Daily Papers

This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from evolutionary-scale protein sequences within a generative self-supervised discrete diffusion probabilistic framework, which generalizes language modeling for proteins in a principled way. After pre-training, DPLM exhibits the ability to generate structurally plausible, novel, and diverse protein sequences for unconditional generation. We further demonstrate the proposed diffusion generative pre-training makes DPLM possess a better understanding of proteins, making it a superior representation learner, which can be fine-tuned for various predictive tasks, comparing favorably to ESM2 (Lin et al., 2022). Moreover, DPLM can be tailored for various needs, which showcases its prowess of conditional generation in several ways: (1) conditioning on partial peptide sequences, e.g., generating scaffolds for functional motifs with high success rate; (2) incorporating other modalities as conditioner, e.g., structure-conditioned generation for inverse folding; and (3) steering sequence generation towards desired properties, e.g., satisfying specified secondary structures, through a plug-and-play classifier guidance. Code is released at https://github.com/bytedance/dplm.

Effective and efficient tokenization plays an important role in image representation and generation. Conventional methods, constrained by uniform 2D/1D grid tokenization, are inflexible to represent regions with varying shapes and textures and at different locations, limiting their efficacy of feature representation. In this work, we propose GPSToken, a novel Gaussian Parameterized Spatially-adaptive Tokenization framework, to achieve non-uniform image tokenization by leveraging parametric 2D Gaussians to dynamically model the shape, position, and textures of different image regions. We first employ an entropy-driven algorithm to partition the image into texture-homogeneous regions of variable sizes. Then, we parameterize each region as a 2D Gaussian (mean for position, covariance for shape) coupled with texture features. A specialized transformer is trained to optimize the Gaussian parameters, enabling continuous adaptation of position/shape and content-aware feature extraction. During decoding, Gaussian parameterized tokens are reconstructed into 2D feature maps through a differentiable splatting-based renderer, bridging our adaptive tokenization with standard decoders for end-to-end training. GPSToken disentangles spatial layout (Gaussian parameters) from texture features to enable efficient two-stage generation: structural layout synthesis using lightweight networks, followed by structure-conditioned texture generation. Experiments demonstrate the state-of-the-art performance of GPSToken, which achieves rFID and FID scores of 0.65 and 1.50 on image reconstruction and generation tasks using 128 tokens, respectively. Codes and models of GPSToken can be found at https://github.com/xtudbxk/GPSToken{https://github.com/xtudbxk/GPSToken}.

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation. The code is available at https://github.com/prescient-design/funcbind.

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.

Diffusion Probabilistic Models (DPMs) have recently been employed for image deblurring, formulated as an image-conditioned generation process that maps Gaussian noise to the high-quality image, conditioned on the blurry input. Image-conditioned DPMs (icDPMs) have shown more realistic results than regression-based methods when trained on pairwise in-domain data. However, their robustness in restoring images is unclear when presented with out-of-domain images as they do not impose specific degradation models or intermediate constraints. To this end, we introduce a simple yet effective multiscale structure guidance as an implicit bias that informs the icDPM about the coarse structure of the sharp image at the intermediate layers. This guided formulation leads to a significant improvement of the deblurring results, particularly on unseen domain. The guidance is extracted from the latent space of a regression network trained to predict the clean-sharp target at multiple lower resolutions, thus maintaining the most salient sharp structures. With both the blurry input and multiscale guidance, the icDPM model can better understand the blur and recover the clean image. We evaluate a single-dataset trained model on diverse datasets and demonstrate more robust deblurring results with fewer artifacts on unseen data. Our method outperforms existing baselines, achieving state-of-the-art perceptual quality while keeping competitive distortion metrics.

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

Recent conditional image generation methods produce images of remarkable diversity, fidelity and realism. However, the majority of these methods allow conditioning only on labels or text prompts, which limits their level of control over the generation result. In this paper, we introduce MaskSketch, an image generation method that allows spatial conditioning of the generation result using a guiding sketch as an extra conditioning signal during sampling. MaskSketch utilizes a pre-trained masked generative transformer, requiring no model training or paired supervision, and works with input sketches of different levels of abstraction. We show that intermediate self-attention maps of a masked generative transformer encode important structural information of the input image, such as scene layout and object shape, and we propose a novel sampling method based on this observation to enable structure-guided generation. Our results show that MaskSketch achieves high image realism and fidelity to the guiding structure. Evaluated on standard benchmark datasets, MaskSketch outperforms state-of-the-art methods for sketch-to-image translation, as well as unpaired image-to-image translation approaches.

Recently, symbolic music generation has become a focus of numerous deep learning research. Structure as an important part of music, contributes to improving the quality of music, and an increasing number of works start to study the hierarchical structure. In this study, we delve into the multi-level structures within music from macro-level and micro-level hierarchies. At the macro-level hierarchy, we conduct phrase segmentation algorithm to explore how phrases influence the overall development of music, and at the micro-level hierarchy, we design skeleton notes extraction strategy to explore how skeleton notes within each phrase guide the melody generation. Furthermore, we propose a novel Phrase-level Cross-Attention mechanism to capture the intrinsic relationship between macro-level hierarchy and micro-level hierarchy. Moreover, in response to the current lack of research on Chinese-style music, we construct our Small Tunes Dataset: a substantial collection of MIDI files comprising 10088 Small Tunes, a category of traditional Chinese Folk Songs. This dataset serves as the focus of our study. We generate Small Tunes songs utilizing the extracted skeleton notes as conditions, and experiment results indicate that our proposed model, Small Tunes Transformer, outperforms other state-of-the-art models. Besides, we design three novel objective evaluation metrics to evaluate music from both rhythm and melody dimensions.

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.

Despite the availability of large-scale 3D datasets and advancements in 3D generative models, the complexity and uneven quality of 3D geometry and texture data continue to hinder the performance of 3D generation techniques. In most existing approaches, 3D geometry and texture are generated in separate stages using different models and non-unified representations, frequently leading to unsatisfactory coherence between geometry and texture. To address these challenges, we propose a novel framework for joint generation of 3D geometry and texture. Specifically, we focus in generate a versatile 2.5D representations that can be seamlessly transformed between 2D and 3D. Our approach begins by integrating multiview RGB, normal, and coordinate images into a unified representation, termed as 2.5D latents. Next, we adapt pre-trained 2D foundation models for high-fidelity 2.5D generation, utilizing both text and image conditions. Finally, we introduce a lightweight 2.5D-to-3D refiner-decoder framework that efficiently generates detailed 3D representations from 2.5D images. Extensive experiments demonstrate that our model not only excels in generating high-quality 3D objects with coherent structure and color from text and image inputs but also significantly outperforms existing methods in geometry-conditioned texture generation.

This paper investigates the fundamental discontinuity between the latest two Segment Anything Models: SAM2 and SAM3. We explain why the expertise in prompt-based segmentation of SAM2 does not transfer to the multimodal concept-driven paradigm of SAM3. SAM2 operates through spatial prompts points, boxes, and masks yielding purely geometric and temporal segmentation. In contrast, SAM3 introduces a unified vision-language architecture capable of open-vocabulary reasoning, semantic grounding, contrastive alignment, and exemplar-based concept understanding. We structure this analysis through five core components: (1) a Conceptual Break Between Prompt-Based and Concept-Based Segmentation, contrasting spatial prompt semantics of SAM2 with multimodal fusion and text-conditioned mask generation of SAM3; (2) Architectural Divergence, detailing pure vision-temporal design of SAM2 versus integration of vision-language encoders, geometry and exemplar encoders, fusion modules, DETR-style decoders, object queries, and ambiguity-handling via Mixture-of-Experts in SAM3; (3) Dataset and Annotation Differences, contrasting SA-V video masks with multimodal concept-annotated corpora of SAM3; (4) Training and Hyperparameter Distinctions, showing why SAM2 optimization knowledge does not apply to SAM3; and (5) Evaluation, Metrics, and Failure Modes, outlining the transition from geometric IoU metrics to semantic, open-vocabulary evaluation. Together, these analyses establish SAM3 as a new class of segmentation foundation model and chart future directions for the emerging concept-driven segmentation era.

Personalized vaccines and T-cell immunotherapies depend critically on identifying peptide-MHC class I (pMHC-I) interactions capable of eliciting potent immune responses. However, current benchmarks and models inherit biases present in mass-spectrometry and binding-assay datasets, limiting discovery of novel peptide ligands. To address this issue, we introduce a structure-guided benchmark of pMHC-I peptides designed using diffusion models conditioned on crystal structure interaction distances. Spanning twenty high-priority HLA alleles, this benchmark is independent of previously characterized peptides yet reproduces canonical anchor residue preferences, indicating structural generalization without experimental dataset bias. Using this resource, we demonstrate that state-of-the-art sequence-based predictors perform poorly at recognizing the binding potential of these structurally stable designs, indicating allele-specific limitations invisible in conventional evaluations. Our geometry-aware design pipeline yields peptides with high predicted structural integrity and higher residue diversity than existing datasets, representing a key resource for unbiased model training and evaluation. Our code, and data are available at: https://github.com/sermare/struct-mhc-dev.

Talking head video generation aims to animate a human face in a still image with dynamic poses and expressions using motion information derived from a target-driving video, while maintaining the person's identity in the source image. However, dramatic and complex motions in the driving video cause ambiguous generation, because the still source image cannot provide sufficient appearance information for occluded regions or delicate expression variations, which produces severe artifacts and significantly degrades the generation quality. To tackle this problem, we propose to learn a global facial representation space, and design a novel implicit identity representation conditioned memory compensation network, coined as MCNet, for high-fidelity talking head generation.~Specifically, we devise a network module to learn a unified spatial facial meta-memory bank from all training samples, which can provide rich facial structure and appearance priors to compensate warped source facial features for the generation. Furthermore, we propose an effective query mechanism based on implicit identity representations learned from the discrete keypoints of the source image. It can greatly facilitate the retrieval of more correlated information from the memory bank for the compensation. Extensive experiments demonstrate that MCNet can learn representative and complementary facial memory, and can clearly outperform previous state-of-the-art talking head generation methods on VoxCeleb1 and CelebV datasets. Please check our https://github.com/harlanhong/ICCV2023-MCNET{Project}.

The creation of 3D assets with explicit, editable part structures is crucial for advancing interactive applications, yet most generative methods produce only monolithic shapes, limiting their utility. We introduce OmniPart, a novel framework for part-aware 3D object generation designed to achieve high semantic decoupling among components while maintaining robust structural cohesion. OmniPart uniquely decouples this complex task into two synergistic stages: (1) an autoregressive structure planning module generates a controllable, variable-length sequence of 3D part bounding boxes, critically guided by flexible 2D part masks that allow for intuitive control over part decomposition without requiring direct correspondences or semantic labels; and (2) a spatially-conditioned rectified flow model, efficiently adapted from a pre-trained holistic 3D generator, synthesizes all 3D parts simultaneously and consistently within the planned layout. Our approach supports user-defined part granularity, precise localization, and enables diverse downstream applications. Extensive experiments demonstrate that OmniPart achieves state-of-the-art performance, paving the way for more interpretable, editable, and versatile 3D content.

Deep neural networks have brought remarkable breakthroughs in medical image analysis. However, due to their data-hungry nature, the modest dataset sizes in medical imaging projects might be hindering their full potential. Generating synthetic data provides a promising alternative, allowing to complement training datasets and conducting medical image research at a larger scale. Diffusion models recently have caught the attention of the computer vision community by producing photorealistic synthetic images. In this study, we explore using Latent Diffusion Models to generate synthetic images from high-resolution 3D brain images. We used T1w MRI images from the UK Biobank dataset (N=31,740) to train our models to learn about the probabilistic distribution of brain images, conditioned on covariables, such as age, sex, and brain structure volumes. We found that our models created realistic data, and we could use the conditioning variables to control the data generation effectively. Besides that, we created a synthetic dataset with 100,000 brain images and made it openly available to the scientific community.

Multimodal Large Language Models (MLLMs) with unified architectures excel across a wide range of vision-language tasks, yet aligning them with personalized image generation remains a significant challenge. Existing methods for MLLMs are frequently subject-specific, demanding a data-intensive fine-tuning process for every new subject, which limits their scalability. In this paper, we introduce MM-R1, a framework that integrates a cross-modal Chain-of-Thought (X-CoT) reasoning strategy to unlock the inherent potential of unified MLLMs for personalized image generation. Specifically, we structure personalization as an integrated visual reasoning and generation process: (1) grounding subject concepts by interpreting and understanding user-provided images and contextual cues, and (2) generating personalized images conditioned on both the extracted subject representations and user prompts. To further enhance the reasoning capability, we adopt Grouped Reward Proximal Policy Optimization (GRPO) to explicitly align the generation. Experiments demonstrate that MM-R1 unleashes the personalization capability of unified MLLMs to generate images with high subject fidelity and strong text alignment in a zero-shot manner.

Controllable face generation poses critical challenges in generative modeling due to the intricate balance required between semantic controllability and photorealism. While existing approaches struggle with disentangling semantic controls from generation pipelines, we revisit the architectural potential of Diffusion Transformers (DiTs) through the lens of expert specialization. This paper introduces Face-MoGLE, a novel framework featuring: (1) Semantic-decoupled latent modeling through mask-conditioned space factorization, enabling precise attribute manipulation; (2) A mixture of global and local experts that captures holistic structure and region-level semantics for fine-grained controllability; (3) A dynamic gating network producing time-dependent coefficients that evolve with diffusion steps and spatial locations. Face-MoGLE provides a powerful and flexible solution for high-quality, controllable face generation, with strong potential in generative modeling and security applications. Extensive experiments demonstrate its effectiveness in multimodal and monomodal face generation settings and its robust zero-shot generalization capability. Project page is available at https://github.com/XavierJiezou/Face-MoGLE.

Large-scale scene data is essential for training and testing in robot learning. Neural reconstruction methods have promised the capability of reconstructing large physically-grounded outdoor scenes from captured sensor data. However, these methods have baked-in static environments and only allow for limited scene control -- they are functionally constrained in scene and trajectory diversity by the captures from which they are reconstructed. In contrast, generating driving data with recent image or video diffusion models offers control, however, at the cost of geometry grounding and causality. In this work, we aim to bridge this gap and present a method that directly generates large-scale 3D driving scenes with accurate geometry, allowing for causal novel view synthesis with object permanence and explicit 3D geometry estimation. The proposed method combines the generation of a proxy geometry and environment representation with score distillation from learned 2D image priors. We find that this approach allows for high controllability, enabling the prompt-guided geometry and high-fidelity texture and structure that can be conditioned on map layouts -- producing realistic and geometrically consistent 3D generations of complex driving scenes.

Real-world databases are predominantly relational, comprising multiple interlinked tables that contain complex structural and statistical dependencies. Learning generative models on relational data has shown great promise in generating synthetic data and imputing missing values. However, existing methods often struggle to capture this complexity, typically reducing relational data to conditionally generated flat tables and imposing limiting structural assumptions. To address these limitations, we introduce RelDiff, a novel diffusion generative model that synthesizes complete relational databases by explicitly modeling their foreign key graph structure. RelDiff combines a joint graph-conditioned diffusion process across all tables for attribute synthesis, and a 2K+SBM graph generator based on the Stochastic Block Model for structure generation. The decomposition of graph structure and relational attributes ensures both high fidelity and referential integrity, both of which are crucial aspects of synthetic relational database generation. Experiments on 11 benchmark datasets demonstrate that RelDiff consistently outperforms prior methods in producing realistic and coherent synthetic relational databases. Code is available at https://github.com/ValterH/RelDiff.

Multimodal embeddings are widely used in downstream tasks such as multimodal retrieval, enabling alignment of interleaved modalities in a shared representation space. While recent studies show that Multimodal Large Language Models (MLLMs) can serve as strong embedding extractors, existing approaches treat embedding extraction as a direct encoding step, overlooking the fact that MLLMs possess the generative capability for reasoning that could be leveraged to enhance representation quality. In this work, we explore how to explicitly incorporate reasoning into the embedding process. To this end, we propose Reasoning Guided Embeddings (RGE), which preserves the generative rationale process of MLLMs and couples it with contrastive training. Our method first enables the model to perform structured rationale generation conditioned on the instruction, and then extracts representations after reasoning has unfolded. This simple design enhances the context-conditional inference signals within the embedding, leading to improved multimodal representation quality. Experiments on the MMEB benchmark show that reasoning-guided conditioning improves multimodal retrieval performance by 4.9% over the non-reasoning baseline, confirming that explicit reasoning can effectively enhance embedding quality.

The EMelodyGen system focuses on emotional melody generation in ABC notation controlled by the musical feature template. Owing to the scarcity of well-structured and emotionally labeled sheet music, we designed a template for controlling emotional melody generation by statistical correlations between musical features and emotion labels derived from small-scale emotional symbolic music datasets and music psychology conclusions. We then automatically annotated a large, well-structured sheet music collection with rough emotional labels by the template, converted them into ABC notation, and reduced label imbalance by data augmentation, resulting in a dataset named Rough4Q. Our system backbone pre-trained on Rough4Q can achieve up to 99% music21 parsing rate and melodies generated by our template can lead to a 91% alignment on emotional expressions in blind listening tests. Ablation studies further validated the effectiveness of the feature controls in the template. Available code and demos are at https://github.com/monetjoe/EMelodyGen.

Generative models offer a scalable and flexible paradigm for simulating complex environments, yet current approaches fall short in addressing the domain-specific requirements of autonomous driving - such as multi-agent interactions, fine-grained control, and multi-camera consistency. We introduce GAIA-2, Generative AI for Autonomy, a latent diffusion world model that unifies these capabilities within a single generative framework. GAIA-2 supports controllable video generation conditioned on a rich set of structured inputs: ego-vehicle dynamics, agent configurations, environmental factors, and road semantics. It generates high-resolution, spatiotemporally consistent multi-camera videos across geographically diverse driving environments (UK, US, Germany). The model integrates both structured conditioning and external latent embeddings (e.g., from a proprietary driving model) to facilitate flexible and semantically grounded scene synthesis. Through this integration, GAIA-2 enables scalable simulation of both common and rare driving scenarios, advancing the use of generative world models as a core tool in the development of autonomous systems. Videos are available at https://wayve.ai/thinking/gaia-2.

Recently, visually-situated text parsing (VsTP) has experienced notable advancements, driven by the increasing demand for automated document understanding and the emergence of Generative Large Language Models (LLMs) capable of processing document-based questions. Various methods have been proposed to address the challenging problem of VsTP. However, due to the diversified targets and heterogeneous schemas, previous works usually design task-specific architectures and objectives for individual tasks, which inadvertently leads to modal isolation and complex workflow. In this paper, we propose a unified paradigm for parsing visually-situated text across diverse scenarios. Specifically, we devise a universal model, called OmniParser, which can simultaneously handle three typical visually-situated text parsing tasks: text spotting, key information extraction, and table recognition. In OmniParser, all tasks share the unified encoder-decoder architecture, the unified objective: point-conditioned text generation, and the unified input & output representation: prompt & structured sequences. Extensive experiments demonstrate that the proposed OmniParser achieves state-of-the-art (SOTA) or highly competitive performances on 7 datasets for the three visually-situated text parsing tasks, despite its unified, concise design. The code is available at https://github.com/AlibabaResearch/AdvancedLiterateMachinery.

In this paper, we propose Img2CAD, the first approach to our knowledge that uses 2D image inputs to generate CAD models with editable parameters. Unlike existing AI methods for 3D model generation using text or image inputs often rely on mesh-based representations, which are incompatible with CAD tools and lack editability and fine control, Img2CAD enables seamless integration between AI-based 3D reconstruction and CAD software. We have identified an innovative intermediate representation called Structured Visual Geometry (SVG), characterized by vectorized wireframes extracted from objects. This representation significantly enhances the performance of generating conditioned CAD models. Additionally, we introduce two new datasets to further support research in this area: ABC-mono, the largest known dataset comprising over 200,000 3D CAD models with rendered images, and KOCAD, the first dataset featuring real-world captured objects alongside their ground truth CAD models, supporting further research in conditioned CAD model generation.

Interactions with large language models (LLMs) often yield long and detailed responses, leveraging both parametric knowledge and retrieval-augmented generation (RAG). While these responses can provide rich insights, they often include redundant or less engaging content not aligned with user interests. This issue becomes apparent when users specify particular subtopics to include or exclude -- termed coverage-conditioned (C^2) queries -- as LLMs often struggle to provide tailored responses. To address this challenge, we investigate the role of query outlines, sequences of subqueries designed to guide LLMs in generating responses that meet specific user requirements. To systematically create and evaluate these outlines, we introduce QTree, a dataset of 10K hierarchical sets of information-seeking subqueries that define structured boundaries for outline creation and evaluation in C^2 scenarios. Additionally, we develop QPlanner, a 7B language model trained to generate customized outlines within boundaries of QTree. We evaluate the effectiveness of the generated outlines through automatic and human judgements, focusing on their impact within retrieval-augmented generation (RAG) systems. Experimental results demonstrate that QPlanner, especially when trained with alignment techniques like DPO, generates higher-quality outlines that better fulfill diverse user needs.

We introduce PartCrafter, the first structured 3D generative model that jointly synthesizes multiple semantically meaningful and geometrically distinct 3D meshes from a single RGB image. Unlike existing methods that either produce monolithic 3D shapes or follow two-stage pipelines, i.e., first segmenting an image and then reconstructing each segment, PartCrafter adopts a unified, compositional generation architecture that does not rely on pre-segmented inputs. Conditioned on a single image, it simultaneously denoises multiple 3D parts, enabling end-to-end part-aware generation of both individual objects and complex multi-object scenes. PartCrafter builds upon a pretrained 3D mesh diffusion transformer (DiT) trained on whole objects, inheriting the pretrained weights, encoder, and decoder, and introduces two key innovations: (1) A compositional latent space, where each 3D part is represented by a set of disentangled latent tokens; (2) A hierarchical attention mechanism that enables structured information flow both within individual parts and across all parts, ensuring global coherence while preserving part-level detail during generation. To support part-level supervision, we curate a new dataset by mining part-level annotations from large-scale 3D object datasets. Experiments show that PartCrafter outperforms existing approaches in generating decomposable 3D meshes, including parts that are not directly visible in input images, demonstrating the strength of part-aware generative priors for 3D understanding and synthesis. Code and training data will be released.

We introduce Goal-Conditioned Visual Navigation Instruction Generation (GoViG), a new task that aims to autonomously generate precise and contextually coherent navigation instructions solely from egocentric visual observations of initial and goal states. Unlike conventional approaches that rely on structured inputs such as semantic annotations or environmental maps, GoViG exclusively leverages raw egocentric visual data, substantially improving its adaptability to unseen and unstructured environments. Our method addresses this task by decomposing it into two interconnected subtasks: (1) visual forecasting, which predicts intermediate visual states bridging the initial and goal views; and (2) instruction generation, which synthesizes linguistically coherent instructions grounded in both observed and anticipated visuals. These subtasks are integrated within an autoregressive multimodal large language model trained with tailored objectives to ensure spatial accuracy and linguistic clarity. Furthermore, we introduce two complementary multimodal reasoning strategies, one-pass and interleaved reasoning, to mimic incremental human cognitive processes during navigation. To evaluate our method, we propose the R2R-Goal dataset, combining diverse synthetic and real-world trajectories. Empirical results demonstrate significant improvements over state-of-the-art methods, achieving superior BLEU-4 and CIDEr scores along with robust cross-domain generalization.

Extensive LLM applications demand efficient structured generations, particularly for LR(1) grammars, to produce outputs in specified formats (e.g., JSON). Existing methods primarily parse LR(1) grammars into a pushdown automaton (PDA), leading to runtime execution overhead for context-dependent token processing, especially inefficient under large inference batches. To address these issues, we propose Pre^3 that exploits deterministic pushdown automata (DPDA) to optimize the constrained LLM decoding efficiency. First, by precomputing prefix-conditioned edges during the preprocessing, Pre^3 enables ahead-of-time edge analysis and thus makes parallel transition processing possible. Second, by leveraging the prefix-conditioned edges, Pre^3 introduces a novel approach that transforms LR(1) transition graphs into DPDA, eliminating the need for runtime path exploration and achieving edge transitions with minimal overhead. Pre^3 can be seamlessly integrated into standard LLM inference frameworks, reducing time per output token (TPOT) by up to 40% and increasing throughput by up to 36% in our experiments. Our code is available at https://github.com/ModelTC/lightllm.

In text-driven 3D scene generation, object layout serves as a crucial intermediate representation that bridges high-level language instructions with detailed geometric output. It not only provides a structural blueprint for ensuring physical plausibility but also supports semantic controllability and interactive editing. However, the learning capabilities of current 3D indoor layout generation models are constrained by the limited scale, diversity, and annotation quality of existing datasets. To address this, we introduce M3DLayout, a large-scale, multi-source dataset for 3D indoor layout generation. M3DLayout comprises 15,080 layouts and over 258k object instances, integrating three distinct sources: real-world scans, professional CAD designs, and procedurally generated scenes. Each layout is paired with detailed structured text describing global scene summaries, relational placements of large furniture, and fine-grained arrangements of smaller items. This diverse and richly annotated resource enables models to learn complex spatial and semantic patterns across a wide variety of indoor environments. To assess the potential of M3DLayout, we establish a benchmark using a text-conditioned diffusion model. Experimental results demonstrate that our dataset provides a solid foundation for training layout generation models. Its multi-source composition enhances diversity, notably through the Inf3DLayout subset which provides rich small-object information, enabling the generation of more complex and detailed scenes. We hope that M3DLayout can serve as a valuable resource for advancing research in text-driven 3D scene synthesis.

Reasoning remains a challenging task for large language models (LLMs), especially within the logically constrained environment of automated theorem proving (ATP), due to sparse rewards and the vast scale of proofs. These challenges are amplified in benchmarks like PutnamBench, which contains university-level problems requiring complex, multi-step reasoning. To address this, we introduce self-generated goal-conditioned MDPs (sG-MDPs), a new framework in which agents generate and pursue their subgoals based on the evolving proof state. Given this more structured generation of goals, the resulting problem becomes more amenable to search. We then apply Monte Carlo Tree Search (MCTS)-like algorithms to solve the sG-MDP, instantiating our approach in Bourbaki (7B), a modular system that can ensemble multiple 7B LLMs for subgoal generation and tactic synthesis. On PutnamBench, Bourbaki (7B) solves 26 problems, achieving new state-of-the-art results with models at this scale.

Music generation has attracted growing interest with the advancement of deep generative models. However, generating music conditioned on textual descriptions, known as text-to-music, remains challenging due to the complexity of musical structures and high sampling rate requirements. Despite the task's significance, prevailing generative models exhibit limitations in music quality, computational efficiency, and generalization. This paper introduces JEN-1, a universal high-fidelity model for text-to-music generation. JEN-1 is a diffusion model incorporating both autoregressive and non-autoregressive training. Through in-context learning, JEN-1 performs various generation tasks including text-guided music generation, music inpainting, and continuation. Evaluations demonstrate JEN-1's superior performance over state-of-the-art methods in text-music alignment and music quality while maintaining computational efficiency. Our demos are available at http://futureverse.com/research/jen/demos/jen1

We show that the GPS tags contained in photo metadata provide a useful control signal for image generation. We train GPS-to-image models and use them for tasks that require a fine-grained understanding of how images vary within a city. In particular, we train a diffusion model to generate images conditioned on both GPS and text. The learned model generates images that capture the distinctive appearance of different neighborhoods, parks, and landmarks. We also extract 3D models from 2D GPS-to-image models through score distillation sampling, using GPS conditioning to constrain the appearance of the reconstruction from each viewpoint. Our evaluations suggest that our GPS-conditioned models successfully learn to generate images that vary based on location, and that GPS conditioning improves estimated 3D structure.

Generating videos from text has proven to be a significant challenge for existing generative models. We tackle this problem by training a conditional generative model to extract both static and dynamic information from text. This is manifested in a hybrid framework, employing a Variational Autoencoder (VAE) and a Generative Adversarial Network (GAN). The static features, called "gist," are used to sketch text-conditioned background color and object layout structure. Dynamic features are considered by transforming input text into an image filter. To obtain a large amount of data for training the deep-learning model, we develop a method to automatically create a matched text-video corpus from publicly available online videos. Experimental results show that the proposed framework generates plausible and diverse videos, while accurately reflecting the input text information. It significantly outperforms baseline models that directly adapt text-to-image generation procedures to produce videos. Performance is evaluated both visually and by adapting the inception score used to evaluate image generation in GANs.

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However, most existing methods consider molecular generation for protein pockets independently while neglecting the underlying connections such as subpocket-level similarities. Subpockets are the local protein environments of ligand fragments and pockets with similar subpockets may bind the same molecular fragment (motif) even though their overall structures are different. Therefore, the trained models can hardly generalize to unseen protein pockets in real-world applications. In this paper, we propose a novel method DrugGPS for generalizable structure-based drug design. With the biochemical priors, we propose to learn subpocket prototypes and construct a global interaction graph to model the interactions between subpocket prototypes and molecular motifs. Moreover, a hierarchical graph transformer encoder and motif-based 3D molecule generation scheme are used to improve the model's performance. The experimental results show that our model consistently outperforms baselines in generating realistic drug candidates with high affinities in challenging out-of-distribution settings.

This paper shows how Long Short-term Memory recurrent neural networks can be used to generate complex sequences with long-range structure, simply by predicting one data point at a time. The approach is demonstrated for text (where the data are discrete) and online handwriting (where the data are real-valued). It is then extended to handwriting synthesis by allowing the network to condition its predictions on a text sequence. The resulting system is able to generate highly realistic cursive handwriting in a wide variety of styles.

Generative models have recently shown great promise for accelerating the design and discovery of new functional materials. Conditional generation enhances this capacity by allowing inverse design, where specific desired properties can be requested during the generation process. However, conditioning of transformer-based approaches, in particular, is constrained by discrete tokenisation schemes and the risk of catastrophic forgetting during fine-tuning. This work introduces CrystaLLM-π (property injection), a conditional autoregressive framework that integrates continuous property representations directly into the transformer's attention mechanism. Two architectures, Property-Key-Value (PKV) Prefix attention and PKV Residual attention, are presented. These methods bypass inefficient sequence-level tokenisation and preserve foundational knowledge from unsupervised pre-training on Crystallographic Information Files (CIFs) as textual input. We establish the efficacy of these mechanisms through systematic robustness studies and evaluate the framework's versatility across two distinct tasks. First, for structure recovery, the model processes high-dimensional, heterogeneous X-ray diffraction patterns, achieving structural accuracy competitive with specialised models and demonstrating applications to experimental structure recovery and polymorph differentiation. Second, for materials discovery, the model is fine-tuned on a specialised photovoltaic dataset to generate novel, stable candidates validated by Density Functional Theory (DFT). It implicitly learns to target optimal band gap regions for high photovoltaic efficiency, demonstrating a capability to map complex structure-property relationships. CrystaLLM-π provides a unified, flexible, and computationally efficient framework for inverse materials design.

The Cambrian explosion of easily accessible pre-trained diffusion models suggests a demand for methods that combine multiple different pre-trained diffusion models without incurring the significant computational burden of re-training a larger combined model. In this paper, we cast the problem of combining multiple pre-trained diffusion models at the generation stage under a novel proposed framework termed superposition. Theoretically, we derive superposition from rigorous first principles stemming from the celebrated continuity equation and design two novel algorithms tailor-made for combining diffusion models in SuperDiff. SuperDiff leverages a new scalable It\^o density estimator for the log likelihood of the diffusion SDE which incurs no additional overhead compared to the well-known Hutchinson's estimator needed for divergence calculations. We demonstrate that SuperDiff is scalable to large pre-trained diffusion models as superposition is performed solely through composition during inference, and also enjoys painless implementation as it combines different pre-trained vector fields through an automated re-weighting scheme. Notably, we show that SuperDiff is efficient during inference time, and mimics traditional composition operators such as the logical OR and the logical AND. We empirically demonstrate the utility of using SuperDiff for generating more diverse images on CIFAR-10, more faithful prompt conditioned image editing using Stable Diffusion, and improved unconditional de novo structure design of proteins. https://github.com/necludov/super-diffusion

Enabling agentic AI systems to adapt their problem-solving approaches based on post-training interactions remains a fundamental challenge. While systems that update and maintain a memory at inference time have been proposed, existing designs only steer the system by modifying textual input to a language model or agent, which means that they cannot change sampling parameters, remove tools, modify system prompts, or switch between agentic and workflow paradigms. On the other hand, systems that adapt more flexibly require offline optimization and remain static once deployed. We present Experience-Guided Reasoner (EGuR), which generates tailored strategies -- complete computational procedures involving LLM calls, tools, sampling parameters, and control logic -- dynamically at inference time based on accumulated experience. We achieve this using an LLM-based meta-strategy -- a strategy that outputs strategies -- enabling adaptation of all strategy components (prompts, sampling parameters, tool configurations, and control logic). EGuR operates through two components: a Guide generates multiple candidate strategies conditioned on the current problem and structured memory of past experiences, while a Consolidator integrates execution feedback to improve future strategy generation. This produces complete, ready-to-run strategies optimized for each problem, which can be cached, retrieved, and executed as needed without wasting resources. Across five challenging benchmarks (AIME 2025, 3-SAT, and three Big Bench Extra Hard tasks), EGuR achieves up to 14% accuracy improvements over the strongest baselines while reducing computational costs by up to 111x, with both metrics improving as the system gains experience.

Structured representations such as keypoints are widely used in pose transfer, conditional image generation, animation, and 3D reconstruction. However, their supervised learning requires expensive annotation for each target domain. We propose a self-supervised method that learns to disentangle object structure from the appearance with a graph of 2D keypoints linked by straight edges. Both the keypoint location and their pairwise edge weights are learned, given only a collection of images depicting the same object class. The resulting graph is interpretable, for example, AutoLink recovers the human skeleton topology when applied to images showing people. Our key ingredients are i) an encoder that predicts keypoint locations in an input image, ii) a shared graph as a latent variable that links the same pairs of keypoints in every image, iii) an intermediate edge map that combines the latent graph edge weights and keypoint locations in a soft, differentiable manner, and iv) an inpainting objective on randomly masked images. Although simpler, AutoLink outperforms existing self-supervised methods on the established keypoint and pose estimation benchmarks and paves the way for structure-conditioned generative models on more diverse datasets. Project website: https://xingzhehe.github.io/autolink/.

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

Generative models trained at scale can now produce text, video, and more recently, scientific data such as crystal structures. In applications of generative approaches to materials science, and in particular to crystal structures, the guidance from the domain expert in the form of high-level instructions can be essential for an automated system to output candidate crystals that are viable for downstream research. In this work, we formulate end-to-end language-to-structure generation as a multi-objective optimization problem, and propose Generative Hierarchical Materials Search (GenMS) for controllable generation of crystal structures. GenMS consists of (1) a language model that takes high-level natural language as input and generates intermediate textual information about a crystal (e.g., chemical formulae), and (2) a diffusion model that takes intermediate information as input and generates low-level continuous value crystal structures. GenMS additionally uses a graph neural network to predict properties (e.g., formation energy) from the generated crystal structures. During inference, GenMS leverages all three components to conduct a forward tree search over the space of possible structures. Experiments show that GenMS outperforms other alternatives of directly using language models to generate structures both in satisfying user request and in generating low-energy structures. We confirm that GenMS is able to generate common crystal structures such as double perovskites, or spinels, solely from natural language input, and hence can form the foundation for more complex structure generation in near future.

Discovering novel materials is critical for technological advancements such as solar cells, batteries, and carbon capture. However, the development of new materials is constrained by a slow and expensive trial-and-error process. To accelerate this pipeline, we introduce PLaID++, a Large Language Model (LLM) fine-tuned for stable and property-guided crystal generation. We fine-tune Qwen-2.5 7B to generate crystal structures using a novel Wyckoff-based text representation. We show that generation can be effectively guided with a reinforcement learning technique based on Direct Preference Optimization (DPO), with sampled structures categorized by their stability, novelty, and space group. By encoding symmetry constraints directly into text and guiding model outputs towards desirable chemical space, PLaID++ generates structures that are thermodynamically stable, unique, and novel at a sim50\% greater rate than prior methods and conditionally generates structures with desired space group properties. Our experiments highlight the effectiveness of iterative DPO, achieving sim115\% and sim50\% improvements in unconditional and space group conditioned generation, respectively, compared to fine-tuning alone. Our work demonstrates the potential of adapting post-training techniques from natural language processing to materials design, paving the way for targeted and efficient discovery of novel materials.

We propose a novel interpretation technique to explain the behavior of structured output models, which learn mappings between an input vector to a set of output variables simultaneously. Because of the complex relationship between the computational path of output variables in structured models, a feature can affect the value of output through other ones. We focus on one of the outputs as the target and try to find the most important features utilized by the structured model to decide on the target in each locality of the input space. In this paper, we assume an arbitrary structured output model is available as a black box and argue how considering the correlations between output variables can improve the explanation performance. The goal is to train a function as an interpreter for the target output variable over the input space. We introduce an energy-based training process for the interpreter function, which effectively considers the structural information incorporated into the model to be explained. The effectiveness of the proposed method is confirmed using a variety of simulated and real data sets.

Strong inductive biases enable learning from little data and help generalization outside of the training distribution. Popular neural architectures such as Transformers lack strong structural inductive biases for seq2seq NLP tasks on their own. Consequently, they struggle with systematic generalization beyond the training distribution, e.g. with extrapolating to longer inputs, even when pre-trained on large amounts of text. We show how a structural inductive bias can be efficiently injected into a seq2seq model by pre-training it to simulate structural transformations on synthetic data. Specifically, we inject an inductive bias towards Finite State Transducers (FSTs) into a Transformer by pre-training it to simulate FSTs given their descriptions. Our experiments show that our method imparts the desired inductive bias, resulting in improved systematic generalization and better few-shot learning for FST-like tasks. Our analysis shows that fine-tuned models accurately capture the state dynamics of the unseen underlying FSTs, suggesting that the simulation process is internalized by the fine-tuned model.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Despite rapid advancements in the capabilities of generative models, pretrained text-to-image models still struggle in capturing the semantics conveyed by complex prompts that compound multiple objects and instance-level attributes. Consequently, we are witnessing growing interests in integrating additional structural constraints, typically in the form of coarse bounding boxes, to better guide the generation process in such challenging cases. In this work, we take the idea of structural guidance a step further by making the observation that contemporary image generation models can directly provide a plausible fine-grained structural initialization. We propose a technique that couples this image-based structural guidance with LLM-based instance-level instructions, yielding output images that adhere to all parts of the text prompt, including object counts, instance-level attributes, and spatial relations between instances.

Generative Adversarial Networks (GANs) struggle to generate structured objects like molecules and game maps. The issue is that structured objects must satisfy hard requirements (e.g., molecules must be chemically valid) that are difficult to acquire from examples alone. As a remedy, we propose Constrained Adversarial Networks (CANs), an extension of GANs in which the constraints are embedded into the model during training. This is achieved by penalizing the generator proportionally to the mass it allocates to invalid structures. In contrast to other generative models, CANs support efficient inference of valid structures (with high probability) and allows to turn on and off the learned constraints at inference time. CANs handle arbitrary logical constraints and leverage knowledge compilation techniques to efficiently evaluate the disagreement between the model and the constraints. Our setup is further extended to hybrid logical-neural constraints for capturing very complex constraints, like graph reachability. An extensive empirical analysis shows that CANs efficiently generate valid structures that are both high-quality and novel.

Generation of graphs is a major challenge for real-world tasks that require understanding the complex nature of their non-Euclidean structures. Although diffusion models have achieved notable success in graph generation recently, they are ill-suited for modeling the topological properties of graphs since learning to denoise the noisy samples does not explicitly learn the graph structures to be generated. To tackle this limitation, we propose a generative framework that models the topology of graphs by explicitly learning the final graph structures of the diffusion process. Specifically, we design the generative process as a mixture of endpoint-conditioned diffusion processes which is driven toward the predicted graph that results in rapid convergence. We further introduce a simple parameterization of the mixture process and develop an objective for learning the final graph structure, which enables maximum likelihood training. Through extensive experimental validation on general graph and 2D/3D molecule generation tasks, we show that our method outperforms previous generative models, generating graphs with correct topology with both continuous (e.g. 3D coordinates) and discrete (e.g. atom types) features. Our code is available at https://github.com/harryjo97/GruM.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

De novo 3D molecule generation is a pivotal task in drug discovery. However, many recent geometric generative models struggle to produce high-quality 3D structures, even if they maintain 2D validity and topological stability. To tackle this issue and enhance the learning of effective molecular generation dynamics, we present Megalodon-a family of scalable transformer models. These models are enhanced with basic equivariant layers and trained using a joint continuous and discrete denoising co-design objective. We assess Megalodon's performance on established molecule generation benchmarks and introduce new 3D structure benchmarks that evaluate a model's capability to generate realistic molecular structures, particularly focusing on energetics. We show that Megalodon achieves state-of-the-art results in 3D molecule generation, conditional structure generation, and structure energy benchmarks using diffusion and flow matching. Furthermore, doubling the number of parameters in Megalodon to 40M significantly enhances its performance, generating up to 49x more valid large molecules and achieving energy levels that are 2-10x lower than those of the best prior generative models.

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present opportunities to enhance generative design to directly optimize expensive high-fidelity oracles and provide actionable insights to domain experts. Here, we propose Beam Enumeration to exhaustively enumerate the most probable sub-sequences from language-based molecular generative models and show that molecular substructures can be extracted. When coupled with reinforcement learning, extracted substructures become meaningful, providing a source of explainability and improving sample efficiency through self-conditioned generation. Beam Enumeration is generally applicable to any language-based molecular generative model and notably further improves the performance of the recently reported Augmented Memory algorithm, which achieved the new state-of-the-art on the Practical Molecular Optimization benchmark for sample efficiency. The combined algorithm generates more high reward molecules and faster, given a fixed oracle budget. Beam Enumeration shows that improvements to explainability and sample efficiency for molecular design can be made synergistic.

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Recipe generation from food images and ingredients is a challenging task, which requires the interpretation of the information from another modality. Different from the image captioning task, where the captions usually have one sentence, cooking instructions contain multiple sentences and have obvious structures. To help the model capture the recipe structure and avoid missing some cooking details, we propose a novel framework: Decomposing Generation Networks (DGN) with structure prediction, to get more structured and complete recipe generation outputs. Specifically, we split each cooking instruction into several phases, and assign different sub-generators to each phase. Our approach includes two novel ideas: (i) learning the recipe structures with the global structure prediction component and (ii) producing recipe phases in the sub-generator output component based on the predicted structure. Extensive experiments on the challenging large-scale Recipe1M dataset validate the effectiveness of our proposed model, which improves the performance over the state-of-the-art results.

Advancements in generative models have sparked significant interest in generating images while adhering to specific structural guidelines. Scene graph to image generation is one such task of generating images which are consistent with the given scene graph. However, the complexity of visual scenes poses a challenge in accurately aligning objects based on specified relations within the scene graph. Existing methods approach this task by first predicting a scene layout and generating images from these layouts using adversarial training. In this work, we introduce a novel approach to generate images from scene graphs which eliminates the need of predicting intermediate layouts. We leverage pre-trained text-to-image diffusion models and CLIP guidance to translate graph knowledge into images. Towards this, we first pre-train our graph encoder to align graph features with CLIP features of corresponding images using a GAN based training. Further, we fuse the graph features with CLIP embedding of object labels present in the given scene graph to create a graph consistent CLIP guided conditioning signal. In the conditioning input, object embeddings provide coarse structure of the image and graph features provide structural alignment based on relationships among objects. Finally, we fine tune a pre-trained diffusion model with the graph consistent conditioning signal with reconstruction and CLIP alignment loss. Elaborate experiments reveal that our method outperforms existing methods on standard benchmarks of COCO-stuff and Visual Genome dataset.

We present Probabilistic Structure Integration (PSI), a system for learning richly controllable and flexibly promptable world models from data. PSI consists of a three-step cycle. The first step, Probabilistic prediction, involves building a probabilistic graphical model Psi of the data, in the form of a random-access autoregressive sequence model. Psi supports a complete set of learned conditional distributions describing the dependence of any variables in the data on any other set of variables. In step 2, Structure extraction, we show how to extract underlying low-dimensional properties in the data, corresponding to a diverse set of meaningful "intermediate structures", in a zero-shot fashion via causal inference on Psi. Step 3, Integration, completes the cycle by converting these structures into new token types that are then continually mixed back into the training diet as conditioning signals and prediction targets. Each such cycle augments the capabilities of Psi, both allowing it to model the underlying data better, and creating new control handles -- akin to an LLM-like universal prompting language. We train an instance of Psi on 1.4 trillion tokens of internet video data; we use it to perform a variety of useful video prediction and understanding inferences; we extract state-of-the-art optical flow, self-supervised depth and object segmentation; and we use these structures to support a full cycle of predictive improvements.

Previous works on Natural Language Generation (NLG) from structured data have primarily focused on surface-level descriptions of record sequences. However, for complex structured data, e.g., multi-row tables, it is often desirable for an NLG system to describe interesting facts from logical inferences across records. If only provided with the table, it is hard for existing models to produce controllable and high-fidelity logical generations. In this work, we formulate logical level NLG as generation from logical forms in order to obtain controllable, high-fidelity, and faithful generations. We present a new large-scale dataset, Logic2Text, with 10,753 descriptions involving common logic types paired with the underlying logical forms. The logical forms show diversified graph structure of free schema, which poses great challenges on the model's ability to understand the semantics. We experiment on (1) Fully-supervised training with the full datasets, and (2) Few-shot setting, provided with hundreds of paired examples; We compare several popular generation models and analyze their performances. We hope our dataset can encourage research towards building an advanced NLG system capable of natural, faithful, and human-like generation. The dataset and code are available at https://github.com/czyssrs/Logic2Text.

We introduce 3DShape2VecSet, a novel shape representation for neural fields designed for generative diffusion models. Our shape representation can encode 3D shapes given as surface models or point clouds, and represents them as neural fields. The concept of neural fields has previously been combined with a global latent vector, a regular grid of latent vectors, or an irregular grid of latent vectors. Our new representation encodes neural fields on top of a set of vectors. We draw from multiple concepts, such as the radial basis function representation and the cross attention and self-attention function, to design a learnable representation that is especially suitable for processing with transformers. Our results show improved performance in 3D shape encoding and 3D shape generative modeling tasks. We demonstrate a wide variety of generative applications: unconditioned generation, category-conditioned generation, text-conditioned generation, point-cloud completion, and image-conditioned generation.

Although Large Language Models achieve strong success in many tasks, they still suffer from hallucinations and knowledge deficiencies in real-world applications. Many knowledge graph-based retrieval-augmented generation (KG-RAG) methods enhance the quality and credibility of LLMs by leveraging structure and semantic information in KGs as external knowledge bases. However, these methods struggle to effectively incorporate structure information, either incurring high computational costs or underutilizing available knowledge. Inspired by smoothing operations in graph representation learning, we propose path pooling, a simple, training-free strategy that introduces structure information through a novel path-centric pooling operation. It seamlessly integrates into existing KG-RAG methods in a plug-and-play manner, enabling richer structure information utilization. Extensive experiments demonstrate that incorporating the path pooling into the state-of-the-art KG-RAG method consistently improves performance across various settings while introducing negligible additional cost.

Sequential dependencies present a fundamental bottleneck in deploying large-scale autoregressive models, particularly for real-time applications. While traditional optimization approaches like pruning and quantization often compromise model quality, recent advances in generation-refinement frameworks demonstrate that this trade-off can be significantly mitigated. This survey presents a comprehensive taxonomy of generation-refinement frameworks, analyzing methods across autoregressive sequence tasks. We categorize methods based on their generation strategies (from simple n-gram prediction to sophisticated draft models) and refinement mechanisms (including single-pass verification and iterative approaches). Through systematic analysis of both algorithmic innovations and system-level implementations, we examine deployment strategies across computing environments and explore applications spanning text, images, and speech generation. This systematic examination of both theoretical frameworks and practical implementations provides a foundation for future research in efficient autoregressive decoding.

We introduce a framework for automatically defining and learning deep generative models with problem-specific structure. We tackle problem domains that are more traditionally solved by algorithms such as sorting, constraint satisfaction for Sudoku, and matrix factorization. Concretely, we train diffusion models with an architecture tailored to the problem specification. This problem specification should contain a graphical model describing relationships between variables, and often benefits from explicit representation of subcomputations. Permutation invariances can also be exploited. Across a diverse set of experiments we improve the scaling relationship between problem dimension and our model's performance, in terms of both training time and final accuracy. Our code can be found at https://github.com/plai-group/gsdm.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Generative Adversarial Nets [8] were recently introduced as a novel way to train generative models. In this work we introduce the conditional version of generative adversarial nets, which can be constructed by simply feeding the data, y, we wish to condition on to both the generator and discriminator. We show that this model can generate MNIST digits conditioned on class labels. We also illustrate how this model could be used to learn a multi-modal model, and provide preliminary examples of an application to image tagging in which we demonstrate how this approach can generate descriptive tags which are not part of training labels.

A growing body of research has demonstrated the inability of NLP models to generalize compositionally and has tried to alleviate it through specialized architectures, training schemes, and data augmentation, among other approaches. In this work, we study a different approach: training on instances with diverse structures. We propose a model-agnostic algorithm for subsampling such sets of instances from a labeled instance pool with structured outputs. Evaluating on both compositional template splits and traditional IID splits of 5 semantic parsing datasets of varying complexity, we show that structurally diverse training using our algorithm leads to comparable or better generalization than prior algorithms in 9 out of 10 dataset-split type pairs. In general, we find structural diversity to consistently improve sample efficiency compared to random train sets. Moreover, we show that structurally diverse sampling yields comprehensive test sets that are a lot more challenging than IID test sets. Finally, we provide two explanations for improved generalization from diverse train sets: 1) improved coverage of output substructures, and 2) a reduction in spurious correlations between these substructures.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

Recent advances in autoregressive (AR) models have demonstrated their potential to rival diffusion models in image synthesis. However, for complex spatially-conditioned generation, current AR approaches rely on fine-tuning the pre-trained model, leading to significant training costs. In this paper, we propose the Efficient Control Model (ECM), a plug-and-play framework featuring a lightweight control module that introduces control signals via a distributed architecture. This architecture consists of context-aware attention layers that refine conditional features using real-time generated tokens, and a shared gated feed-forward network (FFN) designed to maximize the utilization of its limited capacity and ensure coherent control feature learning. Furthermore, recognizing the critical role of early-stage generation in determining semantic structure, we introduce an early-centric sampling strategy that prioritizes learning early control sequences. This approach reduces computational cost by lowering the number of training tokens per iteration, while a complementary temperature scheduling during inference compensates for the resulting insufficient training of late-stage tokens. Extensive experiments on scale-based AR models validate that our method achieves high-fidelity and diverse control over image generation, surpassing existing baselines while significantly improving both training and inference efficiency.

We introduce nested diffusion models, an efficient and powerful hierarchical generative framework that substantially enhances the generation quality of diffusion models, particularly for images of complex scenes. Our approach employs a series of diffusion models to progressively generate latent variables at different semantic levels. Each model in this series is conditioned on the output of the preceding higher-level models, culminating in image generation. Hierarchical latent variables guide the generation process along predefined semantic pathways, allowing our approach to capture intricate structural details while significantly improving image quality. To construct these latent variables, we leverage a pre-trained visual encoder, which learns strong semantic visual representations, and modulate its capacity via dimensionality reduction and noise injection. Across multiple datasets, our system demonstrates significant enhancements in image quality for both unconditional and class/text conditional generation. Moreover, our unconditional generation system substantially outperforms the baseline conditional system. These advancements incur minimal computational overhead as the more abstract levels of our hierarchy work with lower-dimensional representations.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

Large Language Models (LLMs) have demonstrated remarkable capabilities in natural language generation and reasoning. However, their integration into automated software ecosystems is often hindered by the "Structure Gap" - the inherent tension between the probabilistic nature of token generation and the deterministic requirements of structured data formats (e.g., JSON, XML). Traditional Supervised Fine-Tuning (SFT) often fails to enforce strict syntactic constraints, leading to "hallucinated" keys or malformed structures, while constrained decoding methods impose significant inference latency. In this paper, we propose a lightweight, efficient Reinforcement Learning (RL) framework to bridge this gap. We introduce a novel Multi-dimensional Reward Function that decomposes the structured output task into a hierarchy of constraints: structural integrity, format correctness, content accuracy, and validity. Leveraging Gradient Regularized Policy Optimization (GRPO), we enable the model to internalize these constraints without the need for a separate critic network, reducing peak VRAM usage by 40% compared to PPO. We validate our approach on multiple tasks, including complex recipe generation and structured math reasoning (GSM8K-JSON). Experimental results demonstrate that our method achieves 89.7% structural accuracy and 92.1% JSON validity, significantly outperforming both zero-shot baselines (e.g., GPT-3.5) and SFT on larger models like LLaMA-3-8B. Furthermore, we provide a detailed analysis of training dynamics, revealing a distinct self-paced curriculum where the model sequentially acquires syntactic proficiency before semantic accuracy. Our model is publicly available at https://huggingface.co/Freakz3z/Qwen-JSON.

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem. This introduces a new paradigm of multitask language models which seamlessly bridge sequence regression and conditional sequence generation. We thoroughly demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction tasks of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a highly competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by a novel, alternating training scheme that enables the model to decorate seed sequences by desired properties, e.g., to optimize reaction yield. In sum, the RT is the first report of a multitask model that concurrently excels at predictive and generative tasks in biochemistry. This finds particular application in property-driven, local exploration of the chemical or protein space and could pave the road toward foundation models in material design. The code to reproduce all experiments of the paper is available at: https://github.com/IBM/regression-transformer

Heterogeneous tabular data poses unique challenges in generative modelling due to its fundamentally different underlying data structure compared to homogeneous modalities, such as images and text. Although previous research has sought to adapt the successes of generative modelling in homogeneous modalities to the tabular domain, defining an effective generator for tabular data remains an open problem. One major reason is that the evaluation criteria inherited from other modalities often fail to adequately assess whether tabular generative models effectively capture or utilise the unique structural information encoded in tabular data. In this paper, we carefully examine the limitations of the prevailing evaluation framework and introduce TabStruct, a novel evaluation benchmark that positions structural fidelity as a core evaluation dimension. Specifically, TabStruct evaluates the alignment of causal structures in real and synthetic data, providing a direct measure of how effectively tabular generative models learn the structure of tabular data. Through extensive experiments using generators from eight categories on seven datasets with expert-validated causal graphical structures, we show that structural fidelity offers a task-independent, domain-agnostic evaluation dimension. Our findings highlight the importance of tabular data structure and offer practical guidance for developing more effective and robust tabular generative models. Code is available at https://github.com/SilenceX12138/TabStruct.

Large monolithic generative models trained on massive amounts of data have become an increasingly dominant approach in AI research. In this paper, we argue that we should instead construct large generative systems by composing smaller generative models together. We show how such a compositional generative approach enables us to learn distributions in a more data-efficient manner, enabling generalization to parts of the data distribution unseen at training time. We further show how this enables us to program and construct new generative models for tasks completely unseen at training. Finally, we show that in many cases, we can discover separate compositional components from data.

With the advent of neural language models, the performance of code generation has been significantly boosted. However, the problem of repetitions during the generation process continues to linger. Previous work has primarily focused on content repetition, which is merely a fraction of the broader repetition problem in code generation. A more prevalent and challenging problem is structural repetition. In structural repetition, the repeated code appears in various patterns but possesses a fixed structure, which can be inherently reflected in grammar. In this paper, we formally define structural repetition and propose an efficient decoding approach called RPG, which stands for Repetition Penalization based on Grammar, to alleviate the repetition problems in code generation for LLMs. Specifically, RPG first leverages grammar rules to identify repetition problems during code generation, and then strategically decays the likelihood of critical tokens that contribute to repetitions, thereby mitigating them in code generation. To facilitate this study, we construct a new dataset CodeRepetEval to comprehensively evaluate approaches for mitigating the repetition problems in code generation. Extensive experimental results demonstrate that RPG substantially outperforms the best-performing baselines on CodeRepetEval dataset as well as HumanEval and MBPP benchmarks, effectively reducing repetitions and enhancing the quality of generated code.

Prediction sets have recently been shown to be a promising strategy for quantifying the uncertainty of deep neural networks in a way that provides theoretical guarantees. However, existing techniques have largely targeted settings where the space of labels is simple, so prediction sets can be arbitrary subsets of labels. For structured prediction problems where the space of labels is exponential in size, even prediction sets containing a small fraction of all labels can be exponentially large. In the context of code generation, we propose a solution that considers a restricted set of prediction sets that can compactly be represented as partial programs, which are programs with portions replaced with holes. Given a trained code generation model, our algorithm leverages a programming language's abstract syntax tree to generate a set of programs such that the correct program is in the set with high-confidence. Valuable applications of our algorithm include a Codex-style code generator with holes in uncertain parts of the generated code, which provides a partial program with theoretical guarantees. We evaluate our approach on PICARD (a T5 model for SQL semantic parsing) and Codex (a GPT model for over a dozen programming languages, including Python), demonstrating that our approach generates compact PAC prediction sets. This is the first research contribution that generates PAC prediction sets for generative code models.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

A deep generative model such as a GAN learns to model a rich set of semantic and physical rules about the target distribution, but up to now, it has been obscure how such rules are encoded in the network, or how a rule could be changed. In this paper, we introduce a new problem setting: manipulation of specific rules encoded by a deep generative model. To address the problem, we propose a formulation in which the desired rule is changed by manipulating a layer of a deep network as a linear associative memory. We derive an algorithm for modifying one entry of the associative memory, and we demonstrate that several interesting structural rules can be located and modified within the layers of state-of-the-art generative models. We present a user interface to enable users to interactively change the rules of a generative model to achieve desired effects, and we show several proof-of-concept applications. Finally, results on multiple datasets demonstrate the advantage of our method against standard fine-tuning methods and edit transfer algorithms.

We propose a new approach for generative modeling based on training a neural network to be idempotent. An idempotent operator is one that can be applied sequentially without changing the result beyond the initial application, namely f(f(z))=f(z). The proposed model f is trained to map a source distribution (e.g, Gaussian noise) to a target distribution (e.g. realistic images) using the following objectives: (1) Instances from the target distribution should map to themselves, namely f(x)=x. We define the target manifold as the set of all instances that f maps to themselves. (2) Instances that form the source distribution should map onto the defined target manifold. This is achieved by optimizing the idempotence term, f(f(z))=f(z) which encourages the range of f(z) to be on the target manifold. Under ideal assumptions such a process provably converges to the target distribution. This strategy results in a model capable of generating an output in one step, maintaining a consistent latent space, while also allowing sequential applications for refinement. Additionally, we find that by processing inputs from both target and source distributions, the model adeptly projects corrupted or modified data back to the target manifold. This work is a first step towards a ``global projector'' that enables projecting any input into a target data distribution.

We formalize constraint-based structure learning of the "true" causal graph from observed data when unobserved variables are also existent. We provide conditions for a "natural" family of constraint-based structure-learning algorithms that output graphs that are Markov equivalent to the causal graph. Under the faithfulness assumption, this natural family contains all exact structure-learning algorithms. We also provide a set of assumptions, under which any natural structure-learning algorithm outputs Markov equivalent graphs to the causal graph. These assumptions can be thought of as a relaxation of faithfulness, and most of them can be directly tested from (the underlying distribution) of the data, particularly when one focuses on structural causal models. We specialize the definitions and results for structural causal models.

We propose fine-tuning large language models for generation of stable materials. While unorthodox, fine-tuning large language models on text-encoded atomistic data is simple to implement yet reliable, with around 90% of sampled structures obeying physical constraints on atom positions and charges. Using energy above hull calculations from both learned ML potentials and gold-standard DFT calculations, we show that our strongest model (fine-tuned LLaMA-2 70B) can generate materials predicted to be metastable at about twice the rate (49% vs 28%) of CDVAE, a competing diffusion model. Because of text prompting's inherent flexibility, our models can simultaneously be used for unconditional generation of stable material, infilling of partial structures and text-conditional generation. Finally, we show that language models' ability to capture key symmetries of crystal structures improves with model scale, suggesting that the biases of pretrained LLMs are surprisingly well-suited for atomistic data.

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

Sequence generation applications require satisfying semantic constraints, such as ensuring that programs are correct, using certain keywords, or avoiding undesirable content. Language models, whether fine-tuned or prompted with few-shot demonstrations, frequently violate these constraints, and lack a mechanism to iteratively revise their outputs. Moreover, some powerful language models are of extreme scale or inaccessible, making it inefficient, if not infeasible, to update their parameters for task-specific adaptation. We present Self-Correction, an approach that decouples an imperfect base generator (an off-the-shelf language model or supervised sequence-to-sequence model) from a separate corrector that learns to iteratively correct imperfect generations. To train the corrector, we propose an online training procedure that can use either scalar or natural language feedback on intermediate imperfect generations. We show that Self-Correction improves upon the base generator in three diverse generation tasks - mathematical program synthesis, lexically-constrained generation, and toxicity control - even when the corrector is much smaller than the base generator.

Molecular structure elucidation from spectra is a foundational problem in chemistry, with profound implications for compound identification, synthesis, and drug development. Traditional methods rely heavily on expert interpretation and lack scalability. Pioneering machine learning methods have introduced retrieval-based strategies, but their reliance on finite libraries limits generalization to novel molecules. Generative models offer a promising alternative, yet most adopt autoregressive SMILES-based architectures that overlook 3D geometry and struggle to integrate diverse spectral modalities. In this work, we present DiffSpectra, a generative framework that directly infers both 2D and 3D molecular structures from multi-modal spectral data using diffusion models. DiffSpectra formulates structure elucidation as a conditional generation process. Its denoising network is parameterized by Diffusion Molecule Transformer, an SE(3)-equivariant architecture that integrates topological and geometric information. Conditioning is provided by SpecFormer, a transformer-based spectral encoder that captures intra- and inter-spectral dependencies from multi-modal spectra. Extensive experiments demonstrate that DiffSpectra achieves high accuracy in structure elucidation, recovering exact structures with 16.01% top-1 accuracy and 96.86% top-20 accuracy through sampling. The model benefits significantly from 3D geometric modeling, SpecFormer pre-training, and multi-modal conditioning. These results highlight the effectiveness of spectrum-conditioned diffusion modeling in addressing the challenge of molecular structure elucidation. To our knowledge, DiffSpectra is the first framework to unify multi-modal spectral reasoning and joint 2D/3D generative modeling for de novo molecular structure elucidation.

Graphs can be leveraged to model polyphonic multitrack symbolic music, where notes, chords and entire sections may be linked at different levels of the musical hierarchy by tonal and rhythmic relationships. Nonetheless, there is a lack of works that consider graph representations in the context of deep learning systems for music generation. This paper bridges this gap by introducing a novel graph representation for music and a deep Variational Autoencoder that generates the structure and the content of musical graphs separately, one after the other, with a hierarchical architecture that matches the structural priors of music. By separating the structure and content of musical graphs, it is possible to condition generation by specifying which instruments are played at certain times. This opens the door to a new form of human-computer interaction in the context of music co-creation. After training the model on existing MIDI datasets, the experiments show that the model is able to generate appealing short and long musical sequences and to realistically interpolate between them, producing music that is tonally and rhythmically consistent. Finally, the visualization of the embeddings shows that the model is able to organize its latent space in accordance with known musical concepts.

We present a comprehensive evaluation of structured decoding for text-to-table generation with large language models (LLMs). While previous work has primarily focused on unconstrained generation of tables, the impact of enforcing structural constraints during generation remains underexplored. We systematically compare schema-guided (structured) decoding to standard one-shot prompting across three diverse benchmarks - E2E, Rotowire, and Livesum - using open-source LLMs of up to 32B parameters, assessing the performance of table generation approaches in resource-constrained settings. Our experiments cover a wide range of evaluation metrics at cell, row, and table levels. Results demonstrate that structured decoding significantly enhances the validity and alignment of generated tables, particularly in scenarios demanding precise numerical alignment (Rotowire), but may degrade performance in contexts involving densely packed textual information (E2E) or extensive aggregation over lengthy texts (Livesum). We further analyze the suitability of different evaluation metrics and discuss the influence of model size.

Estimating the structure of directed acyclic graphs (DAGs, also known as Bayesian networks) is a challenging problem since the search space of DAGs is combinatorial and scales superexponentially with the number of nodes. Existing approaches rely on various local heuristics for enforcing the acyclicity constraint. In this paper, we introduce a fundamentally different strategy: We formulate the structure learning problem as a purely continuous optimization problem over real matrices that avoids this combinatorial constraint entirely. This is achieved by a novel characterization of acyclicity that is not only smooth but also exact. The resulting problem can be efficiently solved by standard numerical algorithms, which also makes implementation effortless. The proposed method outperforms existing ones, without imposing any structural assumptions on the graph such as bounded treewidth or in-degree. Code implementing the proposed algorithm is open-source and publicly available at https://github.com/xunzheng/notears.

Generating simulations to train intelligent agents in game-playing and robotics from natural language input, from user input or task documentation, remains an open-ended challenge. Existing approaches focus on parts of this challenge, such as generating reward functions or task hyperparameters. Unlike previous work, we introduce FACTORSIM that generates full simulations in code from language input that can be used to train agents. Exploiting the structural modularity specific to coded simulations, we propose to use a factored partially observable Markov decision process representation that allows us to reduce context dependence during each step of the generation. For evaluation, we introduce a generative simulation benchmark that assesses the generated simulation code's accuracy and effectiveness in facilitating zero-shot transfers in reinforcement learning settings. We show that FACTORSIM outperforms existing methods in generating simulations regarding prompt alignment (e.g., accuracy), zero-shot transfer abilities, and human evaluation. We also demonstrate its effectiveness in generating robotic tasks.

Auto-regressive language models factorize sequence probabilities and are trained by minimizing the negative log-likelihood (NLL) objective. While empirically powerful, a deep theoretical understanding of why this simple objective yields such versatile representations remains elusive. This work introduces a unifying analytical framework using Markov Categories (MCs) to deconstruct the AR generation process and the NLL objective. We model the single-step generation map as a composition of Markov kernels in the category Stoch. This compositional view, when enriched with statistical divergences, allows us to dissect information flow and learned geometry. Our framework makes three main contributions. First, we provide a formal, information-theoretic rationale for the success of modern speculative decoding methods like EAGLE, quantifying the information surplus in hidden states that these methods exploit. Second, we formalize how NLL minimization forces the model to learn not just the next token, but the data's intrinsic conditional stochasticity, a process we analyze using categorical entropy. Third, and most centrally, we prove that NLL training acts as an implicit form of spectral contrastive learning. By analyzing the information geometry of the model's prediction head, we show that NLL implicitly forces the learned representation space to align with the eigenspectrum of a predictive similarity operator, thereby learning a geometrically structured space without explicit contrastive pairs. This compositional and information-geometric perspective reveals the deep structural principles underlying the effectiveness of modern LMs. Project Page: https://github.com/asiresearch/lm-theory

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

Text-to-image generative models have become a prominent and powerful tool that excels at generating high-resolution realistic images. However, guiding the generative process of these models to consider detailed forms of conditioning reflecting style and/or structure information remains an open problem. In this paper, we present LoRAdapter, an approach that unifies both style and structure conditioning under the same formulation using a novel conditional LoRA block that enables zero-shot control. LoRAdapter is an efficient, powerful, and architecture-agnostic approach to condition text-to-image diffusion models, which enables fine-grained control conditioning during generation and outperforms recent state-of-the-art approaches

Reliably generating structured outputs has become a critical capability for modern language model (LM) applications. Constrained decoding has emerged as the dominant technology across sectors for enforcing structured outputs during generation. Despite its growing adoption, little has been done with the systematic evaluation of the behaviors and performance of constrained decoding. Constrained decoding frameworks have standardized around JSON Schema as a structured data format, with most uses guaranteeing constraint compliance given a schema. However, there is poor understanding of the effectiveness of the methods in practice. We present an evaluation framework to assess constrained decoding approaches across three critical dimensions: efficiency in generating constraint-compliant outputs, coverage of diverse constraint types, and quality of the generated outputs. To facilitate this evaluation, we introduce JSONSchemaBench, a benchmark for constrained decoding comprising 10K real-world JSON schemas that encompass a wide range of constraints with varying complexity. We pair the benchmark with the existing official JSON Schema Test Suite and evaluate six state-of-the-art constrained decoding frameworks, including Guidance, Outlines, Llamacpp, XGrammar, OpenAI, and Gemini. Through extensive experiments, we gain insights into the capabilities and limitations of constrained decoding on structured generation with real-world JSON schemas. Our work provides actionable insights for improving constrained decoding frameworks and structured generation tasks, setting a new standard for evaluating constrained decoding and structured generation. We release JSONSchemaBench at https://github.com/guidance-ai/jsonschemabench

Beginning with text and images, generative AI has expanded to audio, video, computer code, and molecules. Yet, if generative AI is the answer, what is the question? We explore the foundations of generation as a distinct machine learning task with connections to prediction, compression, and decision-making. We survey five major generative model families: autoregressive models, variational autoencoders, normalizing flows, generative adversarial networks, and diffusion models. We then introduce a probabilistic framework that emphasizes the distinction between density estimation and generation. We review a game-theoretic framework with a two-player adversary-learner setup to study generation. We discuss post-training modifications that prepare generative models for deployment. We end by highlighting some important topics in socially responsible generation such as privacy, detection of AI-generated content, and copyright and IP. We adopt a task-first framing of generation, focusing on what generation is as a machine learning problem, rather than only on how models implement it.

Given an unconditional diffusion model and a predictor for a target property of interest (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. Existing methods, though effective in various individual applications, often lack theoretical grounding and rigorous testing on extensive benchmarks. As a result, they could even fail on simple tasks, and applying them to a new problem becomes unavoidably difficult. This paper introduces a novel algorithmic framework encompassing existing methods as special cases, unifying the study of training-free guidance into the analysis of an algorithm-agnostic design space. Via theoretical and empirical investigation, we propose an efficient and effective hyper-parameter searching strategy that can be readily applied to any downstream task. We systematically benchmark across 7 diffusion models on 16 tasks with 40 targets, and improve performance by 8.5% on average. Our framework and benchmark offer a solid foundation for conditional generation in a training-free manner.

We propose a general and efficient framework to control auto-regressive generation models with NeurAlly-Decomposed Oracle (NADO). Given a pre-trained base language model and a sequence-level boolean oracle function, we propose to decompose the oracle function into token-level guidance to steer the base model in text generation. Specifically, the token-level guidance is approximated by a neural model trained with examples sampled from the base model, demanding no additional auxiliary labeled data. Based on posterior regularization, we present the closed-form optimal solution to incorporate the token-level guidance into the base model for controllable generation. We further provide a theoretical analysis of how the approximation quality of NADO affects the controllable generation results. Experiments conducted on two applications: (1) text generation with lexical constraints and (2) machine translation with formality control demonstrate that our framework efficiently guides the base model towards the given oracle while maintaining high generation quality.

We propose a new representation for encoding 3D shapes as neural fields. The representation is designed to be compatible with the transformer architecture and to benefit both shape reconstruction and shape generation. Existing works on neural fields are grid-based representations with latents defined on a regular grid. In contrast, we define latents on irregular grids, enabling our representation to be sparse and adaptive. In the context of shape reconstruction from point clouds, our shape representation built on irregular grids improves upon grid-based methods in terms of reconstruction accuracy. For shape generation, our representation promotes high-quality shape generation using auto-regressive probabilistic models. We show different applications that improve over the current state of the art. First, we show results for probabilistic shape reconstruction from a single higher resolution image. Second, we train a probabilistic model conditioned on very low resolution images. Third, we apply our model to category-conditioned generation. All probabilistic experiments confirm that we are able to generate detailed and high quality shapes to yield the new state of the art in generative 3D shape modeling.

We propose a unified Generative Adversarial Network (GAN) for controllable image-to-image translation, i.e., transferring an image from a source to a target domain guided by controllable structures. In addition to conditioning on a reference image, we show how the model can generate images conditioned on controllable structures, e.g., class labels, object keypoints, human skeletons, and scene semantic maps. The proposed model consists of a single generator and a discriminator taking a conditional image and the target controllable structure as input. In this way, the conditional image can provide appearance information and the controllable structure can provide the structure information for generating the target result. Moreover, our model learns the image-to-image mapping through three novel losses, i.e., color loss, controllable structure guided cycle-consistency loss, and controllable structure guided self-content preserving loss. Also, we present the Fr\'echet ResNet Distance (FRD) to evaluate the quality of the generated images. Experiments on two challenging image translation tasks, i.e., hand gesture-to-gesture translation and cross-view image translation, show that our model generates convincing results, and significantly outperforms other state-of-the-art methods on both tasks. Meanwhile, the proposed framework is a unified solution, thus it can be applied to solving other controllable structure guided image translation tasks such as landmark guided facial expression translation and keypoint guided person image generation. To the best of our knowledge, we are the first to make one GAN framework work on all such controllable structure guided image translation tasks. Code is available at https://github.com/Ha0Tang/GestureGAN.

This paper presents a pioneering methodology, termed StructTuning, to efficiently transform foundation Large Language Models (LLMs) into domain specialists. It significantly minimizes the training corpus requirement to a mere 0.3% while achieving an impressive 50% of traditional knowledge injection performance. Our method is inspired by the educational processes for human students, particularly how structured domain knowledge from textbooks is absorbed and then applied to tackle real-world challenges through specific exercises. Based on this, we propose a novel two-stage knowledge injection strategy: Structure-aware Continual Pre-Training (SCPT) and Structure-aware Supervised Fine-Tuning (SSFT). In the SCPT phase, we organize the training data into an auto-generated taxonomy of domain knowledge, enabling LLMs to effectively memorize textual segments linked to specific expertise within the taxonomy's architecture. Subsequently, in the SSFT phase, we explicitly prompt models to reveal the underlying knowledge structure in their outputs, leveraging this structured domain insight to address practical problems adeptly. Our ultimate method has undergone extensive evaluations across model architectures and scales, using closed-book question-answering tasks on LongBench and MMedBench datasets. Remarkably, our method matches 50% of the improvement displayed by the state-of-the-art MMedLM2 on MMedBench, but with only 0.3% quantity of the training corpus. This breakthrough showcases the potential to scale up our StructTuning for stronger domain-specific LLMs. Code will be made public soon.

Generating visual layouts is an essential ingredient of graphic design. The ability to condition layout generation on a partial subset of component attributes is critical to real-world applications that involve user interaction. Recently, diffusion models have demonstrated high-quality generative performances in various domains. However, it is unclear how to apply diffusion models to the natural representation of layouts which consists of a mix of discrete (class) and continuous (location, size) attributes. To address the conditioning layout generation problem, we introduce DLT, a joint discrete-continuous diffusion model. DLT is a transformer-based model which has a flexible conditioning mechanism that allows for conditioning on any given subset of all the layout component classes, locations, and sizes. Our method outperforms state-of-the-art generative models on various layout generation datasets with respect to different metrics and conditioning settings. Additionally, we validate the effectiveness of our proposed conditioning mechanism and the joint continuous-diffusion process. This joint process can be incorporated into a wide range of mixed discrete-continuous generative tasks.

Toward combining inductive reasoning with perception abilities, we develop techniques for neurosymbolic program synthesis where perceptual input is first parsed by neural nets into a low-dimensional interpretable representation, which is then processed by a synthesized program. We explore several techniques for relaxing the problem and jointly learning all modules end-to-end with gradient descent: multitask learning; amortized inference; overparameterization; and a differentiable strategy for penalizing lengthy programs. Collectedly this toolbox improves the stability of gradient-guided program search, and suggests ways of learning both how to perceive input as discrete abstractions, and how to symbolically process those abstractions as programs.

Program synthesis or code generation aims to generate a program that satisfies a problem specification. Recent approaches using large-scale pretrained language models (LMs) have shown promising results, yet they have some critical limitations. In particular, they often follow a standard supervised fine-tuning procedure to train a code generation model only from the pairs of natural-language problem descriptions and ground-truth programs. Such paradigm largely ignores some important but potentially useful signals in the problem specification such as unit tests, which thus often results in poor performance when solving complex unseen coding tasks. To address the limitations, we propose "CodeRL", a new framework for program synthesis tasks through pretrained LMs and deep reinforcement learning (RL). Specifically, during training, we treat the code-generating LM as an actor network, and introduce a critic network that is trained to predict the functional correctness of generated programs and provide dense feedback signals to the actor. During inference, we introduce a new generation procedure with a critical sampling strategy that allows a model to automatically regenerate programs based on feedback from example unit tests and critic scores. For the model backbones, we extended the encoder-decoder architecture of CodeT5 with enhanced learning objectives, larger model sizes, and better pretraining data. Our method not only achieves new SOTA results on the challenging APPS benchmark, but also shows strong zero-shot transfer capability with new SOTA results on the simpler MBPP benchmark.

Self-supervised learning excels at learning representations from large amounts of data. At the same time, generative models offer the complementary property of learning information about the underlying data generation process. In this study, we aim at establishing a principled connection between these two paradigms and highlight the benefits of their complementarity. In particular, we perform an analysis of self-supervised learning objectives, elucidating the underlying probabilistic graphical models and presenting a standardized methodology for their derivation from first principles. The analysis suggests a natural means of integrating self-supervised learning with likelihood-based generative models. We instantiate this concept within the realm of cluster-based self-supervised learning and energy models, introducing a lower bound proven to reliably penalize the most important failure modes and unlocking full unification. Our theoretical findings are substantiated through experiments on synthetic and real-world data, including SVHN, CIFAR10, and CIFAR100, demonstrating that our objective function allows to jointly train a backbone network in a discriminative and generative fashion, consequently outperforming existing self-supervised learning strategies in terms of clustering, generation and out-of-distribution detection performance by a wide margin. We also demonstrate that the solution can be integrated into a neuro-symbolic framework to tackle a simple yet non-trivial instantiation of the symbol grounding problem. The code is publicly available at https://github.com/emsansone/GEDI.

Large Language Models (LLMs) rely on instruction samples for alignment, but creating these datasets poses challenges, particularly in expert-dependent tasks like coding, which can be cost-prohibitive. One approach to mitigate these challenges is synthesizing data using another LLM. In this paper, we introduce a scalable method for generating synthetic instructions to enhance the code generation capability of LLMs. The proposed algorithm, Genetic-Instruct, mimics evolutionary processes, utilizing self-instruction to create numerous synthetic samples from a limited number of seeds. Genetic-Instruct is designed for efficient scaling of the generation process. Fine-tuning multiple coding LLMs with the synthetic samples demonstrates a significant improvement in their code generation accuracy compared to the baselines.

Activation steering methods were shown to be effective in conditioning language model generation by additively intervening over models' intermediate representations. However, the evaluation of these techniques has so far been limited to single conditioning properties and synthetic settings. In this work, we conduct a comprehensive evaluation of various activation steering strategies, highlighting the property-dependent nature of optimal parameters to ensure a robust effect throughout generation. To address this issue, we propose Dynamic Activation Composition, an information-theoretic approach to modulate the steering intensity of one or more properties throughout generation. Our experiments on multi-property steering show that our method successfully maintains high conditioning while minimizing the impact of conditioning on generation fluency.

We propose a new framework for estimating generative models via an adversarial process, in which we simultaneously train two models: a generative model G that captures the data distribution, and a discriminative model D that estimates the probability that a sample came from the training data rather than G. The training procedure for G is to maximize the probability of D making a mistake. This framework corresponds to a minimax two-player game. In the space of arbitrary functions G and D, a unique solution exists, with G recovering the training data distribution and D equal to 1/2 everywhere. In the case where G and D are defined by multilayer perceptrons, the entire system can be trained with backpropagation. There is no need for any Markov chains or unrolled approximate inference networks during either training or generation of samples. Experiments demonstrate the potential of the framework through qualitative and quantitative evaluation of the generated samples.

Recent Meta-learning for Black-Box Optimization (MetaBBO) methods harness neural networks to meta-learn configurations of traditional black-box optimizers. Despite their success, they are inevitably restricted by the limitations of predefined hand-crafted optimizers. In this paper, we present Symbol, a novel framework that promotes the automated discovery of black-box optimizers through symbolic equation learning. Specifically, we propose a Symbolic Equation Generator (SEG) that allows closed-form optimization rules to be dynamically generated for specific tasks and optimization steps. Within Symbol, we then develop three distinct strategies based on reinforcement learning, so as to meta-learn the SEG efficiently. Extensive experiments reveal that the optimizers generated by Symbol not only surpass the state-of-the-art BBO and MetaBBO baselines, but also exhibit exceptional zero-shot generalization abilities across entirely unseen tasks with different problem dimensions, population sizes, and optimization horizons. Furthermore, we conduct in-depth analyses of our Symbol framework and the optimization rules that it generates, underscoring its desirable flexibility and interpretability.

We propose TR0N, a highly general framework to turn pre-trained unconditional generative models, such as GANs and VAEs, into conditional models. The conditioning can be highly arbitrary, and requires only a pre-trained auxiliary model. For example, we show how to turn unconditional models into class-conditional ones with the help of a classifier, and also into text-to-image models by leveraging CLIP. TR0N learns a lightweight stochastic mapping which "translates" between the space of conditions and the latent space of the generative model, in such a way that the generated latent corresponds to a data sample satisfying the desired condition. The translated latent samples are then further improved upon through Langevin dynamics, enabling us to obtain higher-quality data samples. TR0N requires no training data nor fine-tuning, yet can achieve a zero-shot FID of 10.9 on MS-COCO, outperforming competing alternatives not only on this metric, but also in sampling speed -- all while retaining a much higher level of generality. Our code is available at https://github.com/layer6ai-labs/tr0n.

While score-based generative models are the model of choice across diverse domains, there are limited tools available for controlling inference-time behavior in a principled manner, e.g. for composing multiple pretrained models. Existing classifier-free guidance methods use a simple heuristic to mix conditional and unconditional scores to approximately sample from conditional distributions. However, such methods do not approximate the intermediate distributions, necessitating additional 'corrector' steps. In this work, we provide an efficient and principled method for sampling from a sequence of annealed, geometric-averaged, or product distributions derived from pretrained score-based models. We derive a weighted simulation scheme which we call Feynman-Kac Correctors (FKCs) based on the celebrated Feynman-Kac formula by carefully accounting for terms in the appropriate partial differential equations (PDEs). To simulate these PDEs, we propose Sequential Monte Carlo (SMC) resampling algorithms that leverage inference-time scaling to improve sampling quality. We empirically demonstrate the utility of our methods by proposing amortized sampling via inference-time temperature annealing, improving multi-objective molecule generation using pretrained models, and improving classifier-free guidance for text-to-image generation. Our code is available at https://github.com/martaskrt/fkc-diffusion.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

Recent advances in diffusion models have demonstrated impressive capability in generating high-quality images for simple prompts. However, when confronted with complex prompts involving multiple objects and hierarchical structures, existing models struggle to accurately follow instructions, leading to issues such as concept omission, confusion, and poor compositionality. To address these limitations, we propose a Hierarchical Compositional Generative framework (HiCoGen) built upon a novel Chain of Synthesis (CoS) paradigm. Instead of monolithic generation, HiCoGen first leverages a Large Language Model (LLM) to decompose complex prompts into minimal semantic units. It then synthesizes these units iteratively, where the image generated in each step provides crucial visual context for the next, ensuring all textual concepts are faithfully constructed into the final scene. To further optimize this process, we introduce a reinforcement learning (RL) framework. Crucially, we identify that the limited exploration of standard diffusion samplers hinders effective RL. We theoretically prove that sample diversity is maximized by concentrating stochasticity in the early generation stages and, based on this insight, propose a novel Decaying Stochasticity Schedule to enhance exploration. Our RL algorithm is then guided by a hierarchical reward mechanism that jointly evaluates the image at the global, subject, and relationship levels. We also construct HiCoPrompt, a new text-to-image benchmark with hierarchical prompts for rigorous evaluation. Experiments show our approach significantly outperforms existing methods in both concept coverage and compositional accuracy.

Recent advancements in generative modeling have made it possible to generate high-quality content from context information, but a key question remains: how to teach models to know when to generate content? To answer this question, this study proposes a novel event generative model that draws its statistical intuition from marked temporal point processes, and offers a clean, flexible, and computationally efficient solution for a wide range of applications involving multi-dimensional marks. We aim to capture the distribution of the point process without explicitly specifying the conditional intensity or probability density. Instead, we use a conditional generator that takes the history of events as input and generates the high-quality subsequent event that is likely to occur given the prior observations. The proposed framework offers a host of benefits, including exceptional efficiency in learning the model and generating samples, as well as considerable representational power to capture intricate dynamics in multi- or even high-dimensional event space. Our numerical results demonstrate superior performance compared to other state-of-the-art baselines.

Program synthesis methods aim to automatically generate programs restricted to a language that can explain a given specification of input-output pairs. While purely symbolic approaches suffer from a combinatorial search space, recent methods leverage neural networks to learn distributions over program structures to narrow this search space significantly, enabling more efficient search. However, for challenging problems, it remains difficult to train models to perform program synthesis in one shot, making test-time search essential. Most neural methods lack structured search mechanisms during inference, relying instead on stochastic sampling or gradient updates, which can be inefficient. In this work, we propose the Latent Program Network (LPN), a general algorithm for program induction that learns a distribution over latent programs in a continuous space, enabling efficient search and test-time adaptation. We explore how to train these networks to optimize for test-time computation and demonstrate the use of gradient-based search both during training and at test time. We evaluate LPN on ARC-AGI, a program synthesis benchmark that evaluates performance by generalizing programs to new inputs rather than explaining the underlying specification. We show that LPN can generalize beyond its training distribution and adapt to unseen tasks by utilizing test-time computation, outperforming algorithms without test-time adaptation mechanisms.

We consider the task of data-to-text generation, which aims to create textual output from non-linguistic input. We focus on generating long-form text, i.e., documents with multiple paragraphs, and propose a neural model enhanced with a planning component responsible for organizing high-level information in a coherent and meaningful way. We infer latent plans sequentially with a structured variational model, while interleaving the steps of planning and generation. Text is generated by conditioning on previous variational decisions and previously generated text. Experiments on two data-to-text benchmarks (RotoWire and MLB) show that our model outperforms strong baselines and is sample efficient in the face of limited training data (e.g., a few hundred instances).

Discovering the underlying relationships among variables from temporal observations has been a longstanding challenge in numerous scientific disciplines, including biology, finance, and climate science. The dynamics of such systems are often best described using continuous-time stochastic processes. Unfortunately, most existing structure learning approaches assume that the underlying process evolves in discrete-time and/or observations occur at regular time intervals. These mismatched assumptions can often lead to incorrect learned structures and models. In this work, we introduce a novel structure learning method, SCOTCH, which combines neural stochastic differential equations (SDE) with variational inference to infer a posterior distribution over possible structures. This continuous-time approach can naturally handle both learning from and predicting observations at arbitrary time points. Theoretically, we establish sufficient conditions for an SDE and SCOTCH to be structurally identifiable, and prove its consistency under infinite data limits. Empirically, we demonstrate that our approach leads to improved structure learning performance on both synthetic and real-world datasets compared to relevant baselines under regular and irregular sampling intervals.

In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data. A new accuracy schedule is proposed to improve the sampling quality by significantly reducing the reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with the state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

Models need appropriate inductive biases to effectively learn from small amounts of data and generalize systematically outside of the training distribution. While Transformers are highly versatile and powerful, they can still benefit from enhanced structural inductive biases for seq2seq tasks, especially those involving syntactic transformations, such as converting active to passive voice or semantic parsing. In this paper, we propose to strengthen the structural inductive bias of a Transformer by intermediate pre-training to perform synthetically generated syntactic transformations of dependency trees given a description of the transformation. Our experiments confirm that this helps with few-shot learning of syntactic tasks such as chunking, and also improves structural generalization for semantic parsing. Our analysis shows that the intermediate pre-training leads to attention heads that keep track of which syntactic transformation needs to be applied to which token, and that the model can leverage these attention heads on downstream tasks.

Crystal structure generation is a foundational challenge in materials discovery, particularly in designing functional inorganic crystalline materials with desired properties. Most existing diffusion-based generative models for crystals rely on complex, hand-crafted priors and modular architectures to separately model atom types, atomic positions, and lattice parameters. These methods often require customized diffusion processes and conditional denoising, which can introduce additional model complexities and inconsistencies. Here we introduce DiffCrysGen, a fully data-driven, score-based diffusion model that jointly learns the distribution of all structural components in crystalline materials. With crystal structure representation as unified 2D matrices, DiffCrysGen bypasses the need for task-specific priors or decoupled modules, enabling end-to-end generation of atom types, fractional coordinates, and lattice parameters within a single framework. Our model learns crystallographic symmetry and chemical validity directly from large-scale datasets, allowing it to scale to complex materials discovery tasks. As a demonstration, we applied DiffCrysGen to the design of rare-earth-free magnetic materials with high saturation magnetization, showing its effectiveness in generating stable, diverse, and property-aligned candidates for sustainable magnet applications.

LLMs have demonstrated commendable performance across diverse domains. Nevertheless, formulating high-quality prompts to assist them in their work poses a challenge for non-AI experts. Existing research in prompt engineering suggests somewhat scattered optimization principles and designs empirically dependent prompt optimizers. Unfortunately, these endeavors lack a structural design, incurring high learning costs and it is not conducive to the iterative updating of prompts, especially for non-AI experts. Inspired by structured reusable programming languages, we propose LangGPT, a structural prompt design framework. Furthermore, we introduce Minstrel, a multi-generative agent system with reflection to automate the generation of structural prompts. Experiments and the case study illustrate that structural prompts generated by Minstrel or written manually significantly enhance the performance of LLMs. Furthermore, we analyze the ease of use of structural prompts through a user survey in our online community.

Text-conditioned image generation models often generate incorrect associations between entities and their visual attributes. This reflects an impaired mapping between linguistic binding of entities and modifiers in the prompt and visual binding of the corresponding elements in the generated image. As one notable example, a query like ``a pink sunflower and a yellow flamingo'' may incorrectly produce an image of a yellow sunflower and a pink flamingo. To remedy this issue, we propose SynGen, an approach which first syntactically analyses the prompt to identify entities and their modifiers, and then uses a novel loss function that encourages the cross-attention maps to agree with the linguistic binding reflected by the syntax. Specifically, we encourage large overlap between attention maps of entities and their modifiers, and small overlap with other entities and modifier words. The loss is optimized during inference, without retraining or fine-tuning the model. Human evaluation on three datasets, including one new and challenging set, demonstrate significant improvements of SynGen compared with current state of the art methods. This work highlights how making use of sentence structure during inference can efficiently and substantially improve the faithfulness of text-to-image generation.