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May 15

Domain Elastic Transform: Bayesian Function Registration for High-Dimensional Scientific Data

Nonrigid registration is conventionally divided into point set registration, which aligns sparse geometries, and image registration, which aligns continuous intensity fields on regular grids. However, this dichotomy creates a critical bottleneck for emerging scientific data, such as spatial transcriptomics, where high-dimensional vector-valued functions, e.g., gene expression, are defined on irregular, sparse manifolds. Consequently, researchers currently face a forced choice: either sacrifice single-cell resolution via voxelization to utilize image-based tools, or ignore the critical functional signal to utilize geometric tools. To resolve this dilemma, we propose Domain Elastic Transform (DET), a grid-free probabilistic framework that unifies geometric and functional alignment. By treating data as functions on irregular domains, DET registers high-dimensional signals directly without binning. We formulate the problem within a rigorous Bayesian framework, modeling domain deformation as an elastic motion guided by a joint spatial-functional likelihood. The method is fully unsupervised and scalable, utilizing feature-sensitive downsampling to handle massive atlases. We demonstrate that DET achieves 92\% topological preservation on MERFISH data where state-of-the-art optimal transport methods struggle (<5\%), and successfully registers whole-embryo Stereo-seq atlases across developmental stages -- a task involving massive scale and complex nonrigid growth. The implementation of DET is available on {https://github.com/ohirose/bcpd} (since Mar, 2025).

  • 2 authors
·
Mar 21

Reasoning or Rhetoric? An Empirical Analysis of Moral Reasoning Explanations in Large Language Models

Do large language models reason morally, or do they merely sound like they do? We investigate whether LLM responses to moral dilemmas exhibit genuine developmental progression through Kohlberg's stages of moral development, or whether alignment training instead produces reasoning-like outputs that superficially resemble mature moral judgment without the underlying developmental trajectory. Using an LLM-as-judge scoring pipeline validated across three judge models, we classify more than 600 responses from 13 LLMs spanning a range of architectures, parameter scales, and training regimes across six classical moral dilemmas, and conduct ten complementary analyses to characterize the nature and internal coherence of the resulting patterns. Our results reveal a striking inversion: responses overwhelmingly correspond to post-conventional reasoning (Stages 5-6) regardless of model size, architecture, or prompting strategy, the effective inverse of human developmental norms, where Stage 4 dominates. Most strikingly, a subset of models exhibit moral decoupling: systematic inconsistency between stated moral justification and action choice, a form of logical incoherence that persists across scale and prompting strategy and represents a direct reasoning consistency failure independent of rhetorical sophistication. Model scale carries a statistically significant but practically small effect; training type has no significant independent main effect; and models exhibit near-robotic cross-dilemma consistency producing logically indistinguishable responses across semantically distinct moral problems. We posit that these patterns constitute evidence for moral ventriloquism: the acquisition, through alignment training, of the rhetorical conventions of mature moral reasoning without the underlying developmental trajectory those conventions are meant to represent.

  • 4 authors
·
Mar 23 2

Children's Intelligence Tests Pose Challenges for MLLMs? KidGym: A 2D Grid-Based Reasoning Benchmark for MLLMs

Multimodal Large Language Models (MLLMs) combine the linguistic strengths of LLMs with the ability to process multimodal data, enbaling them to address a broader range of visual tasks. Because MLLMs aim at more general, human-like competence than language-only models, we take inspiration from the Wechsler Intelligence Scales - an established battery for evaluating children by decomposing intelligence into interpretable, testable abilities. We introduce KidGym, a comprehensive 2D grid-based benchmark for assessing five essential capabilities of MLLMs: Execution, Perception Reasoning, Learning, Memory and Planning. The benchmark comprises 12 unique tasks, each targeting at least one core capability, specifically designed to guage MLLMs' adaptability and developmental potential, mirroring the stages of children's cognitive growth. Additionally, our tasks encompass diverse scenarios and objects with randomly generated layouts, ensuring a more accurate and robust evluation of MLLM capabilities. KidGym is designed to be fully user-customizable and extensible, allowing researchers to create new evaluation scenarios and adjust difficuly levels to accommodate the rapidly growing MLLM community. Through the evaluation of state-of-the-art MLLMs using KidGym, we identified significant insights into model capabilities and revealed several limitations of current models. We release our benchmark at: https://bobo-ye.github.io/KidGym/.

  • 10 authors
·
Mar 31

GrowliFlower: An image time series dataset for GROWth analysis of cauLIFLOWER

This article presents GrowliFlower, a georeferenced, image-based UAV time series dataset of two monitored cauliflower fields of size 0.39 and 0.60 ha acquired in 2020 and 2021. The dataset contains RGB and multispectral orthophotos from which about 14,000 individual plant coordinates are derived and provided. The coordinates enable the dataset users the extraction of complete and incomplete time series of image patches showing individual plants. The dataset contains collected phenotypic traits of 740 plants, including the developmental stage as well as plant and cauliflower size. As the harvestable product is completely covered by leaves, plant IDs and coordinates are provided to extract image pairs of plants pre and post defoliation, to facilitate estimations of cauliflower head size. Moreover, the dataset contains pixel-accurate leaf and plant instance segmentations, as well as stem annotations to address tasks like classification, detection, segmentation, instance segmentation, and similar computer vision tasks. The dataset aims to foster the development and evaluation of machine learning approaches. It specifically focuses on the analysis of growth and development of cauliflower and the derivation of phenotypic traits to foster the development of automation in agriculture. Two baseline results of instance segmentation at plant and leaf level based on the labeled instance segmentation data are presented. The entire data set is publicly available.

  • 9 authors
·
Apr 1, 2022

How do Transformers Learn Implicit Reasoning?

Recent work suggests that large language models (LLMs) can perform multi-hop reasoning implicitly -- producing correct answers without explicitly verbalizing intermediate steps -- but the underlying mechanisms remain poorly understood. In this paper, we study how such implicit reasoning emerges by training transformers from scratch in a controlled symbolic environment. Our analysis reveals a three-stage developmental trajectory: early memorization, followed by in-distribution generalization, and eventually cross-distribution generalization. We find that training with atomic triples is not necessary but accelerates learning, and that second-hop generalization relies on query-level exposure to specific compositional structures. To interpret these behaviors, we introduce two diagnostic tools: cross-query semantic patching, which identifies semantically reusable intermediate representations, and a cosine-based representational lens, which reveals that successful reasoning correlates with the cosine-base clustering in hidden space. This clustering phenomenon in turn provides a coherent explanation for the behavioral dynamics observed across training, linking representational structure to reasoning capability. These findings provide new insights into the interpretability of implicit multi-hop reasoning in LLMs, helping to clarify how complex reasoning processes unfold internally and offering pathways to enhance the transparency of such models.

  • 11 authors
·
May 29, 2025

Perception, Reason, Think, and Plan: A Survey on Large Multimodal Reasoning Models

Reasoning lies at the heart of intelligence, shaping the ability to make decisions, draw conclusions, and generalize across domains. In artificial intelligence, as systems increasingly operate in open, uncertain, and multimodal environments, reasoning becomes essential for enabling robust and adaptive behavior. Large Multimodal Reasoning Models (LMRMs) have emerged as a promising paradigm, integrating modalities such as text, images, audio, and video to support complex reasoning capabilities and aiming to achieve comprehensive perception, precise understanding, and deep reasoning. As research advances, multimodal reasoning has rapidly evolved from modular, perception-driven pipelines to unified, language-centric frameworks that offer more coherent cross-modal understanding. While instruction tuning and reinforcement learning have improved model reasoning, significant challenges remain in omni-modal generalization, reasoning depth, and agentic behavior. To address these issues, we present a comprehensive and structured survey of multimodal reasoning research, organized around a four-stage developmental roadmap that reflects the field's shifting design philosophies and emerging capabilities. First, we review early efforts based on task-specific modules, where reasoning was implicitly embedded across stages of representation, alignment, and fusion. Next, we examine recent approaches that unify reasoning into multimodal LLMs, with advances such as Multimodal Chain-of-Thought (MCoT) and multimodal reinforcement learning enabling richer and more structured reasoning chains. Finally, drawing on empirical insights from challenging benchmarks and experimental cases of OpenAI O3 and O4-mini, we discuss the conceptual direction of native large multimodal reasoning models (N-LMRMs), which aim to support scalable, agentic, and adaptive reasoning and planning in complex, real-world environments.

HIT-TMG Lychee Team
·
May 7, 2025 4

Adaptation and learning of molecular networks as a description of cancer development at the systems-level: Potential use in anti-cancer therapies

There is a widening recognition that cancer cells are products of complex developmental processes. Carcinogenesis and metastasis formation are increasingly described as systems-level, network phenomena. Here we propose that malignant transformation is a two-phase process, where an initial increase of system plasticity is followed by a decrease of plasticity at late stages of carcinogenesis as a model of cellular learning. We describe the hallmarks of increased system plasticity of early, tumor initiating cells, such as increased noise, entropy, conformational and phenotypic plasticity, physical deformability, cell heterogeneity and network rearrangements. Finally, we argue that the large structural changes of molecular networks during cancer development necessitate a rather different targeting strategy in early and late phase of carcinogenesis. Plastic networks of early phase cancer development need a central hit, while rigid networks of late stage primary tumors or established metastases should be attacked by the network influence strategy, such as by edgetic, multi-target, or allo-network drugs. Cancer stem cells need special diagnosis and targeting, since their dormant and rapidly proliferating forms may have more rigid, or more plastic networks, respectively. The extremely high ability to change their rigidity/plasticity may be a key differentiating hallmark of cancer stem cells. The application of early stage-optimized anti-cancer drugs to late-stage patients may be a reason of many failures in anti-cancer therapies. Our hypotheses presented here underlie the need for patient-specific multi-target therapies applying the correct ratio of central hits and network influences -- in an optimized sequence.

  • 6 authors
·
Jun 14, 2013