FM-fMRI: Event Conditioned Flow Matching for Rest-to-Task fMRI Time-Series Synthesis

Task-based fMRI provides a direct readout of task-evoked neural dynamics, but it is expensive and difficult to acquire at scale, motivating rest-to-task synthesis from widely available resting-state fMRI (rsfMRI). We propose FM-fMRI, an event-conditioned flow-matching model that learns a continuous-time conditional vector field to generate task ROI time series from a subject's rsfMRI and the task event information. The formulation enables fast ODE-based sampling and flexible conditioning over heterogeneous event schedules. Rather than optimizing for pointwise reconstruction, we evaluated generated signals using complementary criteria that probe temporal and spectral structure, subject and group-level connectome consistency, and distributional alignment. On the public Human Connectome Project and internal BioPoint autism cohort, FM-fMRI achieves the strongest spectral and connectivity agreement and improved distribution-level matching over conditional diffusion, generative adversarial networks (GANs), and variational autoencoders (VAEs) baselines. Furthermore, we augment the BioPoint cohort by synthesizing task-fMRI ROI time series with our method, improving downstream autism classification and demonstrating practical utility in data-limited clinical settings. The code will be available on GitHub.

ProteinOPD: Towards Effective and Efficient Preference Alignment for Protein Design

Designing proteins with desired functions or properties represents a core goal in synthetic biology and drug discovery. Recent advances in protein language models (PLMs) have enabled the generation of highly designable protein sequences, while preference alignment provides a promising way to steer designs toward desired functions and properties. Nevertheless, they often trigger catastrophic forgetting of pretrained knowledge, degrading basic designability and failing to balance multiple competing objectives. To address these issues, we draw inspiration from On-Policy Distillation (OPD), an advanced post-training method renowned for mitigating catastrophic forgetting through its mode-seeking nature. In this work, we propose ProteinOPD, a multi-objective preference alignment framework that can effectively balance multiple preference objectives while maintaining the inherent designability of PLMs. ProteinOPD adapts a pretrained PLM into preference-specific teachers and distills their knowledge into a shared student via token-level OPD on the student's own trajectories. During this process, the student is aligned to a unique normalized geometric consensus of weighted teachers while ensuring bounded optimization under conflicts. This bridges the gap for OPD in multi-objective/teacher alignment. Extensive experiments show that ProteinOPD achieves substantial gains on target preference objectives without compromising the designability, with an 8x training speedup over RL-based alignment competitors.

Learning the Interaction Prior for Protein-Protein Interaction Prediction: A Model-Agnostic Approach

Protein-protein interactions (PPIs) are fundamental to cellular function and disease mechanisms. Current learning-based PPI predictors focus on learning powerful protein representations but neglect designing specialized classification heads. They mainly rely on generic aggregating methods like concatenation or dot products, which lack biological insight. Motivated by the biological "L3 rule", where multiple length-3 paths between a pair of proteins indicate their interaction likelihood, our study addresses this gap by designing a biologically informed PPI classifier. In this paper, we provide empirical evidence that popular PPI datasets strongly support the L3 rule. We propose an L3-path-regularized graph prompt learning method called L3-PPI, which can generate a prompt graph with virtual L3 paths based on protein representations and controls the number of paths. L3-PPI reformulates the classification of protein embedding pairs into a graph-level classification task over the generated prompt graph. This lightweight module seamlessly integrates with PPI predictors as a plug-and-play component, injecting the interaction prior of complementarity to enhance performance. Extensive experiments show that L3-PPI achieves superior performance enhancements over advanced competitors.

Subject-Specific Low-Field MRI Synthesis via a Neural Operator

Low-field (LF) magnetic resonance imaging (MRI) improves accessibility and reduces costs but generally has lower signal-to-noise ratios and degraded contrast compared to high field (HF) MRI, limiting its clinical utility. Simulating LF MRI from HF MRI enables virtual evaluation of novel imaging devices and development of LF algorithms. Existing low field simulators rely on noise injection and smoothing, which fail to capture the contrast degradation seen in LF acquisitions. To this end, we introduce an end-to-end LF-MRI synthesis framework that learns HF to LF image degradation directly from a small number of paired HF-LF MRIs. Specifically, we introduce a novel HF to LF coordinate-image decoupled neural operator (H2LO) to model the underlying degradation process, and tailor it to capture high-frequency noise textures and image structure. Experimental results in T1w and T2w MRI demonstrate that H2LO produces more faithful simulated low-field images than existing parameterized noise synthesis models and popular image-to-image translation models. Furthermore, it improves performance in downstream image enhancement tasks, showcasing its potential to enhance LF MRI diagnostic capabilities.

TKG-Thinker: Towards Dynamic Reasoning over Temporal Knowledge Graphs via Agentic Reinforcement Learning

Temporal knowledge graph question answering (TKGQA) aims to answer time-sensitive questions by leveraging temporal knowledge bases. While Large Language Models (LLMs) demonstrate significant potential in TKGQA, current prompting strategies constrain their efficacy in two primary ways. First, they are prone to reasoning hallucinations under complex temporal constraints. Second, static prompting limits model autonomy and generalization, as it lack optimization through dynamic interaction with temporal knowledge graphs (TKGs) environments. To address these limitations, we propose \textbf{TKG-Thinker}, a novel agent equipped with autonomous planning and adaptive retrieval capabilities for reasoning over TKGs. Specifically, TKG-Thinker performs in-depth temporal reasoning through dynamic multi-turn interactions with TKGs via a dual-training strategy. We first apply Supervised Fine-Tuning (SFT) with chain-of thought data to instill core planning capabilities, followed by a Reinforcement Learning (RL) stage that leverages multi-dimensional rewards to refine reasoning policies under intricate temporal constraints. Experimental results on benchmark datasets with three open-source LLMs show that TKG-Thinker achieves state-of-the-art performance and exhibits strong generalization across complex TKGQA settings.

RAPTOR: Ridge-Adaptive Logistic Probes

Probing studies what information is encoded in a frozen LLM's layer representations by training a lightweight predictor on top of them. Beyond analysis, probes are often used operationally in probe-then-steer pipelines: a learned concept vector is extracted from a probe and injected via additive activation steering by adding it to a layer representation during the forward pass. The effectiveness of this pipeline hinges on estimating concept vectors that are accurate, directionally stable under ablation, and inexpensive to obtain. Motivated by these desiderata, we propose RAPTOR (Ridge-Adaptive Logistic Probe), a simple L2-regularized logistic probe whose validation-tuned ridge strength yields concept vectors from normalized weights. Across extensive experiments on instruction-tuned LLMs and human-written concept datasets, RAPTOR matches or exceeds strong baselines in accuracy while achieving competitive directional stability and substantially lower training cost; these quantitative results are supported by qualitative downstream steering demonstrations. Finally, using the Convex Gaussian Min-max Theorem (CGMT), we provide a mechanistic characterization of ridge logistic regression in an idealized Gaussian teacher-student model in the high-dimensional few-shot regime, explaining how penalty strength mediates probe accuracy and concept-vector stability and yielding structural predictions that qualitatively align with trends observed on real LLM embeddings.

Molmo2: Open Weights and Data for Vision-Language Models with Video Understanding and Grounding

Today's strongest video-language models (VLMs) remain proprietary. The strongest open-weight models either rely on synthetic data from proprietary VLMs, effectively distilling from them, or do not disclose their training data or recipe. As a result, the open-source community lacks the foundations needed to improve on the state-of-the-art video (and image) language models. Crucially, many downstream applications require more than just high-level video understanding; they require grounding -- either by pointing or by tracking in pixels. Even proprietary models lack this capability. We present Molmo2, a new family of VLMs that are state-of-the-art among open-source models and demonstrate exceptional new capabilities in point-driven grounding in single image, multi-image, and video tasks. Our key contribution is a collection of 7 new video datasets and 2 multi-image datasets, including a dataset of highly detailed video captions for pre-training, a free-form video Q&A dataset for fine-tuning, a new object tracking dataset with complex queries, and an innovative new video pointing dataset, all collected without the use of closed VLMs. We also present a training recipe for this data utilizing an efficient packing and message-tree encoding scheme, and show bi-directional attention on vision tokens and a novel token-weight strategy improves performance. Our best-in-class 8B model outperforms others in the class of open weight and data models on short videos, counting, and captioning, and is competitive on long-videos. On video-grounding Molmo2 significantly outperforms existing open-weight models like Qwen3-VL (35.5 vs 29.6 accuracy on video counting) and surpasses proprietary models like Gemini 3 Pro on some tasks (38.4 vs 20.0 F1 on video pointing and 56.2 vs 41.1 J&F on video tracking).

DAP-MAE: Domain-Adaptive Point Cloud Masked Autoencoder for Effective Cross-Domain Learning

Compared to 2D data, the scale of point cloud data in different domains available for training, is quite limited. Researchers have been trying to combine these data of different domains for masked autoencoder (MAE) pre-training to leverage such a data scarcity issue. However, the prior knowledge learned from mixed domains may not align well with the downstream 3D point cloud analysis tasks, leading to degraded performance. To address such an issue, we propose the Domain-Adaptive Point Cloud Masked Autoencoder (DAP-MAE), an MAE pre-training method, to adaptively integrate the knowledge of cross-domain datasets for general point cloud analysis. In DAP-MAE, we design a heterogeneous domain adapter that utilizes an adaptation mode during pre-training, enabling the model to comprehensively learn information from point clouds across different domains, while employing a fusion mode in the fine-tuning to enhance point cloud features. Meanwhile, DAP-MAE incorporates a domain feature generator to guide the adaptation of point cloud features to various downstream tasks. With only one pre-training, DAP-MAE achieves excellent performance across four different point cloud analysis tasks, reaching 95.18% in object classification on ScanObjectNN and 88.45% in facial expression recognition on Bosphorus.

One Trajectory, One Token: Grounded Video Tokenization via Panoptic Sub-object Trajectory

Effective video tokenization is critical for scaling transformer models for long videos. Current approaches tokenize videos using space-time patches, leading to excessive tokens and computational inefficiencies. The best token reduction strategies degrade performance and barely reduce the number of tokens when the camera moves. We introduce grounded video tokenization, a paradigm that organizes tokens based on panoptic sub-object trajectories rather than fixed patches. Our method aligns with fundamental perceptual principles, ensuring that tokenization reflects scene complexity rather than video duration. We propose TrajViT, a video encoder that extracts object trajectories and converts them into semantically meaningful tokens, significantly reducing redundancy while maintaining temporal coherence. Trained with contrastive learning, TrajViT significantly outperforms space-time ViT (ViT3D) across multiple video understanding benchmarks, e.g., TrajViT outperforms ViT3D by a large margin of 6% top-5 recall in average at video-text retrieval task with 10x token deduction. We also show TrajViT as a stronger model than ViT3D for being the video encoder for modern VideoLLM, obtaining an average of 5.2% performance improvement across 6 VideoQA benchmarks while having 4x faster training time and 18x less inference FLOPs. TrajViT is the first efficient encoder to consistently outperform ViT3D across diverse video analysis tasks, making it a robust and scalable solution.

InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.