MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback

Molecular dynamics (MD) is the canonical in-silico method for atomistic molecular science, simulating molecular behavior from first-principle physics. Designing an MD pipeline for a new system requires substantial expert knowledge: running it on even one molecule is expensive, ruling out trial-and-error. We automate this expert pipeline-design process with an LLM agent. Unlike existing MD agents that orchestrate a predefined tool set, we treat pipeline design as open-ended code generation in which the agent's behavior is reshaped online by verbal reward. Specifically, we build MDForge, an LLM agent whose in-context update rule densifies the sparse reward via a multi-agent debate among physics experts. On three SAMPL host-guest binding free-energy benchmarks, MDForge automatically designs MD pipelines competitive with human experts. Deployed on a library of unseen candidate guests, its CB[7] pipeline discovers a novel binder that wet-lab competition NMR confirms is a high-affinity, picomolar CB[7] binder. Our data and code are available at https://github.com/Zehong-Wang/MDForge.

ProPlay: Procedural World Models for Self-Evolving LLM Agents

Self-evolving agents are expected to improve through interaction without external supervision, but this remains difficult in partially observable environments where agents must explore actively, learn from limited feedback, and decide when to trust prior experience. Existing LLM-agent methods often rely on memory or planning modules, yet they rarely close the loop between them to continually refine an internal understanding of environment dynamics. We introduce ProPlay, a procedural world model that supports procedure-level preplay, where agents can rehearse future procedural paths using the learned world knowledge. Rather than representing experience as isolated rules or low-level action constraints, ProPlay abstracts successful trajectories into procedures and organizes them in a procedure graph that captures causal transitions among task stages. Each transition is associated with a reliability record embedding to estimate its task-specific contribution from past outcomes. Before each episode, ProPlay simulates future procedural trajectories over known graph structures as structured soft guidance; after execution, it refines the graph using environment feedback. Experiments on public benchmarks show that ProPlay consistently improves environment understanding and self-evolution capability over strong baselines. Our code has been released in https://github.com/antman9914/proplay.

SupraBench: A Benchmark for Supramolecular Chemistry

Supramolecular chemistry, which includes the study of non-covalent host-guest assemblies, has advanced various applications. However, designing host-guest systems remains time-consuming, requiring days of dry-lab verification per candidate pair. Although LLMs have emerged as a fast alternative with strong performance on molecular binding tasks, no benchmark currently systematically evaluates LLMs for host-guest reasoning across fundamental supramolecular chemistry tasks, e.g., binding affinity prediction. To this end, we collaborate with domain experts to release the first Supramolecular Benchmark, called SupraBench, to evaluate LLMs in chemistry reasoning. Specifically, we design four fundamental tasks, i.e., binding affinity prediction, top-binder selection, solvent identification, and host-guest description, plus an auxiliary vision-based task for molecular identification. We also release SupraPMC, a curated 16M-token corpus of Supramolecular chemistry articles distilled from Europe PMC, to support the adaptation to the supramolecular domain. We benchmark a broad range of open and proprietary LLMs and find that LLMs leave substantial headroom across all tasks. Domain adaptation pretraining over SupraPMC transfers cleanly to in-distribution regression but trades off against strict letter-format output. Moreover, the difficulty profile differs sharply across task families, revealing distinct failure modes that indicate specific gaps in current supramolecular chemistry reasoning. Our source codes and benchmark datasets are available at https://github.com/Tianyi-Billy-Ma/SupraBench.

Why Semantic Entropy Fails: Geometry-Aware and Calibrated Uncertainty for Policy Optimization

Post-training has become central to improving reasoning and alignment in large language models, where critic-free models enable scalable learning from model-generated outputs but lack principled mechanisms to distinguish informative from noisy signals. Recent approaches leverage response-level measures as uncertainty signals to regulate group-based optimization methods such as GRPO. Yet their empirical success remains unstable and unclear in how they influence optimization dynamics. In this paper, we provide, to our knowledge, the first principled formulation that interprets uncertainty signals as mechanisms for characterizing and regulating gradient variance and learning signal quality. Based on both empirical and theoretical analysis, we identify two critical gaps of current entropy-based estimators: The anisotropic gap and The calibration gap. Motivated by this analysis, we propose Geometric-aware Calibrated Policy Optimization (GCPO), a novel framework integrating geometry-aware measures to capture semantic disagreement with reward-based calibration to align uncertainty with learning signal strength. Experiments on multiple benchmarks show that our approach more faithfully tracks gradient variability and consistently improves post-training performance. Our results highlight the importance of designing uncertainty signals that are aligned with optimization dynamics, offering a principled perspective for robust post-training.

PreScam: A Benchmark for Predicting Scam Progression from Early Conversations

Conversational scams, such as romance and investment scams, are emerging as a major form of online fraud. Unlike one-shot scam lures such as fake lottery or unpaid toll messages, they unfold through multi-turn conversations in which scammers gradually manipulate victims using evolving psychological techniques. However, existing research mainly focuses on static scam detection or synthetic scams, leaving open whether language models can understand how real-world scams progress over time. We introduce PreScam, a benchmark for modeling scam progression from early conversations. Built from user-submitted scam reports, PreScam filters and structures 177,989 raw reports into 11,573 conversational scam instances spanning 20 scam categories. Each instance is hierarchically structured according to the scam lifecycle defined by the proposed scam kill chain, and further annotated at the turn level with scammer psychological actions and victim responses. We benchmark models on two tasks: real-time termination prediction, which estimates whether a conversation is approaching the termination stage, and scammer action prediction, which forecasts the scammer's subsequent actions. Results show a clear gap between surface-level fluency and progression modeling: supervised encoders substantially outperform zero-shot LLMs on real-time termination prediction, while next-action prediction remains only moderately successful even for strong LLMs. Taken together, these results show that current models can capture some scam-related cues, yet still struggle to track how risk escalates and how manipulation unfolds across turns.

On the Safety of Graph Representation Learning

Graph representation learning (GRL) has evolved from topology-only graph embeddings to task-specific supervised GNNs, and more recently to reusable representations and graph foundation models (GFMs). However, existing evaluations mainly measure clean transfer, adaptation, and task coverage. It remains unclear whether GRL methods stay reliable when deployment stresses affect graph signals, graph contexts, label support, structural groups, or predictive evidence. We introduce GRL-Safety, a multi-axis safety evaluation benchmark for GRL. GRL-Safety evaluates twelve representative methods, spanning topology-only embedding methods, supervised GNNs, self-supervised graph models, and GFMs, on twenty-five graph datasets under standardized evaluation conditions while preserving method-native adaptation. The evaluation covers five safety axes: corruption robustness, OOD generalization, class imbalance, fairness, and interpretation, with per-axis and sub-condition reporting rather than a single aggregate score. Our analysis yields three cross-axis insights that can inspire future research. First, safety behavior is shaped by the interaction between representation design and the stressed graph factor, rather than by method family alone. Second, foundation-era methods show axis-specific strengths rather than broad safety dominance. Third, several deployment regimes remain difficult even for the best evaluated method, revealing capability gaps that require new robustness, adaptation, or training objectives beyond model selection. The benchmark, evaluation protocols, and code are available at: https://github.com/GXG-CS/GRL-Safety.

W2T: LoRA Weights Already Know What They Can Do

Each LoRA checkpoint compactly stores task-specific updates in low-rank weight matrices, offering an efficient way to adapt large language models to new tasks and domains. In principle, these weights already encode what the adapter does and how well it performs. In this paper, we ask whether this information can be read directly from the weights, without running the base model or accessing training data. A key obstacle is that a single LoRA update can be factorized in infinitely many ways. Without resolving this ambiguity, models trained on the factors may fit the particular factorization rather than the underlying update. To this end, we propose \methodfull, which maps each LoRA update to a provably canonical form via QR decomposition followed by SVD, so that all equivalent factorizations share the same representation. The resulting components are then tokenized and processed by a Transformer to produce a weight-space embedding. Across language and vision LoRA collections, W2T achieves strong results on attribute classification, performance prediction, and adapter retrieval, demonstrating that LoRA weights reliably indicate model behavior once factorization ambiguity is removed. Code is available at https://github.com/xiaolonghan2000/Weight2Token.

A Survey of Weight Space Learning: Understanding, Representation, and Generation

Neural network weights are typically viewed as the end product of training, while most deep learning research focuses on data, features, and architectures. However, recent advances show that the set of all possible weight values (weight space) itself contains rich structure: pretrained models form organized distributions, exhibit symmetries, and can be embedded, compared, or even generated. Understanding such structures has tremendous impact on how neural networks are analyzed and compared, and on how knowledge is transferred across models, beyond individual training instances. This emerging research direction, which we refer to as Weight Space Learning (WSL), treats neural weights as a meaningful domain for analysis and modeling. This survey provides the first unified taxonomy of WSL. We categorize existing methods into three core dimensions: Weight Space Understanding (WSU), which studies the geometry and symmetries of weights; Weight Space Representation (WSR), which learns embeddings over model weights; and Weight Space Generation (WSG), which synthesizes new weights through hypernetworks or generative models. We further show how these developments enable practical applications, including model retrieval, continual and federated learning, neural architecture search, and data-free reconstruction. By consolidating fragmented progress under a coherent framework, this survey highlights weight space as a learnable, structured domain with growing impact across model analysis, transferring, and weight generation. We release an accompanying resource at https://github.com/Zehong-Wang/Awesome-Weight-Space-Learning.

BHyGNN+: Unsupervised Representation Learning for Heterophilic Hypergraphs

Hypergraph Neural Networks (HyGNNs) have demonstrated remarkable success in modeling higher-order relationships among entities. However, their performance often degrades on heterophilic hypergraphs, where nodes connected by the same hyperedge tend to have dissimilar semantic representations or belong to different classes. While several HyGNNs, including our prior work BHyGNN, have been proposed to address heterophily, their reliance on labeled data significantly limits their applicability in real-world scenarios where annotations are scarce or costly. To overcome this limitation, we introduce BHyGNN+, a self-supervised learning framework that extends BHyGNN for representation learning on heterophilic hypergraphs without requiring ground-truth labels. The core idea of BHyGNN+ is hypergraph duality, a structural transformation where the roles of nodes and hyperedges are interchanged. By contrasting augmented views of a hypergraph against its dual using cosine similarity, our framework captures essential structural patterns in a fully unsupervised manner. Notably, this duality-based formulation eliminates the need for negative samples, a common requirement in existing hypergraph contrastive learning methods that is often difficult to satisfy in practice. Extensive experiments on eleven benchmark datasets demonstrate that BHyGNN+ consistently outperforms state-of-the-art supervised and self-supervised baselines on both heterophilic and homophilic hypergraphs. Our results validate the effectiveness of leveraging hypergraph duality for self-supervised learning and establish a new paradigm for representation learning on challenging, unlabeled hypergraphs.

OPBench: A Graph Benchmark to Combat the Opioid Crisis

The opioid epidemic continues to ravage communities worldwide, straining healthcare systems, disrupting families, and demanding urgent computational solutions. To combat this lethal opioid crisis, graph learning methods have emerged as a promising paradigm for modeling complex drug-related phenomena. However, a significant gap remains: there is no comprehensive benchmark for systematically evaluating these methods across real-world opioid crisis scenarios. To bridge this gap, we introduce OPBench, the first comprehensive opioid benchmark comprising five datasets across three critical application domains: opioid overdose detection from healthcare claims, illicit drug trafficking detection from digital platforms, and drug misuse prediction from dietary patterns. Specifically, OPBench incorporates diverse graph structures, including heterogeneous graphs and hypergraphs, to preserve the rich and complex relational information among drug-related data. To address data scarcity, we collaborate with domain experts and authoritative institutions to curate and annotate datasets while adhering to privacy and ethical guidelines. Furthermore, we establish a unified evaluation framework with standardized protocols, predefined data splits, and reproducible baselines to facilitate fair and systematic comparison among graph learning methods. Through extensive experiments, we analyze the strengths and limitations of existing graph learning methods, thereby providing actionable insights for future research in combating the opioid crisis. Our source code and datasets are available at https://github.com/Tianyi-Billy-Ma/OPBench.