Next-generation multimodal foundation models capable of any-to-any cross-modal generation and multi-turn interaction will serve as core components of artificial general intelligence systems, playing a pivotal role in human-machine interaction. However, most existing multimodal models remain constrained by autoregressive architectures, whose inherent limitations prevent a balanced integration of understanding and generation capabilities. Although hybrid and decoupling strategies have been explored to address these tasks within unified frameworks separately, their redundant, non-integrated designs limit their applicability to broader scenarios, such as cross-modal retrieval. In this work, we introduce NExT-OMNI, an open-source omnimodal foundation model that achieves unified modeling through discrete flow paradigms. By leveraging metric-induced probability paths and kinetic optimal velocities, NExT-OMNI natively supports any-to-any understanding and generation with enhanced response efficiency, while enabling broader application scenarios through concise unified representations rather than task-decoupled designs. Trained on large-scale interleaved text, image, video, and audio data, NExT-OMNI delivers competitive performance on multimodal understanding and generation benchmarks, while outperforming prior unified models in multi-turn multimodal interaction and cross-modal retrieval, highlighting its architectural advantages as a next-generation multimodal foundation model. The code is available at https://github.com/ritzz-ai/Next-OMNI.
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Deep Learning · Generative Models and Autoencoders
Flow-based Generative Models (FGMs) effectively transform noise into complex data distributions. Incorporating Optimal Transport (OT) to couple noise and data during FGM training has been shown to improve the straightness of flow trajectories, enabling more effective inference. However, existing OT-based methods estimate the OT plan using (mini-)batches of sampled noise and data points, which limits their scalability to large and high-dimensional datasets in FGMs. This paper introduces AlignFlow, a novel approach that leverages Semi-Discrete Optimal Transport (SDOT) to enhance the training of FGMs by establishing an explicit, optimal alignment between noise distribution and data points with guaranteed convergence. SDOT computes a transport map by partitioning the noise space into Laguerre cells, each mapped to a corresponding data point. During FGM training, i.i.d. noise samples are paired with data points via the SDOT map. AlignFlow scales well to large datasets and model architectures with negligible computational overhead. Experimental results show that AlignFlow improves the performance of a wide range of state-of-the-art FGM algorithms and can be integrated as a plug-and-play component. Code is available at: https://github.com/konglk1203/AlignFlow.
General Machine Learning · Everything Else
We propose a statistical benchmark for diffusion-posterior-sampling (DPS) algorithms in linear inverse problems. Our test signals are discretized Lévy processes whose posteriors admit efficient Gibbs methods. These Gibbs methods provide gold-standard posterior samples for direct, distribution-level comparisons with DPS algorithms. They can also sample the denoising posteriors in the reverse diffusion, which enables the arbitrary-precision Monte Carlo estimation of various objects that may be needed in the DPS algorithms, such as the expectation or the covariance of the denoising posteriors. In turn, this can be used to isolate algorithmic errors from the errors due to learned components. We instantiate the benchmark with the minimum-mean-squared-error optimality gap and posterior-coverage tests and evaluate popular algorithms on the inverse problems of denoising, deconvolution, imputation, and reconstruction from partial Fourier measurements. We release the benchmark code at https://github.com/zacmar/dps-benchmark and invite the community to contribute and report results.
Deep Learning · Generative Models and Autoencoders
Computation methods for solving entropy-regularized reward optimization—a class of problems widely used for fine-tuning generative models—have advanced rapidly. Among those, Adjoint Matching (AM, Domingo-Enrich et al., 2025) has proven highly effective in continuous state spaces with differentiable rewards. Transferring these practical successes to _discrete_ generative modeling, however, remains particularly challenging and largely unexplored, mainly due to the drastic shift in generative model classes to discrete state spaces, which are nowhere differentiable. In this work, we propose Discrete Adjoint Matching (DAM)—a discrete variant of AM for fine-tuning discrete generative models characterized by Continuous-Time Markov Chains, such as diffusion-based large language models. The core of DAM is the introduction of _discrete adjoint_—an estimator of the optimal solution to the original problem but formulated on discrete domains—from which standard matching frameworks can be applied. This is derived via a purely statistical standpoint, in contrast to the control-theoretic viewpoint in AM, thereby opening up new algorithmic opportunities for general adjoint-based estimators. We showcase DAM’s effectiveness on synthetic and mathematical reasoning tasks.
Computer Vision · Vision Models & Multimodal
Vision-Language Models (VLMs) for radiology report generation are typically trained to mimic the narrative flow of human experts. However, we identify a potential limitation in this conventional paradigm. We hypothesize that optimizing for narrative coherence encourages models to rely on linguistic priors and inter-sentence correlations, which can weaken their grounding in direct visual evidence and lead to factual inaccuracies. To investigate this, we design a controlled experiment demonstrating that as textual context increases, a model's reliance on the input image systematically decays. We propose LLaVA-TA (Topic-guided and Anatomy-aware), a new fine-tuning framework that directly addresses this challenge by re-engineering the generation process. Instead of producing a linear narrative, LLaVA-TA decomposes the report into a set of independent, clinically-relevant topics. By training the model to generate a discrete finding for each topic conditioned on both the full image and its corresponding anatomical region, we reduce the model's reliance on narrative flow and enforce stricter visual grounding. Our experiments show that LLaVA-TA sets a new state of the art on the MIMIC-CXR dataset, significantly improving clinical accuracy on metrics like RadGraph F1 (from 29.4 to 44.0) and CheXpert F1-14 (from 39.5 to 71.5) over strong baselines. Our work demonstrates that dismantling a report's narrative structure to enforce independent, visually-grounded observations is a crucial and effective step toward building more accurate and reliable medical VLMs.
Applications · Language, Speech and Dialog
Masked diffusion models (MDMs) have recently emerged as a novel framework for language modeling. MDMs generate sentences by iteratively denoising masked sequences, filling in [MASK] tokens step by step. Although MDMs support any-order sampling, performance is highly sensitive to the choice of which position to unmask next. Prior work typically relies on rule-based schedules (e.g., max-confidence, max-margin), which provide ad hoc improvements. In contrast, we replace these heuristics with a learned scheduler. Specifically, we cast denoising as a KL–regularized Markov decision process (MDP) with an explicit reference policy and optimize a regularized objective that admits policy-improvement and convergence guarantees under standard assumptions. We prove that the optimized policy under this framework generates samples that more closely match the data distribution than heuristic schedules. Empirically, across four benchmarks, our learned policy consistently outperforms max-confidence: for example, on SUDOKU, where unmasking order is critical, it yields a 22% gain over random and a 12% gain over max-confidence.
Reinforcement Learning · Deep RL
Behavioral Foundation Models (BFMs) proved successful in producing near-optimal policies for arbitrary tasks in a zero-shot manner, requiring no test-time retraining or task-specific fine-tuning. Among the most promising BFMs are the ones that estimate the successor measure learned in an unsupervised way from task-agnostic offline data. However, these methods fail to react to changes in the dynamics, making them inefficient under partial observability or when the transition function changes. This hinders the applicability of BFMs in a real-world setting, e.g., in robotics, where the dynamics can unexpectedly change at test time. In this work, we demonstrate that Forward–Backward (FB) representation, one of the methods from the BFM family, cannot produce reasonable policies under distinct dynamics, leading to an interference among the latent policy representations. To address this, we propose an FB model with a transformer-based belief estimator, which greatly facilitates zero-shot adaptation. Additionally, we show that partitioning the policy encoding space into dynamics-specific clusters, aligned with the context-embedding directions, yields additional gain in performance. Those traits allow our method to respond to the dynamics mismatches observed during training and to generalize to unseen ones. Empirically, in the changing dynamics setting, our approach achieves up to a 2x higher zero-shot returns compared to the baselines for both discrete and continuous tasks.
General Machine Learning · Representation Learning
Learning robust representations from functional magnetic resonance imaging (fMRI) is fundamentally challenged by the temporal irregularity and noise inherent in data from heterogeneous sources. Existing self-supervised learning (SSL) methods often discard critical temporal information by discretizing or averaging fMRI signals. To address this, we introduce a novel framework that reframes SSL as a Stochastic Optimal Control (SOC) problem. Our approach models brain activity as continuous-time latent dynamics, learning a robust representation of brain dynamics by optimizing a control policy that is agnostic to the temporal irregularity. This SOC framework naturally unifies masked autoencoding (MAE) and joint-embedding prediction (JEPA) to extract compact, control-derived representations. Furthermore, a simulation-free inference strategy ensures computational efficiency and scalability for large-scale fMRI datasets. Our model demonstrates state-of-the-art performance across diverse downstream applications, highlighting the potential of the SOC-based continuous-time representation learning framework.
Deep Learning · Algorithms
Binary Neural Networks (BNNs), which constrain both weights and activations to binary values, offer substantial reductions in computational complexity, memory footprint, and energy consumption. These advantages make them particularly well suited for deployment on resource-constrained devices. However, training BNNs via gradient-based optimization remains challenging due to the discrete nature of their variables. The dominant approach, quantization-aware training, circumvents this issue by employing surrogate gradients. Yet, this method requires maintaining latent full-precision parameters and performing the backward pass with floating-point arithmetic, thereby forfeiting the efficiency of binary operations during training. While alternative approaches based on local learning rules exist, they are unsuitable for global credit assignment and for back-propagating errors in multi-layer architectures. This paper introduces Binary Error Propagation (BEP), the first learning algorithm to establish a principled, discrete analog of the backpropagation chain rule. This mechanism enables error signals, represented as binary vectors, to be propagated backward through multiple layers of a neural network. BEP operates entirely on binary variables, with all forward and backward computations performed using only bitwise operations. Crucially, this makes BEP the first solution to enable end-to-end binary training for recurrent neural network architectures. We validate the effectiveness of BEP on both multi-layer perceptrons and recurrent neural networks, demonstrating gains of up to $+6.89$% and $+10.57$% in test accuracy, respectively. The proposed algorithm is released as an open-source repository.
General Machine Learning · Representation Learning
Next token prediction has been the standard training objective used in large language model pretraining. Representations are learned as a result of optimizing for token-level perplexity. We propose Continuous Concept Mixing (CoCoMix), a novel pretraining framework that combines discrete next token prediction with continuous concepts. Specifically, CoCoMix predicts ``continuous concepts'' learned from a pretrained sparse autoencoder and mixes them into the model's hidden state by interleaving with token hidden representations. Through experiments on multiple benchmarks, including language modeling and downstream reasoning tasks, we show that CoCoMix is more sample efficient and consistently outperforms standard next token prediction and knowledge distillation. We find that combining both concept learning and interleaving in an end-to-end framework is critical to performance gains. Furthermore, CoCoMix enhances interpretability and steerability by allowing direct inspection and modification of the predicted concept, offering a transparent way to guide the model’s internal reasoning process.
Discrete diffusion models have demonstrated great promise in modeling various sequence data, ranging from human language to biological sequences. Inspired by the success of RL in language models, there is growing interest in further improving the models by alignment with a certain reward. In this work, we propose an offline preference optimization method to approach trajectory alignment for discrete diffusion models. Instead of applying the reward on the final output and backpropagating the gradient to the entire denoising process, we decompose the problem into a set of stepwise alignment objectives by matching the per-step posterior. This framework enables efficient diffusion optimization, is compatible with arbitrary reward functions, and importantly, yields an equivalent optimal solution under additive factorization of the trajectory reward. Experiments across multiple domains including DNA sequence design, protein inverse folding, and language modeling consistently demonstrate the superiority of our approach. Notably, it achieves an up to 12\% improvement over the most competitive RL-based baseline in terms of predicted activity on DNA sequence design, and further improves the GSM8K score from 78.6 to 81.2 on LLaDA-8B-Instruct for language modeling.
Applications · Health
Multimodal large language models are promising for clinical visual question answering tasks, but scaling to 3D imaging is hindered by high computational costs. Prior methods often rely on 2D slices or fixed-length token compression, disrupting volumetric continuity and obscuring subtle findings. We present Photon, a framework that represents 3D medical volumes with token sequences of variable length. Photon introduces instruction-conditioned token scheduling and surrogate gradient propagation to adaptively reduce tokens during both training and inference, which lowers computational cost while mitigating the attention dilution caused by redundant tokens. It incorporates a custom backpropagation rule with gradient restoration to enable differentiable optimization despite discrete token drop. To stabilize token compression and ensure reliable use of visual evidence, Photon further applies regularization objectives that mitigate language-only bias and improve reliability. Experiments on diverse medical visual question answering tasks show that Photon achieves state-of-the-art accuracy while reducing resource usage and accelerating both training and inference.
Applications · Language, Speech and Dialog
Speech emotion recognition (SER) hinges on front-ends that expose informative time-frequency (TF) structure from raw speech. Classical short-time Fourier and wavelet transforms impose fixed resolution trade-offs, while prior ”superlet” variants rely on integer orders and hand-tuned hyperparameters. We revisit TF analysis from first principles and formulate a learnable continuum of superlet transforms. Starting from DC-corrected analytic Morlet wavelets, we define superlets as multiplicative ensembles of wavelet responses and realize learnable fractional orders via softmax-normalized weights over discrete orders, computed as a logdomain geometric mean. We establish admissibility (zero mean) and continuity in order and frequency, and characterize approximate analyticity by bounding negative-frequency leakage as a function of an effective cycle parameter. Building on these results, we introduce the Learnable Fractional Superlet Transform (LFST), a fully differentiable front-end that jointly optimizes (i) a monotone, logspaced frequency grid, (ii) frequency-dependent base cycles, and (iii) learnable fractional-order weights, all trained end-to-end. LFST further includes a learnable asymmetric hard-thresholding (LAHT) module that promotes sparse, denoised TF activations while preserving transients; we provide sufficient conditions for boundedness and stability under mild cycle and grid constraints. To exploit LFST for SER, we design a compact Spectro-Temporal Emotion Encoder (STEE), achieving strong performance with a parameter budget that is orders of magnitude smaller than large self-supervised models, at the cost of additional frontend computation compared to STFT- or LEAF-based baselines. STEE consumes two-channel TF maps, magnitude S and phase-congruency κ, through a compact multi-scale stack with residual temporal and depthwise-frequency blocks, Adaptive FiLM gating, axial (time-axis) self-attention, global attentive pooling, and a lightweight classifier. The full LFST+STEE system is trained in a standard train-validate-test regime using focal loss with optional class rebalancing, and is validated on IEMOCAP, EMO-DB, and the private NSPL-CRISE dataset under standard protocols. By unifying a principled, learnable TF transform with a compact encoder, LFST+STEE replaces ad hoc front-ends with a mathematically grounded alternative that is differentiable, stable, and adaptable to data, enabling systematic ablations over frequency grids, cycle schedules, and fractional orders within a single end-to-end model. The source code of this paper is shared on the GitHub repository: https://github.com/alaaNfissi/LFST-for-SER.
Scaling inference-time compute for Large Language Models (LLMs) has unlocked unprecedented reasoning capabilities. However, existing inference-time scaling methods typically rely on inefficient and suboptimal discrete search algorithms or trial-and-error prompting to improve the online policy. In this paper, we propose $\nabla$-Reasoner, an iterative generation framework that integrates differentiable optimization over token logits into the decoding loop to refine the policy on the fly. Our core component, Differentiable Textual Optimization (DTO), leverages gradient signals from both the LLM’s likelihood and a reward model to refine textual representations. $\nabla$-Reasoner further incorporates rejection sampling and acceleration design to robustify and speed up decoding. Theoretically, we show that performing inference-time gradient descent in the sample space to maximize reward is dual to aligning an LLM policy via KL-regularized reinforcement learning. Empirically, $\nabla$-Reasoner achieves over 20% accuracy improvement on a challenging mathematical reasoning benchmark, while reducing number of model calls by approximately 10-40% compared to strong baselines. Overall, our work introduces a paradigm shift from zeroth-order search to first-order optimization at test time, offering a cost-effective path to amplify LLM reasoning.
Applications · Chemistry and Drug Discovery
We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules. The model learns to transform a uniform source over all possible tokens into the data distribution. Unlike masked models, its training loss accounts for predictions on all sequence positions at every denoising step, shifting the generation paradigm from completion to refinement, and decoupling the number of sampling steps from the sequence length. For \textit{de novo} generation, InVirtuoGen achieves a stronger quality-diversity pareto frontier than prior fragment-based models and competitive performance on fragment-constrained tasks. For property and lead optimization, we propose a hybrid scheme that combines a genetic algorithm with a Proximal Property Optimization fine-tuning strategy adapted to discrete flows. Our approach sets a new state-of-the-art on the Practical Molecular Optimization benchmark, measured by top-10 AUC across tasks, and yields higher docking scores in lead optimization than previous baselines. InVirtuoGen thus establishes a versatile generative foundation for drug discovery, from early hit finding to multi-objective lead optimization. We further contribute to open science by releasing pretrained checkpoints and code, making our results fully reproducible.
Applications · Chemistry and Drug Discovery
In the era of AI-driven science and engineering, we often want to design discrete objects (e.g., circuits, proteins, materials) in silico according to user-specified properties (e.g., that a protein binds its target). Given a property predictive model, in silico design typically involves training a generative model over the design space (e.g., over the set of all length-L proteins) to concentrate on designs with the desired properties. Distributional optimization, formalized as an estimation of distribution algorithm or as reinforcement learning policy optimization, maximizes an objective function in expectation over samples. Optimizing a distribution over discrete-valued designs is in general challenging due to the combinatorial nature of the design space. However, many property predictors in scientific applications are decomposable in the sense that they can be factorized over design variables in a way that will prove useful. For example, the active site amino acids in a catalytic protein may need to only loosely interact with the rest of the protein for maximal catalytic activity. Current distributional optimization algorithms are unable to make use of such structure, which could dramatically improve the optimization. Herein, we propose and demonstrate use of a new distributional optimization algorithm, Decomposition-Aware Distributional Optimization (DADO), that can leverage any decomposability defined by a junction tree on the design variables. At its core, DADO employs a factorized “search distribution”—a learned generative model—for efficient navigation of the search space, and invokes graph message passing to coordinate optimization across all variables.
Applications · Robotics
Vision-language-action (VLA) models aim to understand natural language instructions and visual observations and execute corresponding actions as an embodied agent. Recent advancements have integrated future images into the understanding-action loop, enabling foresight-driven policies that reduce abstract action prediction to a more tractable inverse kinematics problem. However, existing models either rely on external experts for modality unification or treat image generation and action prediction as separate processes, limiting the benefits of direct synergy between these tasks. In this work, we propose Unified Diffusion VLAs, which tightly couple understanding, generation, and action in a mutually reinforcing manner. Our method optimizes the generation of actions and images jointly through a synchronous denoising diffusion process, where action tokens progressively attend to future image tokens. This iterative refinement enables actions to evolve from initialization with sufficient visual guidance, ensuring precise action execution. We introduce a hybrid attention mechanism and the Joint Discrete Denoising Diffusion Process (JD3P), which integrates multiple modalities into a unified trajectory. We also propose a two-stage training pipeline and several inference-time techniques that optimize performance and efficiency. Our approach achieves state-of-the-art performance on benchmarks such as CALVIN, LIBERO, and SimplerEnv, and we demonstrate its effectiveness through ablation studies and real-world evaluations.
Low-rank optimization has emerged as a promising direction in training large language models (LLMs) to improve running time and reduce the memory usage of adaptive optimizers by constraining learning to a lower-dimensional space. Prior work typically projects gradients of linear layers using approaches based on Singular Value Decomposition (SVD) or QR-decomposition. Applying these techniques individually to each layer in large models is computationally expensive and incurs additional memory costs due to storing the projection matrices. In this work, we propose a computationally efficient and conceptually simple, two-step procedure to approximate SVD/QR-based gradient projections into lower-dimensional spaces by using a predefined orthogonal matrix of the Discrete Cosine Transform (DCT). We dynamically select columns from the DCT matrix based on their alignment with the gradient of each layer. The effective projection matrices are obtained via a simple \texttt{matmul} with the DCT matrix in $O(n^3)$ time, followed by a lightweight sorting step to identify the most relevant basis vectors. For large layers, DCT can be computed via \texttt{Makhoul}'s $N$-point algorithm based on Fast Fourier Transform (FFT) in $O(n^2 \log(n))$ time, yielding speed-ups for low-end GPUs. Due to the predefined nature of the orthogonal bases, they are computed once at the start of training. Our numerical experiments on both pre-training and fine-tuning tasks demonstrate the effectiveness of our dual strategy in approximating optimal low-rank projections, obtaining an approach with rank-independent running time that matches the performance of costly SVD/QR-based methods while achieving faster runtime and reduced memory usage by up to $25\%$ across different model sizes. Our code is available at \href{https://github.com/IST-DASLab/Trion}{\texttt{https://github.com/IST-DASLab/Trion}}.
Deep Learning · Generative Models and Autoencoders
Learning population dynamics involves recovering the underlying process that governs particle evolution, given evolutionary snapshots of samples at discrete time points. Recent methods frame this as an energy minimization problem in probability space and leverage the celebrated JKO scheme for efficient time discretization. In this work, we introduce ``iJKOnet``, an approach that combines the JKO framework with inverse optimization techniques to learn population dynamics. Our method relies on a conventional *end-to-end* adversarial training procedure and does not require restrictive architectural choices, e.g., input-convex neural networks. We establish theoretical guarantees for our methodology and demonstrate improved performance over prior JKO-based methods.
Developing effective representations of protein structures is essential for advancing protein science, particularly for protein generative modeling. Current approaches often grapple with the complexities of the $\operatorname{SE}(3)$ manifold, rely on discrete tokenization, or the need for multiple training objectives, all of which can hinder the model optimization and generalization. We introduce ProteinAE, a novel and streamlined protein diffusion autoencoder designed to overcome these challenges by directly mapping protein backbone coordinates from $\operatorname{E}(3)$ into a continuous, compact latent space. ProteinAE employs a non-equivariant Diffusion Transformer with a bottleneck design for efficient compression and is trained end-to-end with a single flow matching objective, substantially simplifying the optimization pipeline. We demonstrate that ProteinAE achieves state-of-the-art reconstruction quality, outperforming existing autoencoders. The resulting latent space serves as a powerful foundation for a latent diffusion model that bypasses the need for explicit equivariance. This enables efficient, high-quality structure generation that is competitive with leading structure-based approaches and significantly outperforms prior latent-based methods. Code is available at https://github.com/OnlyLoveKFC/ProteinAE_v1.