arXiv subjects

Yixin Wang

Publications and source records attributed to Yixin Wang.

At least 19 recordsLinked to original sources

arXiv2026

Fixed-Dimensional Latent Flow for Generating Variable-Size 3D Molecules

Molecular size is intrinsically linked to composition, structure, and properties, but most 3D molecular generators treat size as a predefined input rather than a quantity to be generated. We introduce Equivariant-Free Transformer-Autoencoded Latent Flow Matching, a two-stage framework that samples a fixed-dimensional latent vector using flow matching and employs an autoregressive Transformer to determine molecular size, atom types, coordinates, and chemical attributes. Canonical atom ordering and rigid-pose alignment enable Transformers without equivariant layers, while decoded attributes guide bond reconstruction. On PCQM4Mv2, unconditional generation yields 87.9\% unique and novel molecules passing sanitization and PoseBusters checks, exceeding baselines with lower end-to-end training and sampling time and higher end-to-end throughput. Across ten target HOMO-LUMO gaps, internal ranking retains 30\% of the screened candidates and increases the density functional theory-verified hit rate within 0.1 eV of the target from 25.0\% to 52.4\%, while largely preserving novelty and diversity. These results demonstrate fixed-dimensional latent generation with autoregressive decoding as a practical approach to molecular design without prespecifying size.

physics.chem-ph↗

arXiv2026

Living with AI Companions: Sustained AI Companionship Predicts Lower Well-Being Through Lower Human Interaction

AI chatbots are increasingly used for companionship, emotional support, and personal self-disclosure; however, how social engagement with these systems unfolds over time and shapes users' well-being remains unclear. To address this, we conducted a two-wave longitudinal study of CharacterAI users, surveying 1,182 participants at baseline and 439 after a mean follow-up of 12 months. We examined how social engagement with AI companions evolves and how these longitudinal engagement patterns may influence well-being through two hypothesized pathways: sustained social engagement over time and the displacement of human social interaction. We found that interaction intensity, companionship use, and self-disclosure all showed substantial continuity over time. Greater interaction intensity at baseline predicted greater subsequent interaction intensity, companionship use, and self-disclosure. Consistent with the longitudinal engagement pathway, sustained social engagement across these dimensions was consistently associated with lower well-being. Results further support the social displacement pathway, indicating that these links were mainly explained by lower in-person social interaction. These findings highlight the importance of designing AI companions that support human social relationships without displacing them.

cs.HC↗

arXiv2026

MMedAgent-Plus: Scaling Multimodal Medical Agents across Modalities, Tasks and Workflows

Medical workflows often require multiple interdependent analyses, but existing specialist and generalist AI models are not designed to coordinate them. We introduce MMedAgent-Plus, a multimodal medical tool-use agent that combines a vision-language planner with 18 leading specialist models spanning 12 tasks and 8 modalities. Through a unified tool interface, the planner selects specialists, executes them in sequence, and synthesizes responses grounded in their outputs. The planner is instruction-tuned on 208,928 samples from 32 public medical benchmarks, covering single- and multi-tool interactions across single and multiple rounds. We separately evaluate tool orchestration, response synthesis, and end-to-end execution on held-out samples. MMedAgent-Plus achieves tool-call accuracies of 91.0%, 98.1%, and 80.7% in single-tool multi-round, multi-tool multi-round, and multi-tool single-round settings, respectively. Given correct tool outputs, MMedAgent-Plus achieves scores of 14.4-14.8 out of 15 for faithfulness, completeness, and conciseness across 600 evaluation samples. In end-to-end execution without pre-supplied tool outputs, MMedAgent-Plus correctly invokes the required specialist in 90.6% of 350 evaluation cases spanning seven tasks. Its final-answer accuracy reaches 0.98, matching the dedicated leading specialist and exceeding the strongest baseline (0.28).

cs.CL↗

arXiv2026

PlotGround: Grounding Plot Digitization in Real Scientific Figures and Their Source Data

Scientific figures often encode quantitative results that are not readily available in machine-readable form, making accurate plot digitization important for verifying and reusing published findings. Yet it remains unclear how accurately current models recover plotted values from real scientific figures, as existing benchmarks rely largely on synthetic charts or cover only a limited range of chart types. We introduce PlotGround, an automated pipeline for building plot digitization benchmarks from real scientific figures and their author-released source data. PlotGround maps figures to source tables, identifies reconstructable panels, and generates quantitative questions with source-grounded reference values. We use PlotGround to construct PlotGround-1k, a human-verified benchmark of 1,119 questions from 1,066 bioRxiv preprints. Across sixteen multimodal models, the best reaches 87.5% accuracy at a $\pm 5\%$ relative-error tolerance. Tightening the tolerance to $\pm 2\%$ lowers every model's accuracy by 11-24 percentage points, revealing a gap between approximate visual reading and precise quantitative recovery. PlotGround's paired figure-source structure lets us compare how accurately the same values are recovered from figures and from source tables. Providing source tables instead of figures raises a coding agent's accuracy from 90.0% to 97.4% while cutting cost by 72%.

cs.CL↗

arXiv2026

Stable Causal Estimation with Optimal Transport

In observational studies, the overlap assumption, also called positivity, is frequently strained in practice. Limited overlap destabilizes widely used estimators such as inverse propensity weighting (IPW), whose variance depends on density ratios that explode as propensity scores approach zero or one. To address this challenge, we propose the Stable Transport Estimator (STE), an optimal transport-based approach for estimating average causal effects when overlap holds but strict overlap fails. Unlike IPW, the variance of STE contains no density-ratio factor; it is governed by the transport map itself and stays finite under bounded moments, even when density ratios diverge. By replacing reweighting with a geometry-aware transport map, STE constructs stable counterfactual comparisons without requiring density estimation or propensity score modeling. STE further extends to settings where the overlap condition is violated: when covariate supports overlap only partially, a linear interpolation transport map enables principled extrapolation with explicit bias-variance trade-offs. We establish consistency, asymptotic normality, and a variance characterization that makes explicit the contribution of the estimated transport map to the asymptotic variance. Across synthetic and real datasets, STE demonstrates improved robustness, reduced bias, and markedly more stable variance compared to existing estimators.

stat.ME↗

arXiv2026

Decoupled Drift-Diffusion World Models for Consistent Future Frame Prediction

World models of visual information predict future image frames conditioned on given action sequences. This predicted scene evolution is driven by deterministic changes such as controlled motion on a robot platform, as well as stochastic changes such as rendering of manipulated objects or previously occluded regions. Our key insight is that the spatial location of these stochastic changes is itself learnable. We leverage this insight by jointly regressing both the deterministic next-state prediction and the spatial uncertainty map, then using the uncertainty map to guide a conditional diffusion process. We propose Decoupled Drift-Diffusion World Model (D3WM), which uses a transformer trained with a Gaussian negative-log-likelihood objective to produce both the deterministic next-state prediction and a spatial map of heteroscedastic aleatoric uncertainty. The learned uncertainty map then provides a structured spatial gate for a conditional diffusion model: deterministic regions are anchored to the predicted state, while uncertain regions, such as disocclusions or dynamic textures, are sampled by the diffusion process. We frame this decomposition under a variance-gated stochastic differential equation that separates deterministic drift from stochastic diffusion. D3WM shows improved results over competitive baselines in two distinct types of action spaces: robotic tabletop manipulation and camera motion.

cs.CV↗

arXiv2026

CoCurve: Cross-Module Co-Pruning Curvature for Structured LLM Pruning

Resource-constrained deployment requires sustaining large language model (LLM) capabilities as models scale under fixed memory and computation budgets. Structured pruning advances this deployment frontier with smaller dense checkpoints, yet deciding what to prune remains bottlenecked by interactions among joint removals. We introduce Cross-Module Co-Pruning Curvature (CoCurve), which formulates structured pruning as set-dependent predictive risk over a unified inventory of attention heads and feed-forward groups. A co-pruning graph built from single-unit forward ablations assigns individual risk to nodes and reinforcement or cancellation to interaction edges, conditioning each decision on the units already removed. We evaluate 6 LLMs (3B--70B) and 3 vision--language models (VLMs) across 3 perplexity corpora, 12 language tasks, and 7 multimodal benchmarks. Across the five-model 20--40% grid and the 70B 10--50% sweep, CoCurve ranks first in 53/60 corpus comparisons (15/15 at 70B); matched-quality interpolation permits 2.2--6.6 more pruning points in 9/10 cases, while CoCurve leads all 6 VLM Avg$_7$ blocks. After the same lightweight recovery, its retained structures remain strongest through 50% pruning, where the 8B checkpoint regains 10.8 Avg$_{12}$ points; physical slicing delivers $1.58\times$ dense prefill throughput with 41% lower peak memory. Mechanism analysis across 10 LLMs and 7 VLMs finds organized within- and cross-module edge structure; matched low-saliency, high-coupling removals degrade 19/20 capability groups by up to 23.7 points.

cs.LG↗

arXiv2026

Conditional Co-Ablation: Recovering Self-Repair Backups in Transformer Circuits

Mechanistic interpretability seeks to explain transformer behavior through circuits: sets of internal components that causally support a behavior. However, self-repair creates a blind spot: ablating a primary component can activate a dormant backup, so a circuit that explains behavior in the intact model can become incomplete under the intervention used to test it. We formulate this gap as conditional circuit completion: given a primary set, identify components that become causally important after its removal. We introduce conditional co-ablation (CoAx), which ranks candidates by growth in ablation effect after primary-set removal. We show that a perfectly dormant backup can be indistinguishable from an irrelevant component to per-unit intact-state scores, whereas its conditional effect change exactly aggregates all interaction orders linking it to the removed set. On GPT-2-small's Indirect Object Identification (IOI) circuit, CoAx recovers the documented backup heads at 0.941 ROC-AUC, versus 0.815 for the strongest intact-state attribution baseline and 0.758 for the matched conditional-energy control. Recovery drops to 0.40 +/- 0.13 AUC for alternative component sets matched in behavioral effect, output displacement, and depth, showing that recovery is specific to the removed circuit. Beyond recovery, the CoAx-selected heads are causally load-bearing: freezing them after primary removal sharply reduces the IOI margin, while adding them to the incomplete circuit reduces incompleteness from 0.75 to 0.21. More broadly, conditional growth aligns with intervention-derived repair in 11/12 held-out instances across 4 mechanism clusters, and CoAx completions outperform matched random completions on all 8 non-GPT-2 models spanning 6 architecture families. Together, causal explanations of self-repairing transformers must account for backup circuitry when primary components fail.

cs.LG↗

arXiv2026

Terminal Shrinkage Averaging Reveals a Schedule-Estimator Interaction in LLM Pretraining

Large language model (LLM) pretraining conventionally returns the raw final iterate. This couples two design choices: the learning-rate schedule that generates the parameter trajectory and the estimator that constructs the deployed model (e.g. the raw final iterate or a checkpoint average). A schedule that promotes optimization progress may differ from one that minimizes variation in the raw final iterate. Separating these choices creates an opportunity to maintain progress late in training while reducing variation in the returned model. To this end, we propose \emph{Terminal Shrinkage Averaging (TSA)}, which interpolates between the raw final iterate and the average of recent checkpoints to balance recent progress against terminal variation. We analyze how TSA changes the preferred terminal learning-rate schedule under a local quadratic approximation and test this interaction through a sequence of controlled NanoChat experiments. Finally, we demonstrate that the resulting gains transfer to depth-22 NanoChat, where the combined schedule and estimator improve validation quality. A qualifying time-to-GPT-2 run also finishes faster than the public baseline used in our experiments, providing preliminary evidence of benchmark acceleration.

cs.LG↗

arXiv2026

Latency-Response Theory Model: Evaluating Large Language Models via Response Accuracy and Chain-of-Thought Length

The proliferation of Large Language Models (LLMs) necessitates valid evaluation methods to provide guidance for both downstream applications and actionable future improvements. The Item Response Theory (IRT) model with Computerized Adaptive Testing has recently emerged as a promising framework for evaluating LLMs via their response accuracy. Beyond simple response accuracy, LLMs' chain of thought (CoT) lengths serve as a vital indicator of their reasoning ability. To leverage the CoT length information to assist LLM evaluation, we propose the \textbf{La}tency-\textbf{R}esponse \textbf{T}heory (LaRT) model, which jointly models both the response accuracy and CoT length by introducing a key correlation parameter between the latent ability and the latent speed. We derive an efficient stochastic approximation Expectation-Maximization algorithm for parameter estimation. We establish rigorous identifiability results for the latent ability and latent speed parameters to ensure the statistical validity of their estimation. Through both theoretical asymptotic analyses and simulation studies, we demonstrate LaRT's advantages over IRT in terms of superior estimation accuracy and shorter confidence intervals for latent trait estimation. To evaluate LaRT in real data, we collect responses from diverse LLMs on popular benchmark datasets. We find that LaRT yields different LLM rankings than IRT and outperforms IRT across multiple key evaluation metrics including predictive power, item efficiency, ranking validity, and LLM evaluation efficiency. Code and data are available at https://github.com/Toby-X/Latency-Response-Theory-Model

stat.ME↗

arXiv2026

Policy Optimization and Statistical Inference for Online Contextual Matrix Games

Online decision making often requires navigating a landscape shaped by both dynamic contexts and strategic interactions. In competitive pricing, for example, hotels must account for both dynamic contextual factors and rivals' strategic responses. Existing approaches address only part of this challenge: contextual bandits optimize single-agent decisions using observable features but ignore multi-player interactions, while online matrix games capture strategic behavior through Nash equilibrium but assume fixed payoffs, ignoring contextual information. How should agents act then when strategic payoffs evolve with contextual signals? We introduce \emph{online contextual matrix games} to integrate contextual information into multi-player online games. We further propose \emph{OnGameLearn}, an online learning algorithm that efficiently balances exploration and exploitation across both player actions and contexts. This approach comes with statistical guarantees: tail bounds for the estimated payoff matrix, the convergence of the estimated Nash equilibrium, the asymptotic normality of the parameter estimators, and the sublinear regret bound. We also develop the notion of \emph{policy value} in matrix games and develop a doubly robust, $\sqrt{T}$-consistent estimator for it. Across simulated studies and a real-world hotel pricing application, we find that OnGameLearn effectively navigates the intertwined challenges of strategic and contextual decision-making.

stat.ML↗

arXiv2026

Weightless Fine-Tuning: Personalizing LLMs via Logit-Space Transport

Supervised fine-tuning (SFT) is a standard approach for adapting LLMs to a target distribution, but in settings such as personalization, where each author requires separate weight access, optimization, storage, and retraining, its costs become prohibitive. We propose Weightless Fine-Tuning (WFT), a training-free decoding-time method that approximates the distributional effect of SFT without weight updates. WFT computes supervised residuals on an author's training sequence and transports them to the current prompt through a cross-prefix transport operator estimated from dropout-induced cross-covariance. The operator captures how a perturbation at one context propagates to predictions at another, replacing gradient-based parameter updates with logit-space corrections. On three LaMP personalization benchmarks, WFT achieves the best average performance across datasets, matches or exceeds SFT on individual tasks, and outperforms other lightweight baselines on average. In a budget-controlled comparison, WFT approaches SFT performance using less than 7% of the effective computation. Logit-level analysis shows a cosine similarity of 0.875 between the logit shifts induced by WFT and SFT over 95% of the next-token probability mass, suggesting that WFT captures the distributional effect of supervised adaptation without modifying model weights.

cs.LG↗

arXiv2026

Causal Inference with Unstructured Outcomes

Causal inference has traditionally centered on scalar outcomes: whether a patient recovers, how much a worker earns, or how many visits a website receives. Modern studies increasingly ask causal questions about outcomes with richer form, such as clinical notes, open-ended survey responses, and images. A hospital may want to know how an AI documentation tool changes the notes physicians write, or how a nurse training program alters what patients say in survey responses. For such outcomes, the usual average treatment effect is ill-defined: one cannot meaningfully subtract one text or image from another. To this end, we propose a causal query for unstructured outcomes. The key idea is to learn what features of the outcome are most causally affected by the treatment, which we call the maximally contrasting feature (MCF). To estimate the MCF, we learn a feature-scoring function that maps each outcome to a scalar and exposes the sharpest contrast between treated and control potential outcomes. We develop identification conditions and estimation algorithms for this query, and extend it to heterogeneous effects by allowing the feature-scoring function to depend on observed covariates. We also handle settings where both the treatment and the outcome are unstructured. Empirical studies on text and images show that the algorithm recovers salient aspects of an outcome changed by a treatment.

stat.ML↗

arXiv2026

Causal Inference with Unstructured Treatments

Causal inference usually concerns a scalar treatment, yet in many problems the treatment is unstructured: a text, an image, or a sequence of clinical decisions. Consider an instructor writing a course description to attract more students: the treatment is the course description, and the outcome is enrollment. The standard target, the average treatment effect of fixing the treatment to one exact value versus another, runs into two problems. It cannot be estimated, because almost no exact description recurs across courses, leaving no comparable group from which to measure its effect; and it would be of little use even if it could, since no one wants every course to carry the same description. What the instructor actually wants to know is which features of a description raise enrollment, and which of those features can be acted on across many courses. To this end, we propose a causal query for unstructured treatments: the maximally influential feature (MIF), the feature of the treatment that most strongly influences the outcome. We formalize the MIF as a binary feature of the treatment, defined by a feature-scoring function, constrained so that both of its values stay well populated, and chosen to maximize the causal effect it induces. Turning the feature on shifts the distribution of treatments toward those that display it, turning it off shifts away, and the MIF effect contrasts the two average potential outcomes. We study identification conditions for the MIF, develop algorithms to estimate it, and make it actionable through a nudging algorithm that revises a treatment along the MIF into an outcome-improving version. We illustrate the MIF algorithm across applications in text, image, and dynamic treatment sequences.

stat.ML↗

arXiv2026

Amortized Bayesian Causal Discovery of Extended Factor Graphs

Learning causal graphs from interventional data is a challenging problem with broad applications. In molecular biology, for example, a central goal is to uncover gene regulatory networks from large-scale perturbation data. An ideal algorithm for this task should scale to thousands of nodes, incorporate interventions even when their targets are unknown, quantify uncertainty, and provide identifiability guarantees. However, existing approaches---e.g. approaches using score-based optimization or approximate Bayesian inference---often fail to meet all of these criteria. To address these limitations, we develop Amortized Bayesian Causal Discovery of Extended Factor Graphs (ABCDEFG). Our method guarantees exact acyclicity, scales to graphs with thousands of nodes, and naturally handles interventions even when their targets are unknown. Additionally, ABCDEFG estimates a posterior distribution whose maximum a posteriori estimate provably identifies the true causal graph up to an equivalence class. On simulated datasets, ABCDEFG achieves state-of-the-art accuracy, producing a well-calibrated posterior distribution while outperforming previous score-based and approximate Bayesian methods. Applied to large-scale single-cell perturbation data, ABCDEFG identifies both established and novel gene targets of growth factors.

stat.ML↗

arXiv2026

Adapting Evidential Neural Networks to Test-Time Neighbor Fusion Improves Molecular Property Prediction

A trained molecular property model can be refined at test time by correcting each prediction with the measured labels of the most similar training molecules, a retraining-free procedure we call neighbor fusion; evidential neural networks make it principled by using their aleatoric and epistemic uncertainty to parameterize a Bayesian update. Our main contribution, PG-EVIKAL, learns a property-distance metric to re-rank structurally similar neighbors by their property relevance before fusion, building on EVIKAL (scalar Kalman filter) and GP-EVIKAL (Gaussian process variant handling correlated neighbors). Evaluated on 16 molecular datasets, PG-EVIKAL reduces RMSE relative to the evidential model baseline on 14 of them, with a median reduction of 19.4%, and improves calibration; in sequential-assay scenarios it further incorporates newly measured molecules, refining predictions as they arrive without retraining. This work demonstrates that evidential uncertainty decomposition is not merely a calibration objective but an actionable inference resource that enables test-time refinement of molecular property predictions.

cs.LG↗

arXiv2026

Bayesian Invariance Modeling of Multi-Environment Data

Invariant prediction [Peters et al., 2016] analyzes feature/outcome data from multiple environments to identify invariant features - those with a stable predictive relationship to the outcome. Such features support generalization to new environments and help reveal causal mechanisms. Previous methods have primarily tackled this problem through hypothesis testing or regularized optimization. Here we develop Bayesian Invariant Prediction (BIP), a probabilistic model for invariant prediction. BIP encodes the indices of invariant features as a latent variable and recover them by posterior inference. Under the assumptions of Peters et al. [2016], the BIP posterior targets the true invariant features. We prove that the posterior is consistent and that greater environment heterogeneity leads to faster posterior contraction. To handle many features, we design an efficient variational approximation called VI-BIP. In simulations and real data, we find that BIP and VI-BIP are more accurate and scalable than existing methods for invariant prediction.

stat.ML↗

arXiv2026

Predictive single cell foundation model for gene regulation and aging with privacy-preserving tabular learning

Pre-trained foundation models (FMs) have begun transforming single-cell genomics, but scaling them raises privacy concerns. Moreover, unlike text data, single-cell data is unordered and exhibits a unique tabular structure that current single-cell FMs overlook. We introduce Tabula, a privacy-preserving FM designed with federated learning (FL) that explicitly models the tabular structure of single-cell data. To deploy Tabula, we further developed Chiron, a decentralized AI agent-enabled platform for collaborative training across institutions without sharing raw data. Beyond strong performance across downstream benchmarks, Tabula reveals combinatorial regulatory logic across diverse biological systems, including hematopoiesis, pancreatic endogenesis, neurogenesis, and cardiogenesis. Using a new scRNA-seq dataset of paired young and aged human fibroblasts, Tabula nominates rejuvenation factors through age- and identity score-guided in silico prioritization, outperforming conventional approaches. Thus, Tabula represents an important advance in single-cell foundation modeling by integrating tabular learning with FL, paving the way toward privacy-preserving virtual cells for human health.

cs.LG↗