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Tianyi Ma

Publications and source records attributed to Tianyi Ma.

At least 37 records · Page 2Linked to original sources
arXiv2026

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.

cs.LG↗
arXiv2026

Food4All: An Agentic Framework and Benchmark for Food Resource Navigation with Adaptive User Understanding

Food assistance referral requires conversational agents to translate underspecified, often noisy help-seeking dialogues into locally valid resource recommendations. We present Food4All, an agentic food-resource referral framework and benchmark grounded in 686 structured Indiana food resources. Food4All couples a food-specific search tool with 300 multi-turn evaluation tasks spanning single food needs, composite cases with access or document constraints, and five non-ideal user interaction traits: unreasonable demands, rambling responses, impatience, incomplete answers, and inconsistent information. We evaluate six Large Language Models (LLMs) on requirement grounding, resource retrieval, final referral correctness, and interaction efficiency. Although the strongest model achieves 96.33% referral accuracy, our diagnostics reveal persistent failures in grounding schedule, eligibility, intake, and document constraints, as well as failures to preserve valid retrieved resources in the final recommendation. Trait-level analysis further shows that different non-ideal behaviors stress different parts of the referral pipeline. Food4All provides a controlled testbed for studying tool-calling agents in constraint-sensitive food assistance referral under realistic user interaction challenges.

cs.CL↗
arXiv2026

Causal Scaffolding for Physical Reasoning: A Benchmark for Causally-Informed Physical World Understanding in VLMs

Understanding and reasoning about the physical world is the foundation of intelligent behavior, yet state-of-the-art vision-language models (VLMs) still fail at causal physical reasoning, often producing plausible but incorrect answers. To address this gap, we introduce CausalPhys, a benchmark of over 3,000 carefully curated video- and image-based questions spanning four domains: Perception, Anticipation, Intervention, and Goal Orientation. Each question is paired with an expert-annotated causal graph capturing object-attribute-event dependencies, enabling interpretable and fine-grained evaluation of causal understanding. Building on this, we formulate a causal-graph-grounded metric that quantitatively measures how well a model's chain-of-thought reasoning aligns with the correct causal relations, moving beyond answer-only accuracy and enabling systematic diagnosis of VLMs' causal reasoning failures. Using this metric, we conduct a comprehensive analysis of leading VLMs, revealing systematic gaps in capturing causal dependencies and underscoring the need for causality-aware learning. To address these limitations, we further propose Causal Rationale-informed Fine-Tuning (CRFT), which explicitly aligns VLM reasoning with causal structures. Extensive experiments demonstrate that CRFT substantially enhances both reasoning accuracy and interpretability across multiple model backbones. By unifying dataset curation, causal evaluation, and causality-informed learning, CausalPhys establishes a strong foundation for advancing modern VLMs toward causally grounded physical reasoning.

cs.DB↗
arXiv2026

SaaS-Bench: Can Computer-Use Agents Leverage Real-World SaaS to Solve Professional Workflows?

Computer-Using Agents (CUAs) are rapidly extending large language models (LLMs) beyond text-based reasoning toward action execution in more complex environments, such as web browsers and graphical user interfaces (GUIs). However, existing web and GUI agent benchmarks often rely on simplified settings, isolated tasks, or short-horizon interactions, making it difficult to assess capabilities of agents in realistic professional workflows. Software-as-a-Service (SaaS) environments are a natural choice for CUA evaluation, as they host a large share of modern digital work and naturally involve dynamic system states, cross-application coordination, domain-specific knowledge, and long-horizon dependencies. To this end, we introduce SaaS-Bench, a benchmark built on 23 deployable SaaS systems across six professional domains, containing 106 tasks grounded in realistic work scenarios. These tasks require long-horizon execution, cover both text-only and multimodal settings, and are evaluated with weighted verification checkpoints that measure strict task completion and partial progress. Experiments show that representative LLM-based agents struggle on SaaS-Bench, with even the strongest model completing fewer than 4% of tasks end-to-end, exposing limitations in planning, state tracking, cross-application context maintenance, and error recovery. Code are available at https://github.com/UniPat-AI/SaaS-Bench for reproduction.

cs.AI↗
arXiv2026

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.

cs.LG↗
arXiv2026

Efficient and Minimax Optimal In-context Nonparametric Regression with Transformers

We study in-context learning for nonparametric regression with $α$-Hölder smooth regression functions, for some $α>0$. We prove that, with $n$ in-context examples and $d$-dimensional regression covariates, a pretrained transformer with $Θ(\log n)$ parameters and $Ω\bigl(n^{2α/(2α+d)}\log^3 n\bigr)$ pretraining sequences can achieve the minimax optimal rate of convergence $O\bigl(n^{-2α/(2α+d)}\bigr)$ in mean squared error. Our result requires substantially fewer transformer parameters and pretraining sequences than previous results in the literature. This is achieved by showing that transformers are able to approximate local polynomial estimators efficiently by implementing a kernel-weighted polynomial basis and then running gradient descent.

stat.ML↗
arXiv2026

Hypergraph Pattern Machine: Compositional Tokenization for Higher-Order Interactions

Hypergraphs model higher-order relations that drive real-world decisions, from drug prescriptions to recommendations. A central structural signal in such data, beyond what pairwise relations can express, is interaction compositionality: whether a higher-order relation is compositional, emergent, or inhibitory with respect to its observed or unobserved sets. In polypharmacy, the regime decides whether a drug should be dropped, kept, or excluded: a compositional drug triple can be safely simplified, an emergent triple requires all drugs jointly, and an inhibitory triple flags a drug that disrupts an existing interaction. However, existing hypergraph learning methods, which merely propagate messages over observed hyperedges, leave this compositional signal unmodeled, allowing dangerous drug combinations to slip through and be misclassified. To this end, we propose the Hypergraph Pattern Machine (HGPM), shifting the paradigm from message passing to learning the compositional pattern of subsets. It tokenizes compositional subsets, organizes them in an inclusion DAG, and trains an inclusion-aware Transformer under masked reconstruction. On ten hypergraph benchmarks, HGPM matches or exceeds state-of-the-art methods. Notably, in a real adverse-event prediction case, HGPM correctly identifies the drug addition that inhibits the side effect among feature-identical candidates, a discrimination existing methods cannot make. The code and data are in https://github.com/KryieZhao/HGPM.git.

cs.LG↗
arXiv2026

Breaking Down and Building Up: Mixture of Skill-Based Vision-and-Language Navigation Agents

Vision-and-Language Navigation (VLN) poses significant challenges for agents to interpret natural language instructions and navigate complex 3D environments. While recent progress has been driven by large-scale pre-training and data augmentation, current methods still struggle to generalize to unseen scenarios, particularly when complex spatial and temporal reasoning is required. In this work, we propose SkillNav, a modular framework that introduces structured, skill-based reasoning into Transformer-based VLN agents. Our method decomposes navigation into a set of interpretable atomic skills (e.g., Vertical Movement, Area and Region Identification, Stop and Pause), each handled by a specialized agent. To support targeted skill training without manual data annotation, we construct a synthetic dataset pipeline that generates diverse, linguistically natural, skill-specific instruction-trajectory pairs. We then introduce a novel training-free Vision-Language Model (VLM)-based router, which dynamically selects the most suitable agent at each time step by aligning sub-goals with visual observations and historical actions. SkillNav obtains competitive results on commonly used benchmarks and establishes state-of-the-art generalization to the GSA-R2R, a benchmark with novel instruction styles and unseen environments.

cs.AI↗
arXiv2026

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.

cs.CL↗
arXiv2026

Optimal In-context Adaptivity and Distributional Robustness of Transformers

We study in-context learning problems where a Transformer is pretrained on tasks drawn from a mixture distribution $π=\sum_{α\in\mathcal{A}} λ_α π_α$, called the pretraining prior, in which each mixture component $π_α$ is a distribution on tasks of a specific difficulty level indexed by $α$. Our goal is to understand the performance of the pretrained Transformer when evaluated on a different test distribution $μ$, consisting of tasks of fixed difficulty $β\in\mathcal{A}$, and with potential distribution shift relative to $π_β$, subject to the chi-squared divergence $χ^2(μ,π_β)$ being at most $κ$. In particular, we consider nonparametric regression problems with random smoothness, and multi-index models with both random smoothness and random effective dimension. We prove that a large Transformer pretrained on sufficient data achieves the optimal rate of convergence corresponding to the difficulty level $β$, uniformly over test distributions $μ$ in the chi-squared divergence ball. Thus, the pretrained Transformer is able to achieve faster rates of convergence on easier tasks and is robust to distribution shift at test time. Finally, we prove that even if an estimator had access to the test distribution $μ$, the convergence rate of its expected risk over $μ$ could not be faster than that of our pretrained Transformers, thereby providing a more appropriate optimality guarantee than minimax lower bounds.

stat.ML↗
arXiv2026

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.

cs.LG↗
arXiv2026

Estimation beyond Missing (Completely) at Random

We study the effects of missingness on the estimation of population parameters. Moving beyond restrictive missing completely at random (MCAR) assumptions, we first formulate a missing data analogue of Huber's arbitrary $ε$-contamination model. For mean estimation with respect to squared Euclidean error loss, we show that the minimax quantiles decompose as a sum of the corresponding minimax quantiles under a heterogeneous, MCAR assumption, and a robust error term, depending on $ε$, that reflects the additional error incurred by departure from MCAR. We next introduce natural classes of realisable $ε$-contamination models, where an MCAR version of a base distribution $P$ is contaminated by an arbitrary missing not at random (MNAR) version of $P$. These classes are rich enough to capture various notions of biased sampling and sensitivity conditions, yet we show that they enjoy improved minimax performance relative to our earlier arbitrary contamination classes for both parametric and nonparametric classes of base distributions. For instance, with a univariate Gaussian base distribution, consistent mean estimation over realisable $ε$-contamination classes is possible even when $ε$ and the proportion of missingness converge (slowly) to 1. We extend our results to the setting of departures from missing at random (MAR) in normal linear regression with a realisable missing response, and also demonstrate that our methods can be made adaptive to the case of unknown $ε$.

math.ST↗
arXiv2026

EvoTaxo: Building and Evolving Taxonomy from Social Media Streams

Constructing taxonomies from social media corpora is challenging because posts are short, noisy, semantically entangled, and temporally dynamic. Existing taxonomy induction methods are largely designed for static corpora and often struggle to balance robustness, scalability, and sensitivity to evolving discourse. We propose EvoTaxo, a LLM-based framework for building and evolving taxonomies from temporally ordered social media streams. Rather than clustering raw posts directly, EvoTaxo converts each post into a structured draft action over the current taxonomy, accumulates structural evidence over time windows, and consolidates candidate edits through dual-view clustering that combines semantic similarity with temporal locality. A refinement-and-arbitration procedure then selects reliable edits before execution, while each node maintains a concept memory bank to preserve semantic boundaries over time. Experiments on two Reddit corpora show that EvoTaxo produces more balanced taxonomies than baselines, with clearer post-to-leaf assignment, better corpus coverage at comparable taxonomy size, and stronger structural quality. A case study on the Reddit community /r/ICE_Raids further shows that EvoTaxo captures meaningful temporal shifts in discourse. Our codebase is available here.

cs.CL↗
arXiv2026

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.

cs.LG↗
arXiv2026

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.

cs.LG↗
arXiv2026

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.

cs.LG↗
arXiv2026

SGCR: A Specification-Grounded Framework for Trustworthy LLM Code Review

Automating code review with Large Language Models (LLMs) shows immense promise, yet practical adoption is hampered by their lack of reliability, context-awareness, and control. To address this, we propose Specification-Grounded Code Review (SGCR), a framework that grounds LLMs in human-authored specifications to produce trustworthy and relevant feedback. SGCR features a novel dual-pathway architecture: an explicit path ensures deterministic compliance with predefined rules derived from these specifications, while an implicit path heuristically discovers and verifies issues beyond those rules. Deployed in a live industrial environment at HiThink Research, SGCR's suggestions achieved a 42% developer adoption rate-a 90.9% relative improvement over a baseline LLM (22%). Our work demonstrates that specification-grounding is a powerful paradigm for bridging the gap between the generative power of LLMs and the rigorous reliability demands of software engineering.

cs.SE↗
arXiv2026

GLEN-Bench: A Graph-Language based Benchmark for Nutritional Health

Nutritional interventions are important for managing chronic health conditions, but current computational methods provide limited support for personalized dietary guidance. We identify three key gaps: (1) dietary pattern studies often ignore real-world constraints such as socioeconomic status, comorbidities, and limited food access; (2) recommendation systems rarely explain why a particular food helps a given patient; and (3) no unified benchmark evaluates methods across the connected tasks needed for nutritional interventions. We introduce GLEN-Bench, the first comprehensive graph-language based benchmark for nutritional health assessment. We combine NHANES health records, FNDDS food composition data, and USDA food-access metrics to build a knowledge graph that links demographics, health conditions, dietary behaviors, poverty-related constraints, and nutrient needs. We test the benchmark using opioid use disorder, where models must detect subtle nutritional differences across disease stages. GLEN-Bench includes three linked tasks: risk detection identifies at-risk individuals from dietary and socioeconomic patterns; recommendation suggests personalized foods that meet clinical needs within resource constraints; and question answering provides graph-grounded, natural-language explanations to facilitate comprehension. We evaluate these graph-language approaches, including graph neural networks, large language models, and hybrid architectures, to establish solid baselines and identify practical design choices. Our analysis identifies clear dietary patterns linked to health risks, providing insights that can guide practical interventions.

cs.CL↗