Mobile manipulators in households must both navigate and manipulate. This requires a compact, semantically rich scene representation that captures where objects are, how they function, and which parts are actionable. Scene graphs are a natural choice, yet prior work often separates spatial and functional relations, treats scenes as static snapshots without object states or temporal updates, and overlooks information most relevant for accomplishing the current task. To overcome these shortcomings, we introduce MomaGraph, a unified scene representation for embodied agents that integrates spatial-functional relationships and part-level interactive elements. However, advancing such a representation requires both suitable data and rigorous evaluation, which have been largely missing. To address this, we construct MomaGraph-Scenes, the first large-scale dataset of richly annotated, task-driven scene graphs in household environments, and design MomaGraph-Bench, a systematic evaluation suite spanning six reasoning capabilities from high-level planning to fine-grained scene understanding. Built upon this foundation, we further develop MomaGraph-R1, a 7B vision–language model trained with reinforcement learning on MomaGraph-Scenes. MomaGraph-R1 predicts task-oriented scene graphs and serves as a zero-shot task planner under a Graph-then-Plan framework. Extensive experiments show that our model achieves state-of-the-art results among open-source models, reaching 71.6% accuracy on the benchmark (+11.4% over the best baseline), while generalizing across public benchmarks and transferring effectively to real-robot experiments. More visualizations and robot demonstrations are available at https://hybridrobotics.github.io/MomaGraph/.
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Applications · Everything Else
Large Language Models (LLMs) have made remarkable progress, surpassing human performance on several benchmarks in domains such as mathematics and coding. A key driver of this progress has been the development of benchmark datasets. In contrast, the financial domain poses higher entry barriers due to its demand for specialized expertise, and benchmarks remain relatively scarce compared to those in mathematics or coding. We introduce EDINET-Bench, an open-source Japanese financial benchmark designed to evaluate LLMs on challenging tasks such as accounting fraud detection, earnings forecasting, and industry classification. EDINET-Bench is constructed from ten years of annual reports filed by Japanese companies. These tasks require models to process entire annual reports and integrate information across multiple tables and textual sections, demanding expert-level reasoning that is challenging even for human professionals. Our experiments show that even state-of-the-art LLMs struggle in this domain, performing only marginally better than logistic regression in binary classification tasks such as fraud detection and earnings forecasting. Our results show that simply providing reports to LLMs in a straightforward setting is not enough. This highlights the need for benchmark frameworks that better reflect the environments in which financial professionals operate, with richer scaffolding such as realistic simulations and task-specific reasoning support to enable more effective problem solving. We make our dataset and code publicly available to support future research.
Optimization · Learning for Optimization
Machine learning (ML) has shown promise for tackling combinatorial optimization (CO), but much of the reported progress relies on small-scale, synthetic benchmarks that fail to capture real-world structure and scale. A core limitation is that ML methods are typically trained and evaluated on synthetic instance generators, leaving open how they perform on irregular, competition-grade, or industrial datasets. We present FrontierCO, a benchmark for evaluating ML-based CO solvers under real-world structure and extreme scale. FrontierCO spans eight CO problems, including routing, scheduling, facility location, and graph problems, with instances drawn from competitions and public repositories (e.g., DIMACS, TSPLib). Each task provides both easy sets (historically challenging but now solvable) and hard sets (open or computationally intensive), alongside standardized training/validation resources. Using FrontierCO, we evaluate 16 representative ML solvers---graph neural approaches, hybrid neural–symbolic methods, and LLM-based agents---against state-of-the-art classical solvers. We find a persistent performance gap that widens under structurally challenging and large instance sizes (e.g., TSP up to 10M nodes; MIS up to 8M), while also identifying cases where ML methods outperform classical solvers. By centering evaluation on real-world structure and orders-of-magnitude larger instances, FrontierCO provides a rigorous basis for advancing ML for CO. Our benchmark is available at https://huggingface.co/datasets/CO-Bench/FrontierCO.
Deep Learning · Everything Else
Information retrieval (IR) evaluation remains challenging due to incomplete IR benchmark datasets that contain unlabeled relevant chunks. While LLMs and LLM-human hybrid strategies reduce costly human effort, they remain prone to LLM overconfidence and ineffective AI-to-human escalation. To address this, we propose DREAM, a multi-round debate-based relevance assessment framework with LLM agents, built on opposing initial stances and iterative reciprocal critique. Through our agreement-based debate, it yields more accurate labeling for certain cases and more reliable AI-to-human escalation for uncertain ones, achieving 95.2% labeling accuracy with only 3.5% human involvement. Using DREAM, we build BRIDGE, a refined benchmark that mitigates evaluation bias and enables fairer retriever comparison by uncovering 29,824 missing relevant chunks. We then re-benchmark IR systems and extend evaluation to RAG, showing that unaddressed holes not only distort retriever rankings but also drive retrieval–generation misalignment. Code and data will be released upon acceptance.
Content Warning: This paper contains examples with harmful content, and the constructed dataset includes samples that may be considered offensive. As large language models (LLMs) continue to advance in capabilities, ensuring their safety against jailbreak attacks remains a critical challenge. In this paper, we introduce a novel safety alignment approach called Answer-Then-Check, which enhances LLM robustness against malicious prompts by applying thinking ability to mitigate jailbreaking problems before producing a final answer to the user. Our method enables models to answer the question in their thoughts directly and then critically evaluate its safety before deciding whether to provide it. To implement this approach, we construct the Reasoned Safety Alignment (ReSA) dataset, comprising 80K samples that teach models to reason through direct responses and then analyze their safety. Experimental results demonstrate that our approach achieves the Pareto frontier with superior safety capability while decreasing over-refusal rates. Notably, the fine-tuned model maintains general reasoning capabilities on benchmarks like MMLU, MATH500, and HumanEval. Besides, our method equips models with the ability to perform safe completion, while post-hoc detection methods can only directly reject sensitive, harmful queries (e.g., self-harm). Our results show that inference-time strategies alone are insufficient, highlighting the necessity of safety training, and we find even $500$ samples can yield performance comparable to the entire dataset, suggesting a promising path for data-efficient safety alignment. The dataset is publicly available at: https://huggingface.co/datasets/ByteDance-Seed/ReSA.
Computer Vision · 3D Rendering & Reconstruction
We present Depth Anything 3 (DA3), a model that predicts spatially consistent geometry from an arbitrary number of visual inputs, with or without known camera poses. In pursuit of minimal modeling, DA3 yields two key insights: a single plain transformer (e.g., vanilla DINOv2 encoder) is sufficient as a backbone without architectural specialization, and a singular depth-ray prediction target obviates the need for complex multi-task learning. Through our teacher-student training paradigm, the model achieves a level of detail and generalization on par with Depth Anything 2 (DA2). We establish a new visual geometry benchmark covering camera pose estimation, any-view geometry and visual rendering. On this benchmark, DA3 sets a new state-of-the-art across all tasks, surpassing prior SOTA VGGT by an average of 35.7\% in camera pose accuracy and 23.6\% in geometric accuracy. Moreover, it outperforms DA2 in monocular depth estimation. All models are trained exclusively on public academic datasets.
Computer Vision · Vision Models & Multimodal
Recent benchmarks and datasets have been proposed to improve spatial reasoning in vision-language models (VLMs), yet existing open resources remain constrained by limited scale, narrow visual diversity, and restricted instruction expressiveness. To address these gaps, we present InternSpatial---the largest open-source dataset for spatial reasoning in VLMs---alongside InternSpatial-Bench, a comprehensive evaluation benchmark designed to assess spatial understanding across diverse instruction formats. InternSpatial contains 12 million question-answer(QA) pairs covering both single-view and multi-view scenarios, sourced from varied visual environments and supporting 19 distinct instruction formats that mirror real-world query patterns. InternSpatial-Bench aims to single-view assessment and also extends multi-view reasoning through a novel rotation estimation task. Experimental validation demonstrates that models trained on \trainset achieve substantial performance improvement of 12.1% on InternSpatial-Bench and 10.7% on VSI-Bench, while preserving competitive performance on general-purpose benchmarks. We expect these resources can advance the development of spatially-capable VLMs for practical applications in robotics and embodied AI systems. Our codes and datasets are publicly available at https://github.com/dengnianchen/intern-spatial.
Computer Vision · 3D Rendering & Reconstruction
Building 4D video representations to model underlying spacetime constitutes a crucial step toward understanding dynamic scenes, yet there is no consensus on the paradigm: current approaches resort to additional estimators such as depth, flow, or tracking, or to heavy per-scene optimization, making them brittle and hard to generalize. In a video, its atomic unit, the pixel, follows a continuous 3D trajectory that unfolds over time, acting as the atomic primitive of dynamics. Recognizing this, we propose to represent any video as a Trajectory Field: a dense mapping that assigns each pixel in each frame to a parametric 3D trajectory. To this end, we introduce Trace Anything, a neural network that predicts the trajectory field in a feed-forward manner. Specifically, for each video frame, the model outputs a series of control point maps, defining parametric trajectories for each pixel. Together, our representation and model directly construct a 4D video representation in a single forward pass, without additional estimators or global alignment. We develop a synthetic data platform to construct a training dataset and a benchmark for trajectory field estimation. Experiments show that Trace Anything surpasses existing methods or performs competitively on the new benchmark and established point tracking benchmarks, with significant efficiency gains. Moreover, it facilitates downstream applications such as goal-conditioned manipulation, simple motion extrapolation, and spatio-temporal fusion. We will release the code, the model weights, and the data platform.
Applications · Time Series
Large Language Models (LLMs) have shown promising performance in time series modeling tasks, but do they truly understand time series data? While multiple benchmarks have been proposed to answer this fundamental question, most are manually curated and focus on narrow domains or specific skill sets. To address this limitation, we propose scalable methods for creating comprehensive time series reasoning benchmarks that combine the flexibility of templates with the creativity of LLM agents. We first develop $\texttt{TimeSeriesExam}$, a multiple-choice benchmark using synthetic time series to evaluate LLMs across five core reasoning categories: pattern recognition, noise understanding, similarity analysis, anomaly detection, and causality. Then, with $\texttt{TimeSeriesExamAgent}$, we scale our approach by automatically generating benchmarks from real-world datasets spanning healthcare, finance and weather domains. Through multi-dimensional quality evaluation, we demonstrate that our automatically generated benchmarks achieve diversity comparable to manually curated alternatives. However, our experiments reveal that LLM performance remains limited in both abstract time series reasoning and domain-specific applications, highlighting ongoing challenges in enabling effective time series understanding in these models. $\texttt{TimeSeriesExamAgent}$ is available at https://github.com/magwiazda/TimeSeriesExamAgent
Applications · Genetics, Cell Biology, Health, etc
Protein-protein interactions (PPIs) are mediated at the residue level. Most sequence-based PPI models consider residue-residue interactions across two proteins, which can yield accurate interaction scores but are too slow to scale. At proteome scale, identifying candidate PPIs requires evaluating nearly *all possible protein pairs*. For $N$ proteins of average length $L$, exhaustive all-against-all search requires $\mathcal{O}(N^2L^2)$ computation, rendering conventional approaches computationally impractical. We introduce RaftPPI, a scalable framework that approximates residue-level PPI modeling while enabling efficient large-scale retrieval. RaftPPI represents residue interactions with a Gaussian kernel, approximated efficiently via structured random Fourier features, and applies a low-rank factorized attention mechanism that admits pooling into a compact embedding per protein. Each protein is encoded once into an indexable embedding, allowing approximate nearest-neighbor search to replace exhaustive pairwise scoring, reducing proteome-wide retrieval from *months* to *minutes* on a single GPU or CPU. On the human proteome with the D-SCRIPT dataset, RaftPPI retrieves the top 20% pairs from $\sim$200M candidate pairs in 5.7 minutes on an A100 GPU, or 3.3 minutes on an Intel Xeon 6980P CPU, covering 75.1% of the true interacting pairs, compared to 4.9 GPU months for the best prior method (61.2%). Across seven benchmarks with sequence- and degree-controlled splits, RaftPPI achieves state-of-the-art PPI classification and retrieval performance, while enabling residue-aware, retrieval-friendly screening at proteome scale.
Applications · Chemistry and Drug Discovery
Deep learning models have driven significant progress in predicting protein function and interactions at the protein level. While these advancements have been invaluable for many biological applications such as enzyme engineering and function annotation, a more detailed perspective is essential for understanding protein functional mechanisms and evaluating the biological knowledge captured by models. This study introduces VenusX, the first benchmark designed to assess protein representation learning with a focus on fine-grained intra-protein functional understanding. VenusX comprises three major task categories across six types of annotations, including residue-level binary classification, fragment-level multi-class classification, and pairwise functional similarity scoring for identifying critical active sites, binding sites, conserved sites, motifs, domains, and epitopes. The benchmark features over 878,000 samples curated from major open-source databases such as InterPro, BioLiP, and SAbDab. By providing mixed-family and cross-family splits at three sequence identity thresholds, our benchmark enables a comprehensive assessment of model performance on both in-distribution and out-of-distribution scenarios. For baseline evaluation, we assess a diverse set of popular and open-source models, including pre-trained protein language models, sequence-structure hybrids, structure-based methods, and alignment-based techniques. Their performance is reported across all benchmark datasets and evaluation settings using multiple metrics, offering a thorough comparison and a strong foundation for future research. Our code (https://github.com/ai4protein/VenusX), data (https://huggingface.co/collections/AI4Protein/venusx-dataset), and a leaderboard (https://ai4protein.github.io/venusx/) are provided as open-source resources.
Applications · Chemistry and Drug Discovery
Peptide therapeutics are widely regarded as the “third generation” of drugs, yet progress in peptide Machine Learning (ML) are hindered by the absence of standardized benchmarks. Here we present \textbf{PepBenchmark}, which unifies datasets, preprocessing, and evaluation protocols for peptide drug discovery. PepBenchmark comprises three components: (1) \textbf{PepBenchData}, a well-curated collection comprising 29 canonical-peptide and 6 non-canonical-peptide datasets across 7 groups, systematically covering key aspects of peptide drug development—representing, to the best of our knowledge, the most comprehensive AI-ready dataset resource to date; (2) \textbf{PepBenchPipeline}, a standardized preprocessing pipeline that ensures consistent dataset cleaning, construction, splitting, and feature transformation, mitigating quality issues common in ad hoc pipelines; and (3) \textbf{PepBenchLeaderboard}, a unified evaluation protocol and leaderboard with strong baselines across 4 major methodological families: Fingerprint-based, GNN-based, PLM-based, and SMILES-based models. Together, PepBenchmark provides the first standardized and comparable foundation for peptide drug discovery, facilitating methodological advances and translation into real-world applications. The data and code are publicly available at \href{https://github.com/ZGCI-AI4S-Pep/PepBenchmark/}{\texttt{https://github.com/ZGCI-AI4S-Pep/PepBenchmark/}}.
Deep Learning · Everything Else
Although probing frozen models has become a standard evaluation paradigm, self-supervised learning in audio defaults to fine-tuning {when pursuing state-of-the-art on AudioSet}. A key reason is that global pooling creates an information bottleneck causing linear probes to misrepresent the embedding quality: The $\texttt{cls}$-token discards crucial token information about dispersed, localized events in audio. This weakness is rooted in the mismatch between the pretraining objective (globally) and the downstream task (localized). Across a comprehensive benchmark of 13 datasets and 6 spectrogram-based encoders, we investigate the global pooling bottleneck. We introduce binarized prototypical probes: a lightweight and simple pooling method that learns prototypes to perform class-wise information aggregation. Despite its simplicity, our method notably outperforms linear and attentive probing. Our work establishes probing as a competitive and efficient paradigm for evaluating audio SSL models, challenging the reliance on costly fine-tuning.
Applications · Chemistry and Drug Discovery
Enzyme Commission (EC) number prediction is vital for elucidating enzyme functions and advancing biotechnology applications. However, current methods struggle to capture the hierarchical relationships among enzymes and often overlook critical structural and active site features. To bridge this gap, we introduce PoinnCARE, a novel framework that jointly encodes and aligns multi-modal data from enzyme sequences, structures, and active sites in hyperbolic space. By integrating graph diffusion and alignment techniques, PoinnCARE mitigates data sparsity and enriches functional representations, while hyperbolic embedding preserves the intrinsic hierarchy of the EC system with theoretical guarantees in low-dimensional spaces. Extensive experiments on four datasets from the CARE benchmark demonstrate that PoinnCARE consistently and significantly outperforms state-of-the-art methods in EC number prediction.
RNA secondary structure forms the basis for folding and function, with non-canonical (NC) interactions indispensable for catalysis, regulation, and molecular recognition. Despite their importance, predicting NC base pairs remains challenging due to the absence of a standardized benchmark for systematic evaluation. To address this, we introduce NC-Bench, the first benchmark dedicated to NC base-pair prediction. NC-Bench provides 925 curated RNA sequences with 6,708 high-quality NC annotations, fine-grained edge and orientation classification tasks, and IsoScore-based embedding evaluation, offering a rigorous foundation for systematic assessment. Building on this, we propose NCfold, a dual-branch framework that couples sequence features with structural priors derived from RNA foundation models (RFMs) via Representative Embedding Fusion (REF) and REF-weighted self-attention. The closed-loop design iteratively refines sequence and structure representations, alleviating data sparsity and enhancing predictive accuracy. Experiments on NC-Bench show that NCfold outperforms existing methods, with zero-shot and ablation studies confirming its effectiveness and underscoring the need for NC-specific benchmarks. Together, NC-Bench and NCfold establish a systematic foundation for NC base-pair prediction, advancing our understanding of RNA structure and enabling next-generation RNA-centric applications. The datasets and codes are publicly available at https://github.com/heqin-zhu/NCBench.
Applications · Chemistry and Drug Discovery
Biomolecular interactions play a critical role in biological processes. While recent breakthroughs like AlphaFold 3 have enabled accurate modeling of biomolecular complex structures, predicting binding affinity remains challenging mainly due to limited high-quality data. Recent methods are often specialized for specific types of biomolecular interactions, limiting their generalizability. In this work, we repurpose AlphaFold 3 for representation learning to predict binding affinity, a non-trivial task that requires shifting from generative structure prediction to encoding observed geometry, simplifying the heavily conditioned trunk module, and designing a framework to jointly capture sequence and structural information. To address these challenges, we introduce the **Atom-level Diffusion Transformer (ADiT)**, which takes sequence and structure as inputs, employs a unified tokenization scheme, integrates diffusion transformers, and removes dependencies on multiple sequence alignments and templates. We pre-train three ADiT variants on the PDB dataset with a denoising objective and evaluate them across protein-ligand, drug-target, protein-protein, and antibody-antigen interactions. The model achieves state-of-the-art or competitive performance across benchmarks, scales effectively with model size, and successfully identifies wet-lab validated affinity-enhancing antibody mutations, establishing a generalizable framework for biomolecular interactions. Our open-source implementation is available at https://github.com/VectorShi/ADiT.
Deep Learning · Everything Else
Given the prohibitive cost of pre-training large language models, it is essential to leverage smaller proxy models to optimize recipes before scaling up. However, this approach becomes challenging for reasoning capabilities, which exhibit \textit{emergent} behavior that only appears reliably at larger model sizes, often exceeding 7B parameters. To address this, we introduce \tsc{rBridge}, showing that small proxies ($\leq$1B) can effectively predict large-model reasoning by aligning more closely with \textbf{(1)} the pre-training objective and \textbf{(2)} the target task. \tsc{rBridge} achieves this by weighting negative log-likelihood with task alignment, using reasoning traces from frontier models as gold labels. In our experiments, \tsc{rBridge} \textbf{(i)} reduces dataset ranking costs by over 100$\times$ relative to the best baseline, \textbf{(ii)} achieves the strongest correlation across six reasoning benchmarks at 1B to 32B scale, and \textbf{(iii)} transfers predictive relationships across pre-training recipes at 1B to 7B scale. These findings indicate that \tsc{rBridge} offers a practical path for exploring reasoning-oriented pre-training at lower cost.
Social Aspects · Fairness, Equity, Justice and Safety
Navigating dilemmas involving conflicting values is challenging even for humans in high-stakes domains, let alone for AI, yet prior work has been limited to everyday scenarios. To close this gap, we introduce CLASH (Character perspective-based LLM Assessments in Situations with High-stakes), a meticulously curated dataset consisting of 345 high-impact dilemmas along with 3,795 individual perspectives of diverse values. CLASH enables the study of critical yet underexplored aspects of value-based decision-making processes, including understanding of decision ambivalence and psychological discomfort as well as capturing the temporal shifts of values in the perspectives of characters. By benchmarking 14 non-thinking and thinking models, we uncover several key findings. (1) Even strong proprietary models, such as GPT-5 and Claude-4-Sonnet, struggle with ambivalent decisions, achieving only 24.06 and 51.01 accuracy. (2) Although LLMs reasonably predict psychological discomfort, they do not adequately comprehend perspectives involving value shifts. (3) Cognitive behaviors that are effective in the math-solving and game strategy domains do not transfer to value reasoning. Instead, new failure patterns emerge, including early commitment and overcommitment. (4) The steerability of LLMs towards a given value is significantly correlated with their value preferences. (5) Finally, LLMs exhibit greater steerability when reasoning from a third-party perspective, although certain values (e.g., safety) benefit uniquely from first-person framing.
Computer Vision · Image and Video Generation
Recent image editing models have achieved impressive results while following natural language editing instructions, but they rely on supervised fine-tuning with large datasets of input-target pairs. This is a critical bottleneck, as such naturally occurring pairs are hard to curate at scale. Current workarounds use synthetic training pairs that leverage the zero-shot capabilities of existing models. However, this can propagate and magnify the artifacts of the pretrained model into the final trained model. In this work, we present a new training paradigm that eliminates the need for paired data entirely. Our approach directly optimizes a few-step diffusion model by unrolling it during training and leveraging feedback from vision-language models (VLMs). For each input and editing instruction, the VLM evaluates if an edit follows the instruction and preserves unchanged content, providing direct gradients for end-to-end optimization. To ensure visual fidelity, we incorporate distribution matching loss (DMD), which constrains generated images to remain within the image manifold learned by pretrained models. We evaluate our method on standard benchmarks and include an extensive ablation study. Without any paired data, our method performs on par with various image editing diffusion models trained on extensive supervised paired data, under the few-step setting. Given the same VLM as the reward model, we also outperform RL-based techniques like Flow-GRPO.
General Machine Learning · Representation Learning
Representation learning of geospatial locations remains a core challenge in achieving general geospatial intelligence, with increasingly diverging philosophies and techniques. While Earth observation paradigms excel at depicting locations in their physical states, we propose that a location’s full characterization requires grounding in both its physical attributes and its internal human activity pattern, the latter being particularly crucial for understanding its human-centric functions. We present MoRA, a human-centric geospatial framework that leverages a mobility graph as its core backbone to fuse various data modalities, aiming to learn embeddings that represent the socio-economic context and functional role of a location. MoRA achieves this through the integration of spatial tokenization, GNNs, and asymmetric contrastive learning to align 100M+ POIs, massive remote sensing imagery, and structured demographic statistics with a billion-edge mobility graph, ensuring the three auxiliary modalities are interpreted through the lens of fundamental human dynamics. To rigorously evaluate the effectiveness of MoRA, we construct a benchmark dataset composed of 9 downstream prediction tasks across social and economic domains. Experiments show that MoRA, with four input modalities and a compact 128-dimensional representation space, achieves superior predictive performances than state-of-the-art models by an average of 12.9\%. Echoing LLM scaling laws, we further demonstrate the scaling behavior in geospatial representation learning. We open-source code and pretrained models at: https://github.com/ylzhouchris/MoRA.