability by requiring prior knowledge of the motion length. Conversely, autoregressive motion models address this limitation by adaptively predicting motion endpoints, at the cost of degraded generation quality and editing capabilities. To address these challenges, we propose Bidirectional Autoregressive Motion Model (BAMM), a novel text-to-motion generation framework. BAMM consists of two key components: (1) a motion tokenizer that transforms 3D human motion into discrete tokens in latent space, and (2) a masked self-attention transformer that autoregressively predicts randomly masked tokens via a hybrid attention masking strategy. By unifying generative masked modeling and autoregressive modeling, BAMM captures rich and bidirectional dependencies among motion tokens, while learning the probabilistic mapping from textual inputs to motion outputs with dynamically-adjusted motion sequence length. This feature enables BAMM to simultaneously achieving high-quality motion generation with enhanced usability and built-in motion editability. Extensive experiments on HumanML3D and KIT-ML datasets demonstrate that BAMM surpasses current state-of-the-art methods in both qualitative and quantitative measures. Our project page is available at https://exitudio.github.io/BAMM-page

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological alternatives, but still require small molecule docking at binding pockets for targeted protein degradation (TPD). The computational design of protein-based binders presents unique opportunities to access undruggable targets, but have often relied on stable 3D structures or predictions for effective binder generation. Recently, we have leveraged the expressive latent spaces of protein language models (pLMs) for the prioritization of peptide binders from sequence alone, which we have then fused to E3 ubiquitin ligase domains, creating a CRISPR-analogous TPD system for target proteins. However, our methods rely on training discriminator models for ranking heuristically or unconditionally-derived guide peptides for their target binding capability. In this work, we introduce PepMLM, a purely target sequence-conditioned de novo generator of linear peptide binders. By employing a novel masking strategy that uniquely positions cognate peptide sequences at the terminus of target protein sequences, PepMLM tasks the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon previously-validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of target substrates in cellular models. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream programmable proteome editing applications.

Recently, the state space model Mamba has demonstrated efficient long-sequence modeling capabilities, particularly for addressing long-sequence visual tasks in 3D medical imaging. However, existing generative self-supervised learning methods have not yet fully unleashed Mamba's potential for handling long-range dependencies because they overlook the inherent causal properties of state space sequences in masked modeling. To address this challenge, we propose a general-purpose pre-training framework called MambaMIM, a masked image modeling method based on a novel TOKen-Interpolation strategy (TOKI) for the selective structure state space sequence, which learns causal relationships of state space within the masked sequence. Further, MambaMIM introduces a bottom-up 3D hybrid masking strategy to maintain a masking consistency across different architectures and can be used on any single or hybrid Mamba architecture to enhance its multi-scale and long-range representation capability. We pre-train MambaMIM on a large-scale dataset of 6.8K CT scans and evaluate its performance across eight public medical segmentation benchmarks. Extensive downstream experiments reveal the feasibility and advancement of using Mamba for medical image pre-training. In particular, when we apply the MambaMIM to a customized architecture that hybridizes MedNeXt and Vision Mamba, we consistently obtain the state-of-the-art segmentation performance. The code is available at: https://github.com/FengheTan9/MambaMIM.

World models play a crucial role in understanding and predicting the dynamics of the world, which is essential for video generation. However, existing world models are confined to specific scenarios such as gaming or driving, limiting their ability to capture the complexity of general world dynamic environments. Therefore, we introduce WorldDreamer, a pioneering world model to foster a comprehensive comprehension of general world physics and motions, which significantly enhances the capabilities of video generation. Drawing inspiration from the success of large language models, WorldDreamer frames world modeling as an unsupervised visual sequence modeling challenge. This is achieved by mapping visual inputs to discrete tokens and predicting the masked ones. During this process, we incorporate multi-modal prompts to facilitate interaction within the world model. Our experiments show that WorldDreamer excels in generating videos across different scenarios, including natural scenes and driving environments. WorldDreamer showcases versatility in executing tasks such as text-to-video conversion, image-tovideo synthesis, and video editing. These results underscore WorldDreamer's effectiveness in capturing dynamic elements within diverse general world environments.

Pre-training and fine-tuning, e.g., BERT, have achieved great success in language understanding by transferring knowledge from rich-resource pre-training task to the low/zero-resource downstream tasks. Inspired by the success of BERT, we propose MAsked Sequence to Sequence pre-training (MASS) for the encoder-decoder based language generation tasks. MASS adopts the encoder-decoder framework to reconstruct a sentence fragment given the remaining part of the sentence: its encoder takes a sentence with randomly masked fragment (several consecutive tokens) as input, and its decoder tries to predict this masked fragment. In this way, MASS can jointly train the encoder and decoder to develop the capability of representation extraction and language modeling. By further fine-tuning on a variety of zero/low-resource language generation tasks, including neural machine translation, text summarization and conversational response generation (3 tasks and totally 8 datasets), MASS achieves significant improvements over the baselines without pre-training or with other pre-training methods. Specially, we achieve the state-of-the-art accuracy (37.5 in terms of BLEU score) on the unsupervised English-French translation, even beating the early attention-based supervised model.

Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language Models (pLMs) aim to unlock insights from the vast space of unlabeled protein sequences by learning rich, semantic representations from primary sequences via masked language modeling. However, these models typically exhibit limited generative capacity. In this work, we introduce the Diffusion Sequence Model (DSM), a novel pLM trained with masked diffusion to enable both high-quality representation learning and generative protein design. DSM builds upon the ESM2 architecture by incorporating a masked forward diffusion process inspired by the LLaDA framework. After training, DSM is capable of generating diverse, biomimetic sequences that align with expected amino acid compositions, secondary structures, and predicted functions, even with 90\% token corruption. Furthermore, DSM's learned representations match or exceed those of similarly sized pLMs on downstream tasks. We also introduce DSM(ppi), a variant fine-tuned to generate protein binders by attending to target sequences. We demonstrate DSM(ppi)'s effectiveness on the challenging Bench-tested Binder Benchmark (BenchBB), where both DSM and DSM(ppi) produce candidates with superior predicted binding affinity compared to known binders. Our results establish masked diffusion as a powerful paradigm for unifying protein representation and generation in a single framework.

Large pretrained language models have recently conquered the area of natural language processing. As an alternative to predominant masked language modelling introduced in BERT, the T5 model has introduced a more general training objective, namely sequence to sequence transformation, which includes masked language model but more naturally fits text generation tasks such as machine translation, summarization, question answering, text simplification, dialogue systems, etc. The monolingual variants of T5 models have been limited to well-resourced languages, while the massively multilingual T5 model supports 101 languages. In contrast, we trained two different sized T5-type sequence to sequence models for morphologically rich Slovene language with much less resources and analyzed their behavior on 11 tasks. Concerning classification tasks, the SloT5 models mostly lag behind the monolingual Slovene SloBERTa model but are useful for the generative tasks.