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Jan 9

A Large-Scale Benchmark of Cross-Modal Learning for Histology and Gene Expression in Spatial Transcriptomics

Spatial transcriptomics enables simultaneous measurement of gene expression and tissue morphology, offering unprecedented insights into cellular organization and disease mechanisms. However, the field lacks comprehensive benchmarks for evaluating multimodal learning methods that leverage both histology images and gene expression data. Here, we present HESCAPE, a large-scale benchmark for cross-modal contrastive pretraining in spatial transcriptomics, built on a curated pan-organ dataset spanning 6 different gene panels and 54 donors. We systematically evaluated state-of-the-art image and gene expression encoders across multiple pretraining strategies and assessed their effectiveness on two downstream tasks: gene mutation classification and gene expression prediction. Our benchmark demonstrates that gene expression encoders are the primary determinant of strong representational alignment, and that gene models pretrained on spatial transcriptomics data outperform both those trained without spatial data and simple baseline approaches. However, downstream task evaluation reveals a striking contradiction: while contrastive pretraining consistently improves gene mutation classification performance, it degrades direct gene expression prediction compared to baseline encoders trained without cross-modal objectives. We identify batch effects as a key factor that interferes with effective cross-modal alignment. Our findings highlight the critical need for batch-robust multimodal learning approaches in spatial transcriptomics. To accelerate progress in this direction, we release HESCAPE, providing standardized datasets, evaluation protocols, and benchmarking tools for the community

  • 9 authors
·
Aug 2, 2025

GeometryZero: Improving Geometry Solving for LLM with Group Contrastive Policy Optimization

Recent advances in large language models (LLMs) have demonstrated remarkable capabilities across diverse domains, particularly in mathematical reasoning, amid which geometry problem solving remains a challenging area where auxiliary construction plays a enssential role. Existing approaches either achieve suboptimal performance or rely on massive LLMs (e.g., GPT-4o), incurring massive computational costs. We posit that reinforcement learning with verifiable reward (e.g., GRPO) offers a promising direction for training smaller models that effectively combine auxiliary construction with robust geometric reasoning. However, directly applying GRPO to geometric reasoning presents fundamental limitations due to its dependence on unconditional rewards, which leads to indiscriminate and counterproductive auxiliary constructions. To address these challenges, we propose Group Contrastive Policy Optimization (GCPO), a novel reinforcement learning framework featuring two key innovations: (1) Group Contrastive Masking, which adaptively provides positive or negative reward signals for auxiliary construction based on contextual utility, and a (2) length reward that promotes longer reasoning chains. Building on GCPO, we develop GeometryZero, a family of affordable-size geometric reasoning models that judiciously determine when to employ auxiliary construction. Our extensive empirical evaluation across popular geometric benchmarks (Geometry3K, MathVista) demonstrates that GeometryZero models consistently outperform baselines (e.g. GRPO), achieving an average improvement of 4.29% across all benchmarks.

  • 7 authors
·
Jun 8, 2025 2

REOBench: Benchmarking Robustness of Earth Observation Foundation Models

Earth observation foundation models have shown strong generalization across multiple Earth observation tasks, but their robustness under real-world perturbations remains underexplored. To bridge this gap, we introduce REOBench, the first comprehensive benchmark for evaluating the robustness of Earth observation foundation models across six tasks and twelve types of image corruptions, including both appearance-based and geometric perturbations. To ensure realistic and fine-grained evaluation, our benchmark focuses on high-resolution optical remote sensing images, which are widely used in critical applications such as urban planning and disaster response. We conduct a systematic evaluation of a broad range of models trained using masked image modeling, contrastive learning, and vision-language pre-training paradigms. Our results reveal that (1) existing Earth observation foundation models experience significant performance degradation when exposed to input corruptions. (2) The severity of degradation varies across tasks, model architectures, backbone sizes, and types of corruption, with performance drop varying from less than 1% to over 20%. (3) Vision-language models show enhanced robustness, particularly in multimodal tasks. REOBench underscores the vulnerability of current Earth observation foundation models to real-world corruptions and provides actionable insights for developing more robust and reliable models.

  • 10 authors
·
May 22, 2025

Improving Reference-based Distinctive Image Captioning with Contrastive Rewards

Distinctive Image Captioning (DIC) -- generating distinctive captions that describe the unique details of a target image -- has received considerable attention over the last few years. A recent DIC method proposes to generate distinctive captions by comparing the target image with a set of semantic-similar reference images, i.e., reference-based DIC (Ref-DIC). It aims to force the generated captions to distinguish between the target image and the reference image. To ensure Ref-DIC models really perceive the unique objects (or attributes) in target images, we propose two new Ref-DIC benchmarks and develop a Transformer-based Ref-DIC baseline TransDIC. The model only extracts visual features from the target image, but also encodes the differences between objects in the target and reference images. Taking one step further, we propose a stronger TransDIC++, which consists of an extra contrastive learning module to make full use of the reference images. This new module is model-agnostic, which can be easily incorporated into various Ref-DIC architectures. Finally, for more trustworthy benchmarking, we propose a new evaluation metric named DisCIDEr for Ref-DIC, which evaluates both the accuracy and distinctiveness of the generated captions. Experimental results demonstrate that our TransDIC++ can generate distinctive captions. Besides, it outperforms several state-of-the-art models on the two new benchmarks over different metrics.

  • 7 authors
·
Jun 25, 2023

HaLP: Hallucinating Latent Positives for Skeleton-based Self-Supervised Learning of Actions

Supervised learning of skeleton sequence encoders for action recognition has received significant attention in recent times. However, learning such encoders without labels continues to be a challenging problem. While prior works have shown promising results by applying contrastive learning to pose sequences, the quality of the learned representations is often observed to be closely tied to data augmentations that are used to craft the positives. However, augmenting pose sequences is a difficult task as the geometric constraints among the skeleton joints need to be enforced to make the augmentations realistic for that action. In this work, we propose a new contrastive learning approach to train models for skeleton-based action recognition without labels. Our key contribution is a simple module, HaLP - to Hallucinate Latent Positives for contrastive learning. Specifically, HaLP explores the latent space of poses in suitable directions to generate new positives. To this end, we present a novel optimization formulation to solve for the synthetic positives with an explicit control on their hardness. We propose approximations to the objective, making them solvable in closed form with minimal overhead. We show via experiments that using these generated positives within a standard contrastive learning framework leads to consistent improvements across benchmarks such as NTU-60, NTU-120, and PKU-II on tasks like linear evaluation, transfer learning, and kNN evaluation. Our code will be made available at https://github.com/anshulbshah/HaLP.

  • 7 authors
·
Apr 1, 2023

VERIFIED: A Video Corpus Moment Retrieval Benchmark for Fine-Grained Video Understanding

Existing Video Corpus Moment Retrieval (VCMR) is limited to coarse-grained understanding, which hinders precise video moment localization when given fine-grained queries. In this paper, we propose a more challenging fine-grained VCMR benchmark requiring methods to localize the best-matched moment from the corpus with other partially matched candidates. To improve the dataset construction efficiency and guarantee high-quality data annotations, we propose VERIFIED, an automatic VidEo-text annotation pipeline to generate captions with RelIable FInE-grained statics and Dynamics. Specifically, we resort to large language models (LLM) and large multimodal models (LMM) with our proposed Statics and Dynamics Enhanced Captioning modules to generate diverse fine-grained captions for each video. To filter out the inaccurate annotations caused by the LLM hallucination, we propose a Fine-Granularity Aware Noise Evaluator where we fine-tune a video foundation model with disturbed hard-negatives augmented contrastive and matching losses. With VERIFIED, we construct a more challenging fine-grained VCMR benchmark containing Charades-FIG, DiDeMo-FIG, and ActivityNet-FIG which demonstrate a high level of annotation quality. We evaluate several state-of-the-art VCMR models on the proposed dataset, revealing that there is still significant scope for fine-grained video understanding in VCMR. Code and Datasets are in https://github.com/hlchen23/VERIFIED{https://github.com/hlchen23/VERIFIED}.

  • 8 authors
·
Oct 11, 2024