LatentChem: From Textual CoT to Latent Thinking in Chemical Reasoning

Chemical large language models (LLMs) predominantly rely on explicit Chain-of-Thought (CoT) in natural language to perform complex reasoning. However, chemical reasoning is inherently continuous and structural, and forcing it into discrete linguistic tokens introduces a fundamental representation mismatch that constrains both efficiency and performance. We introduce LatentChem, a latent reasoning interface that decouples chemical computation from textual generation, enabling models to perform multi-step reasoning directly in continuous latent space while emitting language only for final outputs. Remarkably, we observe a consistent emergent behavior: when optimized solely for task success, models spontaneously internalize reasoning, progressively abandoning verbose textual derivations in favor of implicit latent computation. This shift is not merely stylistic but computationally advantageous. Across diverse chemical reasoning benchmarks, LatentChem achieves a 59.88\% non-tie win rate over strong CoT-based baselines on ChemCoTBench, while delivering a 10.84$\times$ average inference speedup. Our results provide empirical evidence that chemical reasoning is more naturally and effectively realized as continuous latent dynamics rather than discretized linguistic trajectories.

Temporal Graph Pattern Machine

Temporal graph learning is pivotal for deciphering dynamic systems, where the core challenge lies in explicitly modeling the underlying evolving patterns that govern network transformation. However, prevailing methods are predominantly task-centric and rely on restrictive assumptions -- such as short-term dependency modeling, static neighborhood semantics, and retrospective time usage. These constraints hinder the discovery of transferable temporal evolution mechanisms. To address this, we propose the Temporal Graph Pattern Machine (TGPM), a foundation framework that shifts the focus toward directly learning generalized evolving patterns. TGPM conceptualizes each interaction as an interaction patch synthesized via temporally-biased random walks, thereby capturing multi-scale structural semantics and long-range dependencies that extend beyond immediate neighborhoods. These patches are processed by a Transformer-based backbone designed to capture global temporal regularities while adapting to context-specific interaction dynamics. To further empower the model, we introduce a suite of self-supervised pre-training tasks -- specifically masked token modeling and next-time prediction -- to explicitly encode the fundamental laws of network evolution. Extensive experiments show that TGPM consistently achieves state-of-the-art performance in both transductive and inductive link prediction, demonstrating exceptional cross-domain transferability.

Molecular Representations in Implicit Functional Space via Hyper-Networks

Molecular representations fundamentally shape how machine learning systems reason about molecular structure and physical properties. Most existing approaches adopt a discrete pipeline: molecules are encoded as sequences, graphs, or point clouds, mapped to fixed-dimensional embeddings, and then used for task-specific prediction. This paradigm treats molecules as discrete objects, despite their intrinsically continuous and field-like physical nature. We argue that molecular learning can instead be formulated as learning in function space. Specifically, we model each molecule as a continuous function over three-dimensional (3D) space and treat this molecular field as the primary object of representation. From this perspective, conventional molecular representations arise as particular sampling schemes of an underlying continuous object. We instantiate this formulation with MolField, a hyper-network-based framework that learns distributions over molecular fields. To ensure physical consistency, these functions are defined over canonicalized coordinates, yielding invariance to global SE(3) transformations. To enable learning directly over functions, we introduce a structured weight tokenization and train a sequence-based hyper-network to model a shared prior over molecular fields. We evaluate MolField on molecular dynamics and property prediction. Our results show that treating molecules as continuous functions fundamentally changes how molecular representations generalize across tasks and yields downstream behavior that is stable to how molecules are discretized or queried.

Graph is a Substrate Across Data Modalities

Graphs provide a natural representation of relational structure that arises across diverse domains. Despite this ubiquity, graph structure is typically learned in a modality- and task-isolated manner, where graph representations are constructed within individual task contexts and discarded thereafter. As a result, structural regularities across modalities and tasks are repeatedly reconstructed rather than accumulated at the level of intermediate graph representations. This motivates a representation-learning question: how should graph structure be organized so that it can persist and accumulate across heterogeneous modalities and tasks? We adopt a representation-centric perspective in which graph structure is treated as a structural substrate that persists across learning contexts. To instantiate this perspective, we propose G-Substrate, a graph substrate framework that organizes learning around shared graph structures. G-Substrate comprises two complementary mechanisms: a unified structural schema that ensures compatibility among graph representations across heterogeneous modalities and tasks, and an interleaved role-based training strategy that exposes the same graph structure to multiple functional roles during learning. Experiments across multiple domains, modalities, and tasks show that G-Substrate outperforms task-isolated and naive multi-task learning methods.

Why Reasoning Fails to Plan: A Planning-Centric Analysis of Long-Horizon Decision Making in LLM Agents

Large language model (LLM)-based agents exhibit strong step-by-step reasoning capabilities over short horizons, yet often fail to sustain coherent behavior over long planning horizons. We argue that this failure reflects a fundamental mismatch: step-wise reasoning induces a form of step-wise greedy policy that is adequate for short horizons but fails in long-horizon planning, where early actions must account for delayed consequences. From this planning-centric perspective, we study LLM-based agents in deterministic, fully structured environments with explicit state transitions and evaluation signals. Our analysis reveals a core failure mode of reasoning-based policies: locally optimal choices induced by step-wise scoring lead to early myopic commitments that are systematically amplified over time and difficult to recover from. We introduce FLARE (Future-aware Lookahead with Reward Estimation) as a minimal instantiation of future-aware planning to enforce explicit lookahead, value propagation, and limited commitment in a single model, allowing downstream outcomes to influence early decisions. Across multiple benchmarks, agent frameworks, and LLM backbones, FLARE consistently improves task performance and planning-level behavior, frequently allowing LLaMA-8B with FLARE to outperform GPT-4o with standard step-by-step reasoning. These results establish a clear distinction between reasoning and planning.

LongDA: Benchmarking LLM Agents for Long-Document Data Analysis

We introduce LongDA, a data analysis benchmark for evaluating LLM-based agents under documentation-intensive analytical workflows. In contrast to existing benchmarks that assume well-specified schemas and inputs, LongDA targets real-world settings in which navigating long documentation and complex data is the primary bottleneck. To this end, we manually curate raw data files, long and heterogeneous documentation, and expert-written publications from 17 publicly available U.S. national surveys, from which we extract 505 analytical queries grounded in real analytical practice. Solving these queries requires agents to first retrieve and integrate key information from multiple unstructured documents, before performing multi-step computations and writing executable code, which remains challenging for existing data analysis agents. To support the systematic evaluation under this setting, we develop LongTA, a tool-augmented agent framework that enables document access, retrieval, and code execution, and evaluate a range of proprietary and open-source models. Our experiments reveal substantial performance gaps even among state-of-the-art models, highlighting the challenges researchers should consider before applying LLM agents for decision support in real-world, high-stakes analytical settings.

Semantic Refinement with LLMs for Graph Representations

Graph-structured data exhibit substantial heterogeneity in where their predictive signals originate: in some domains, node-level semantics dominate, while in others, structural patterns play a central role. This structure-semantics heterogeneity implies that no graph learning model with a fixed inductive bias can generalize optimally across diverse graph domains. However, most existing methods address this challenge from the model side by incrementally injecting new inductive biases, which remains fundamentally limited given the open-ended diversity of real-world graphs. In this work, we take a data-centric perspective and treat node semantics as a task-adaptive variable. We propose a Data-Adaptive Semantic Refinement framework DAS for graph representation learning, which couples a fixed graph neural network (GNN) and a large language model (LLM) in a closed feedback loop. The GNN provides implicit supervisory signals to guide the semantic refinement of LLM, and the refined semantics are fed back to update the same graph learner. We evaluate our approach on both text-rich and text-free graphs. Results show consistent improvements on structure-dominated graphs while remaining competitive on semantics-rich graphs, demonstrating the effectiveness of data-centric semantic adaptation under structure-semantics heterogeneity.

Graph Prompting for Graph Learning Models: Recent Advances and Future Directions

Graph learning models have demonstrated great prowess in learning expressive representations from large-scale graph data in a wide variety of real-world scenarios. As a prevalent strategy for training powerful graph learning models, the "pre-training, adaptation" scheme first pre-trains graph learning models on unlabeled graph data in a self-supervised manner and then adapts them to specific downstream tasks. During the adaptation phase, graph prompting emerges as a promising approach that learns trainable prompts while keeping the pre-trained graph learning models unchanged. In this paper, we present a systematic review of recent advancements in graph prompting. First, we introduce representative graph pre-training methods that serve as the foundation step of graph prompting. Next, we review mainstream techniques in graph prompting and elaborate on how they design learnable prompts for graph prompting. Furthermore, we summarize the real-world applications of graph prompting from different domains. Finally, we discuss several open challenges in existing studies with promising future directions in this field.

Scalable Graph Generative Modeling via Substructure Sequences

Graph neural networks (GNNs) has been predominantly driven by message-passing, where node representations are iteratively updated via local neighborhood aggregation. Despite their success, message-passing suffers from fundamental limitations -- including constrained expressiveness, over-smoothing, over-squashing, and limited capacity to model long-range dependencies. These issues hinder scalability: increasing data size or model size often fails to yield improved performance, limiting the viability of GNNs as backbones for graph foundation models. In this work, we explore pathways beyond message-passing and introduce Generative Graph Pattern Machine (G$^2$PM), a generative Transformer pre-training framework for graphs. G$^2$PM represents graph instances (nodes, edges, or entire graphs) as sequences of substructures, and employs generative pre-training over the sequences to learn generalizable, transferable representations. Empirically, G$^2$PM demonstrates strong scalability: on the ogbn-arxiv benchmark, it continues to improve with model sizes up to 60M parameters, outperforming prior generative approaches that plateau at significantly smaller scales (e.g., 3M). In addition, we systematically analyze the model design space, highlighting key architectural choices that contribute to its scalability and generalization. Across diverse tasks -- including node classification, graph classification, and transfer learning -- G$^2$PM consistently outperforms strong baselines, establishing a compelling foundation for scalable graph learning. The code and dataset are available at https://github.com/Zehong-Wang/G2PM.

Graph Foundation Models: A Comprehensive Survey

Graph-structured data pervades domains such as social networks, biological systems, knowledge graphs, and recommender systems. While foundation models have transformed natural language processing, vision, and multimodal learning through large-scale pretraining and generalization, extending these capabilities to graphs -- characterized by non-Euclidean structures and complex relational semantics -- poses unique challenges and opens new opportunities. To this end, Graph Foundation Models (GFMs) aim to bring scalable, general-purpose intelligence to structured data, enabling broad transfer across graph-centric tasks and domains. This survey provides a comprehensive overview of GFMs, unifying diverse efforts under a modular framework comprising three key components: backbone architectures, pretraining strategies, and adaptation mechanisms. We categorize GFMs by their generalization scope -- universal, task-specific, and domain-specific -- and review representative methods, key innovations, and theoretical insights within each category. Beyond methodology, we examine theoretical foundations including transferability and emergent capabilities, and highlight key challenges such as structural alignment, heterogeneity, scalability, and evaluation. Positioned at the intersection of graph learning and general-purpose AI, GFMs are poised to become foundational infrastructure for open-ended reasoning over structured data. This survey consolidates current progress and outlines future directions to guide research in this rapidly evolving field. Resources are available at https://github.com/Zehong-Wang/Awesome-Foundation-Models-on-Graphs.