Recovering the dynamics from a few snapshots of a high-dimensional system is a challenging task in statistical physics and machine learning, with important applications in computational biology. Many algorithms have been developed to tackle this problem, based on frameworks such as optimal transport and the Schrödinger bridge. A notable recent framework is Regularized Unbalanced Optimal Transport (RUOT), which integrates both stochastic dynamics and unnormalized distributions. However, since many existing methods do not explicitly enforce optimality conditions, their solutions often struggle to satisfy the principle of least action and meet challenges to converge in a stable and reliable way. To address these issues, we propose Variational RUOT (Var-RUOT), a new framework to solve the RUOT problem. By incorporating the optimal necessary conditions for the RUOT problem into both the parameterization of the search space and the loss function design, Var-RUOT only needs to learn a scalar field to solve the RUOT problem and can search for solutions with lower action. We also examined the challenge of selecting a growth penalty function in the widely used Wasserstein-Fisher-Rao metric and proposed a solution that better aligns with biological priors in Var-RUOT.

Autoregressive models have transformed protein engineering by enabling the generation of novel protein sequences beyond those found in nature. However, their sequential inference introduces significant latency, limiting their utility in highthroughput protein screening. Speculative decoding accelerates generation by employing a lightweight draft model to sample tokens, which a larger target model then verifies and refines. Yet, in protein sequence generation, draft models are typically agnostic to the structural and functional constraints of the target protein, leading to biologically implausible outputs and a shift in the likelihood distribution of generated sequences. We introduce SpecMER (Speculative Decoding via k-mer Guidance), a novel framework that incorporates biological, structural, and functional priors using k-mer motifs extracted from multiple sequence alignments. By scoring candidate sequences in parallel and selecting those most consistent with known biological patterns, SpecMER significantly improves sequence plausibility while retaining the efficiency of speculative decoding. SpecMER achieves 24-32% speedup over standard autoregressive decoding, along with higher acceptance rates and improved sequence likelihoods.

Differentiable economics--the use of deep learning for auction design--has driven progress in multi-item auction design with additive and unit-demand valuations. However, there has been little progress for combinatorial auctions (CAs), even in the simplest and yet important single bidder case, due to exponential growth of the bundle space with the number of items. We address this challenge by introducing a deep network architecture for a menu-based CA, which supports the first dominantstrategy incentive compatible (DSIC), revenue-optimizing single-bidder CA. Our idea is to generate a bundle distribution through an ordinary differential equation (ODE) applied to a tractable initial distribution. Our method, BUNDLEFLOW, learns suitable ODE-based transforms, one for each menu element, to optimize expected revenue. BUNDLEFLOW achieves up to 2.23 higher revenue than baselines on standard CA testbeds and scales up to 500 items.

In this work, we observe a counterintuitive phenomenon in self-supervised learning (SSL): longer training may impair the performance of dense prediction tasks (e.g., semantic segmentation). We refer to this phenomenon as Self-supervised Dense Degradation (SDD) and demonstrate its consistent presence across sixteen state-of-the-art SSL methods with various losses, architectures, and datasets. When the model performs suboptimally on dense tasks at the end of training, measuring the performance during training becomes essential. However, evaluating dense performance effectively without annotations remains an open challenge. To tackle this issue, we introduce a Dense representation Structure Estimator (DSE), composed of a class-relevance measure and an effective dimensionality measure. The proposed DSE is both theoretically grounded and empirically validated to be closely correlated with the downstream performance. Based on this metric, we introduce a straightforward yet effective model selection strategy and a DSE-based regularization method. Experiments on sixteen SSL methods across four benchmarks confirm that model selection improves mIoU by 3.0% on average with negligible computational cost.

With the rapid growth of video generative models (VGMs), it is essential to develop reliable and comprehensive automatic metrics for AI-generated videos (AIGVs). Existing methods either use off-the-shelf models optimized for other tasks or rely on human assessment data to train specialized evaluators. These approaches are constrained to specific evaluation aspects and are difficult to scale with the increasing demands for finer-grained and more comprehensive evaluations. To address this issue, this work investigates the feasibility of using multimodal large language models (MLLMs) as a unified evaluator for AIGVs, leveraging their strong visual perception and language understanding capabilities. To evaluate the performance of automatic metrics in unified AIGV evaluation, we introduce a benchmark called UVE-Bench. UVE-Bench collects videos generated by state-of-the-art VGMs and provides pairwise human preference annotations across 15 evaluation aspects. Using UVE-Bench, we extensively evaluate 18 MLLMs. Our empirical results suggest that while advanced MLLMs (e.g., Qwen2VL-72B and InternVL2.5-78B)

Latent diffusion models (LDMs) dominate high-quality image generation, yet integrating representation learning with generative modeling remains a challenge. We introduce a novel generative image modeling framework that seamlessly bridges this gap by leveraging a diffusion model to jointly model low-level image latents (from a variational autoencoder) and high-level semantic features (from a pretrained self-supervised encoder like DINO). Our latent-semantic diffusion approach learns to generate coherent image-feature pairs from pure noise, significantly enhancing both generative quality and training efficiency, all while requiring only minimal modifications to standard Diffusion Transformer architectures. By eliminating the need for complex distillation objectives, our unified design simplifies training and unlocks a powerful new inference strategy: Representation Guidance, which leverages learned semantics to steer and refine image generation. Evaluated in both conditional and unconditional settings, our method delivers substantial improvements in image quality and training convergence speed, establishing a new direction for representation-aware generative modeling.

Scientific discoveries increasingly rely on complex multimodal reasoning that integrates information-intensive scientific data and domain-specific expertise. Empowered by expert-level scientific benchmarks, scientific Multimodal Large Language Models (MLLMs) hold the potential to significantly enhance this discovery process in realistic workflows. However, current scientific benchmarks mostly focus on evaluating the knowledge understanding capabilities of MLLMs, leading to an inadequate assessment of their perception and reasoning abilities. To address this gap, we present the Scientists First Exam (SFE) benchmark, designed to evaluate the scientific cognitive capacities of MLLMs through three cognitive levels: scientific signal perception, scientific attribute understanding, scientific comparative reasoning. Specifically, SFE comprises 830 expert-verified VQA pairs across three question types, spanning 66 multimodal tasks across five high-value disciplines. Extensive experiments reveal that current state-of-the-art GPT-o3 and InternVL-3 achieve only 34.08% and 26.52% on SFE, highlighting significant room for MLLMs to improve in scientific realms. We hope the insights obtained in SFE will facilitate further developments in AI-enhanced scientific discoveries.

Inspired by the remarkable success of foundation models in language and vision, Graph Foundation Models (GFMs) hold significant promise for broad applicability across diverse graph tasks and domains. However, existing GFMs struggle with unstable few-shot fine-tuning, where both performance and adaptation efficiency exhibit significant fluctuations caused by the randomness in the support sample selection and structural discrepancies between the pre-trained and target graphs. How to fine-tune GFMs robustly and efficiently to enable trustworthy knowledge transfer across domains and tasks is the major challenge. In this paper, we propose GRAVER, a novel Generative gRAph VocabulariEs for Robust GFM fine-tuning framework that tackles the aforementioned instability via generative augmentations. Specifically, to identify transferable units, we analyze and extract key class-specific subgraph patterns by ego-graph disentanglement and validate their transferability both theoretically and empirically. To enable effective pre-training across diverse domains, we leverage a universal task template based on ego-graph similarity and construct graph vocabularies via graphon-based generative experts. To facilitate robust and efficient prompt fine-tuning, we grave the support samples with in-context vocabularies, where the lightweight MoE-CoE network attentively routes knowledge from source domains. Extensive experiments demonstrate the superiority of GRAVER over effectiveness, robustness, and efficiency on downstream few-shot node and graph classification tasks compared with 15 state-of-the-art baselines.

We investigate fingerprints in pretraining datasets for large language models (LLMs) through dataset classification experiments. Building on prior work demonstrating the existence of fingerprints or biases in popular computer vision datasets, we analyze popular open-source pretraining datasets for LLMs derived from CommonCrawl including C4, RefinedWeb, DolmaCC, RedPajama-V2, FineWeb, and DCLM-Baseline. Despite those datasets being obtained with similar curation steps, neural networks can classify surprisingly well which dataset a single text sequence belongs to, significantly better than a human can. This indicates that small differences in filtering and processing pipelines induce fingerprints, that we find are evident in formatting, vocabulary, and content distributions. Such fingerprints can negatively impact cross-dataset generalization. Additionally, we show that these fingerprints propagate through training: sequences generated by models trained on those datasets can be accurately classified by a classifier trained on the original datasets. This can offer insights into data characteristics that are typically undisclosed by LLM developers, including pretraining mixture proportions and finetuning data sources.

Optimal Transport (OT) has emerged as a fundamental tool in machine learning for comparing probability distributions in a geometrically meaningful manner. However, a key limitation of classical OT is its requirement that the source and target distributions have equal total mass, limiting its use in real-world settings involving imbalanced data, noise, outliers, or structural inconsistencies. Partial Transport (PT) addresses this limitation by allowing only a fraction of the mass to be transported, offering greater flexibility and robustness. Nonetheless, similar to OT, PT remains computationally expensive, as it typically involves solving large-scale linear programs-especially in high-dimensional spaces. To alleviate this computational burden, several emerging works have introduced the TreeSliced Wasserstein (TSW) distance, which projects distributions onto tree-metric spaces where OT problems admit closed-form solutions. Building on this line of research, we propose a novel framework that extends the tree-sliced approach to the PT setting, introducing the Partial Tree-Sliced Wasserstein (PartialTSW) distance. Our method is based on the key observation that, within tree-metric space, the PT problem can be equivalently reformulated as a standard balanced OT problem between suitably modified measures. This reformulation enables efficient computation while preserving the adaptability and robustness of partial transport. Our method proves effective across challenging tasks such as outlier removal and addressing class imbalance in image-to-image translation.