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.

Recent advances in diffusion models have enabled high-quality video generation, b making ut the additional training and temporal inference dimension on long significantly videos prohibiti increases vely computational expensive. In costs, this paper diffusion, we models: identify post-softmax a phenomenon attention we term scores Spatiotempor diminish al as Ener spatial gy Decay and temporal in video distance o scalable ver space sparse between and time attention tok in ens nature.

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)

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.

We introduce Oxford Day-and-Night, a large-scale, egocentric dataset for novel view synthesis (NVS) and visual relocalisation under challenging lighting conditions. Existing datasets often lack crucial combinations of features such as ground-truth 3D geometry, wide-ranging lighting variation, and full 6DoF motion. Oxford Day-and-Night addresses these gaps by leveraging Meta ARIA glasses to capture egocentric video and applying multi-session SLAM to estimate camera poses, reconstruct 3D point clouds, and align sequences captured under varying lighting conditions, including both day and night. The dataset spans over 30 km of recorded trajectories and covers an area of 40,000 m2, offering a rich foundation for egocentric 3D vision research. It supports two core benchmarks, NVS and relocalisation, providing a unique platform for evaluating models in realistic and diverse environments.

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.

Graph Convolutional Networks (GCNs) based on linear aggregation have been widely applied across various domains due to their exceptional performance. To enhance performance, these networks often utilize the graph Laplacian norm to suppress the propagation of information from first-order neighbors. However, this approach may dilute valuable interaction information and make the model slowly learn sparse interaction relationships from neighbors, which increases training time and negatively affects performance. To address these issues, we introduce BoostGCN, a novel linear GCN model that focuses on amplifying significant interactions with first-order neighbors, which enables the model to accurately and quickly capture significant relationships. BoostGCN has relatively fixed parameters, making it user-friendly. Experiments on four real-world datasets demonstrate that BoostGCN outperforms existing state-of-the-art GCN models in both performance and efficiency.

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.