Yixin Wang

Yixin Wang, David M. Blei, John P. Cunningham

Variational autoencoders model high-dimensional data by positing low-dimensional latent variables that are mapped through a flexible distribution parametrized by a neural network. Unfortunately, variational autoencoders often suffer from posterior collapse: the posterior of the latent variables is equal to its prior, rendering the variational autoencoder useless as a means to produce meaningful representations. Existing approaches to posterior collapse often attribute it to the use of neural networks or optimization issues due to variational approximation. In this paper, we consider posterior collapse as a problem of latent variable non-identifiability. We prove that the posterior collapses if and only if the latent variables are non-identifiable in the generative model. This fact implies that posterior collapse is not a phenomenon specific to the use of flexible distributions or approximate inference. Rather, it can occur in classical probabilistic models even with exact inference, which we also demonstrate. Based on these results, we propose a class of latent-identifiable variational autoencoders, deep generative models which enforce identifiability without sacrificing flexibility. This model class resolves the problem of latent variable non-identifiability by leveraging bijective Brenier maps and parameterizing them with input convex neural networks, without special variational inference objectives or optimization tricks. Across synthetic and real datasets, latent-identifiable variational autoencoders outperform existing methods in mitigating posterior collapse and providing meaningful representations of the data.

Anastasios N. Angelopoulos, Karl Krauth, Stephen Bates et al. · berkeley

When building recommendation systems, we seek to output a helpful set of items to the user. Under the hood, a ranking model predicts which of two candidate items is better, and we must distill these pairwise comparisons into the user-facing output. However, a learned ranking model is never perfect, so taking its predictions at face value gives no guarantee that the user-facing output is reliable. Building from a pre-trained ranking model, we show how to return a set of items that is rigorously guaranteed to contain mostly good items. Our procedure endows any ranking model with rigorous finite-sample control of the false discovery rate (FDR), regardless of the (unknown) data distribution. Moreover, our calibration algorithm enables the easy and principled integration of multiple objectives in recommender systems. As an example, we show how to optimize for recommendation diversity subject to a user-specified level of FDR control, circumventing the need to specify ad hoc weights of a diversity loss against an accuracy loss. Throughout, we focus on the problem of learning to rank a set of possible recommendations, evaluating our methods on the Yahoo! Learning to Rank and MSMarco datasets.

Jun Ma, Ronald Xie, Shamini Ayyadhury et al.

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.

Kartik Ahuja, Divyat Mahajan, Yixin Wang et al.

Causal representation learning seeks to extract high-level latent factors from low-level sensory data. Most existing methods rely on observational data and structural assumptions (e.g., conditional independence) to identify the latent factors. However, interventional data is prevalent across applications. Can interventional data facilitate causal representation learning? We explore this question in this paper. The key observation is that interventional data often carries geometric signatures of the latent factors' support (i.e. what values each latent can possibly take). For example, when the latent factors are causally connected, interventions can break the dependency between the intervened latents' support and their ancestors'. Leveraging this fact, we prove that the latent causal factors can be identified up to permutation and scaling given data from perfect $do$ interventions. Moreover, we can achieve block affine identification, namely the estimated latent factors are only entangled with a few other latents if we have access to data from imperfect interventions. These results highlight the unique power of interventional data in causal representation learning; they can enable provable identification of latent factors without any assumptions about their distributions or dependency structure.

Dylan Molho, Jiayuan Ding, Zhaoheng Li et al.

Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning through different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.

Han Zhang, Shangen Lu, Yixin Wang et al. · tsinghua

The impacts of link recommendations on social networks are challenging to evaluate, and so far they have been studied in limited settings. Observational studies are restricted in the kinds of causal questions they can answer and naive A/B tests often lead to biased evaluations due to unaccounted network interference. Furthermore, evaluations in simulation settings are often limited to static network models that do not take into account the potential feedback loops between link recommendation and organic network evolution. To this end, we study the impacts of recommendations on social networks in dynamic settings. Adopting a simulation-based approach, we consider an explicit dynamic formation model -- an extension of the celebrated Jackson-Rogers model -- and investigate how link recommendations affect network evolution over time. Empirically, we find that link recommendations have surprising delayed and indirect effects on the structural properties of networks. Specifically, we find that link recommendations can exhibit considerably different impacts in the immediate term and in the long term. For instance, we observe that friend-of-friend recommendations can have an immediate effect in decreasing degree inequality, but in the long term, they can make the degree distribution substantially more unequal. Moreover, we show that the effects of recommendations can persist in networks, in part due to their indirect impacts on natural dynamics even after recommendations are turned off. We show that, in counterfactual simulations, removing the indirect effects of link recommendations can make the network trend faster toward what it would have been under natural growth dynamics.

Yongkai Liu, Helena Feng, Bin Jiang et al.

Predicting outcomes in acute ischemic stroke (AIS) guides clinical decision-making, patient counseling, and resource allocation. Clinical notes contain rich contextual information, but their unstructured nature limits their use in traditional predictive models. We developed and evaluated the Chain-of-Thought (CoT) Outcome Prediction Engine (COPE), a reasoning-enhanced large language model framework, for predicting 90-day functional outcomes after AIS from unstructured clinical notes. This study included 464 AIS patients with discharge summaries and 90-day modified Rankin Scale (mRS) scores. COPE uses a two-step CoT framework based on sequential open-source LLaMA-3-8B models: the first generates clinical reasoning, and the second outputs an mRS prediction. We compared COPE with GPT-4.1, ClinicalBERT, a structured variable-based machine learning model (Clinical ML), and a single-step LLM without CoT. Performance was evaluated using mean absolute error (MAE), accuracy within +/-1 mRS point, and exact accuracy. COPE achieved an MAE of 1.01 (95% CI 0.92-1.11), +/-1 accuracy of 74.4% (69.9, 78.8%), and exact accuracy of 32.8% (28.0, 37.6%), comparable to GPT-4.1 and superior to ClinicalBERT [MAE 1.24 (1.13-1.36)], Clinical ML [1.28 (1.18-1.39)], and the single-step LLM [1.20 (1.09-1.33)]. Subgroup analyses showed consistent performance across sex and age, with slightly higher error among older patients, those undergoing thrombectomy, and those with longer summaries. These findings demonstrate that COPE, a lightweight, interpretable, and privacy-preserving open-source framework, provides an accurate and practical solution for outcome prediction from unstructured clinical text.

Banghua Zhu, Stephen Bates, Zhuoran Yang et al.

We study the hidden-action principal-agent problem in an online setting. In each round, the principal posts a contract that specifies the payment to the agent based on each outcome. The agent then makes a strategic choice of action that maximizes her own utility, but the action is not directly observable by the principal. The principal observes the outcome and receives utility from the agent's choice of action. Based on past observations, the principal dynamically adjusts the contracts with the goal of maximizing her utility. We introduce an online learning algorithm and provide an upper bound on its Stackelberg regret. We show that when the contract space is $[0,1]^m$, the Stackelberg regret is upper bounded by $\widetilde O(\sqrt{m} \cdot T^{1-1/(2m+1)})$, and lower bounded by $Ω(T^{1-1/(m+2)})$, where $\widetilde O$ omits logarithmic factors. This result shows that exponential-in-$m$ samples are sufficient and necessary to learn a near-optimal contract, resolving an open problem on the hardness of online contract design. Moreover, when contracts are restricted to some subset $\mathcal{F} \subset [0,1]^m$, we define an intrinsic dimension of $\mathcal{F}$ that depends on the covering number of the spherical code in the space and bound the regret in terms of this intrinsic dimension. When $\mathcal{F}$ is the family of linear contracts, we show that the Stackelberg regret grows exactly as $Θ(T^{2/3})$. The contract design problem is challenging because the utility function is discontinuous. Bounding the discretization error in this setting has been an open problem. In this paper, we identify a limited set of directions in which the utility function is continuous, allowing us to design a new discretization method and bound its error. This approach enables the first upper bound with no restrictions on the contract and action space.

Binxu Li, Tiankai Yan, Yuanting Pan et al.

Multi-Modal Large Language Models (MLLMs), despite being successful, exhibit limited generality and often fall short when compared to specialized models. Recently, LLM-based agents have been developed to address these challenges by selecting appropriate specialized models as tools based on user inputs. However, such advancements have not been extensively explored within the medical domain. To bridge this gap, this paper introduces the first agent explicitly designed for the medical field, named \textbf{M}ulti-modal \textbf{Med}ical \textbf{Agent} (MMedAgent). We curate an instruction-tuning dataset comprising six medical tools solving seven tasks across five modalities, enabling the agent to choose the most suitable tools for a given task. Comprehensive experiments demonstrate that MMedAgent achieves superior performance across a variety of medical tasks compared to state-of-the-art open-source methods and even the closed-source model, GPT-4o. Furthermore, MMedAgent exhibits efficiency in updating and integrating new medical tools. Codes and models are all available.

Linying Zhang, Lauren R. Richter, Yixin Wang et al.

Healthcare continues to grapple with the persistent issue of treatment disparities, sparking concerns regarding the equitable allocation of treatments in clinical practice. While various fairness metrics have emerged to assess fairness in decision-making processes, a growing focus has been on causality-based fairness concepts due to their capacity to mitigate confounding effects and reason about bias. However, the application of causal fairness notions in evaluating the fairness of clinical decision-making with electronic health record (EHR) data remains an understudied domain. This study aims to address the methodological gap in assessing causal fairness of treatment allocation with electronic health records data. We propose a causal fairness algorithm to assess fairness in clinical decision-making. Our algorithm accounts for the heterogeneity of patient populations and identifies potential unfairness in treatment allocation by conditioning on patients who have the same likelihood to benefit from the treatment. We apply this framework to a patient cohort with coronary artery disease derived from an EHR database to evaluate the fairness of treatment decisions. In addition, we investigate the impact of social determinants of health on the assessment of causal fairness of treatment allocation.

Chinmaya Kausik, Yangyi Lu, Kevin Tan et al.

Evaluating and optimizing policies in the presence of unobserved confounders is a problem of growing interest in offline reinforcement learning. Using conventional methods for offline RL in the presence of confounding can not only lead to poor decisions and poor policies, but also have disastrous effects in critical applications such as healthcare and education. We map out the landscape of offline policy evaluation for confounded MDPs, distinguishing assumptions on confounding based on whether they are memoryless and on their effect on the data-collection policies. We characterize settings where consistent value estimates are provably not achievable, and provide algorithms with guarantees to instead estimate lower bounds on the value. When consistent estimates are achievable, we provide algorithms for value estimation with sample complexity guarantees. We also present new algorithms for offline policy improvement and prove local convergence guarantees. Finally, we experimentally evaluate our algorithms on both a gridworld environment and a simulated healthcare setting of managing sepsis patients. In gridworld, our model-based method provides tighter lower bounds than existing methods, while in the sepsis simulator, our methods significantly outperform confounder-oblivious benchmarks.

Yang Liu, Yao Zhang, Yixin Wang et al.

Recently, the dominant DETR-based approaches apply central-concept spatial prior to accelerate Transformer detector convergency. These methods gradually refine the reference points to the center of target objects and imbue object queries with the updated central reference information for spatially conditional attention. However, centralizing reference points may severely deteriorate queries' saliency and confuse detectors due to the indiscriminative spatial prior. To bridge the gap between the reference points of salient queries and Transformer detectors, we propose SAlient Point-based DETR (SAP-DETR) by treating object detection as a transformation from salient points to instance objects. In SAP-DETR, we explicitly initialize a query-specific reference point for each object query, gradually aggregate them into an instance object, and then predict the distance from each side of the bounding box to these points. By rapidly attending to query-specific reference region and other conditional extreme regions from the image features, SAP-DETR can effectively bridge the gap between the salient point and the query-based Transformer detector with a significant convergency speed. Our extensive experiments have demonstrated that SAP-DETR achieves 1.4 times convergency speed with competitive performance. Under the standard training scheme, SAP-DETR stably promotes the SOTA approaches by 1.0 AP. Based on ResNet-DC-101, SAP-DETR achieves 46.9 AP.

Adam Ousherovitch, Yixin Wang

Modern learning systems excel at interpolation but struggle to generalize to unseen tasks outside the training distribution's support. This failure occurs even in simple settings, such as handling task parameters beyond the training range, and persists despite advances in foundation models. To this end, we develop the Relational Task Extrapolator (RTE), an algorithm designed to enable systematic extrapolation to novel tasks. The key observation is that extrapolation is inherently relational: extrapolating to unseen tasks requires learning how tasks transform into one another. If a model learns the transformation between tasks A and B during training, it can apply that same transformation to relate known tasks to unseen ones at test time. RTE operationalizes this idea by decomposing each target task into a known anchor task and a transformation linking the anchor and target. It then learns a relational operator, mapping an anchor-transformation pair to predictions for the target task. We instantiate RTE across multiple task extrapolation regimes in function prediction, e.g. where target tasks use out-of-range parameters (parameter extrapolation), have greater compositional depth (length extrapolation), and/or recombine function primitives in unseen ways (compositional extrapolation). We further extend RTE to sequence prediction, integrating it into fine-tuning algorithms for foundation models. Across empirical studies, we find that RTE substantially outperforms existing approaches on extrapolation to novel, unseen tasks.

Yixin Wang, Wei Peng, Susan F. Tapert et al.

Publicly available data sets of structural MRIs might not contain specific measurements of brain Regions of Interests (ROIs) that are important for training machine learning models. For example, the curvature scores computed by Freesurfer are not released by the Adolescent Brain Cognitive Development (ABCD) Study. One can address this issue by simply reapplying Freesurfer to the data set. However, this approach is generally computationally and labor intensive (e.g., requiring quality control). An alternative is to impute the missing measurements via a deep learning approach. However, the state-of-the-art is designed to estimate randomly missing values rather than entire measurements. We therefore propose to re-frame the imputation problem as a prediction task on another (public) data set that contains the missing measurements and shares some ROI measurements with the data sets of interest. A deep learning model is then trained to predict the missing measurements from the shared ones and afterwards is applied to the other data sets. Our proposed algorithm models the dependencies between ROI measurements via a graph neural network (GNN) and accounts for demographic differences in brain measurements (e.g. sex) by feeding the graph encoding into a parallel architecture. The architecture simultaneously optimizes a graph decoder to impute values and a classifier in predicting demographic factors. We test the approach, called Demographic Aware Graph-based Imputation (DAGI), on imputing those missing Freesurfer measurements of ABCD (N=3760) by training the predictor on those publicly released by the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA, N=540)...

Zihao Lin, Haibo Wang, Zhiyang Xu et al.

Music-grounded mashup video creation is a challenging form of video non-linear editing, where a system must compose a coherent timeline from large collections of source videos while aligning with music rhythm, user intent, story completeness, and long-range structural constraints. Existing approaches typically rely on fixed pipelines or simplified retrieval-and-concatenation paradigms, limiting their ability to adapt to diverse prompts and heterogeneous source materials. In this paper, we present GLANCE, a global-local coordination multi-agent framework for music-grounded nonlinear video editing. GLANCE adopts a bi-loop architecture for better editing practice: an outer loop performs long-horizon planning and task-graph construction, and an inner loop adopts the "Observe-Think-Act-Verify" flow for segment-wise editing tasks and their refinements. To address the cross-segment and global conflict emerging after subtimelines composition, we introduce a dedicated global-local coordination mechanism with both preventive and corrective components, which includes a novelly designed context controller, conflict region decomposition module, and a bottom-up dynamic negotiation mechanism. To support rigorous evaluation, we construct MVEBench, a new benchmark that factorizes editing difficulty along task type, prompt specificity, and music length, and propose an agent-as-a-judge evaluation framework for scalable multi-dimensional assessment. Experimental results show that GLANCE consistently outperforms prior research baselines and open-source product baselines under the same backbone models. With GPT-4o-mini as the backbone, GLANCE improves over the strongest baseline by 33.2% and 15.6% on two task settings, respectively. Human evaluation further confirms the quality of the generated videos and validates the effectiveness of the proposed evaluation framework.

Xuan Lu, Wei Ai, Yixin Wang et al.

While many organizations have shifted to working remotely during the COVID-19 pandemic, how the remote workforce and the remote teams are influenced by and would respond to this and future shocks remain largely unknown. Software developers have relied on remote collaborations long before the pandemic, working in virtual teams (GitHub repositories). The dynamics of these repositories through the pandemic provide a unique opportunity to understand how remote teams react under shock. This work presents a systematic analysis. We measure the overall effect of the early pandemic on public GitHub repositories by comparing their sizes and productivity with the counterfactual outcomes forecasted as if there were no pandemic. We find that the productivity level and the number of active members of these teams vary significantly during different periods of the pandemic. We then conduct a finer-grained investigation and study the heterogeneous effects of the shock on individual teams. We find that the resilience of a team is highly correlated to certain properties of the team before the pandemic. Through a bootstrapped regression analysis, we reveal which types of teams are robust or fragile to the shock.

Karl Krauth, Yixin Wang, Michael I. Jordan

Recommender systems play a key role in shaping modern web ecosystems. These systems alternate between (1) making recommendations (2) collecting user responses to these recommendations, and (3) retraining the recommendation algorithm based on this feedback. During this process the recommender system influences the user behavioral data that is subsequently used to update it, thus creating a feedback loop. Recent work has shown that feedback loops may compromise recommendation quality and homogenize user behavior, raising ethical and performance concerns when deploying recommender systems. To address these issues, we propose the Causal Adjustment for Feedback Loops (CAFL), an algorithm that provably breaks feedback loops using causal inference and can be applied to any recommendation algorithm that optimizes a training loss. Our main observation is that a recommender system does not suffer from feedback loops if it reasons about causal quantities, namely the intervention distributions of recommendations on user ratings. Moreover, we can calculate this intervention distribution from observational data by adjusting for the recommender system's predictions of user preferences. Using simulated environments, we demonstrate that CAFL improves recommendation quality when compared to prior correction methods.

Cameron Gruich, Varun Madhavan, Yixin Wang et al.

It is critical that machine learning (ML) model predictions be trustworthy for high-throughput catalyst discovery approaches. Uncertainty quantification (UQ) methods allow estimation of the trustworthiness of an ML model, but these methods have not been well explored in the field of heterogeneous catalysis. Herein, we investigate different UQ methods applied to a crystal graph convolutional neural network (CGCNN) to predict adsorption energies of molecules on alloys from the Open Catalyst 2020 (OC20) dataset, the largest existing heterogeneous catalyst dataset. We apply three UQ methods to the adsorption energy predictions, namely k-fold ensembling, Monte Carlo dropout, and evidential regression. The effectiveness of each UQ method is assessed based on accuracy, sharpness, dispersion, calibration, and tightness. Evidential regression is demonstrated to be a powerful approach for rapidly obtaining tunable, competitively trustworthy UQ estimates for heterogeneous catalysis applications when using neural networks. Recalibration of model uncertainties is shown to be essential in practical screening applications of catalysts using uncertainties.

Celestine Mendler-Dünner, Frances Ding, Yixin Wang

Predictions about people, such as their expected educational achievement or their credit risk, can be performative and shape the outcome that they aim to predict. Understanding the causal effect of these predictions on the eventual outcomes is crucial for foreseeing the implications of future predictive models and selecting which models to deploy. However, this causal estimation task poses unique challenges: model predictions are usually deterministic functions of input features and highly correlated with outcomes. This can make the causal effects of predictions on outcomes impossible to disentangle from the direct effect of the covariates. We study this problem through the lens of causal identifiability, and despite the hardness of this problem in full generality, we highlight three natural scenarios where the causal relationship between covariates, predictions and outcomes can be identified from observational data: randomization in predictions, overparameterization of the predictive model deployed during data collection, and discrete prediction outputs. Empirically we show that given our identifiability conditions hold, standard variants of supervised learning that predict from predictions by treating the prediction as an input feature can indeed find transferable functional relationships that allow for conclusions about newly deployed predictive models. These positive results fundamentally rely on model predictions being recorded during data collection, bringing forward the importance of rethinking standard data collection practices to enable progress towards a better understanding of social outcomes and performative feedback loops.

Eric Czech, Zhiwei Xu, Yael Elmatad et al.

Chinchilla Approach 2 is among the most widely used methods for fitting neural scaling laws. Its parabolic approximation introduces systematic biases in compute-optimal allocation estimates, even on noise-free synthetic data. Applied to published Llama 3 IsoFLOP data at open frontier compute scales, these biases imply a parameter underallocation corresponding to 6.5% of the $3.8\times10^{25}$ FLOP training budget and \$1.4M (90% CI: \$412K-\$2.9M) in unnecessary compute at 50% H100 MFU. Simulated multimodal model misallocations show even greater opportunity costs due to higher loss surface asymmetry. Three sources of this error are examined: IsoFLOP sampling grid width (Taylor approximation accuracy), uncentered IsoFLOP sampling, and loss surface asymmetry ($α\neq β$). Chinchilla Approach 3 largely eliminates these biases but is often regarded as less data-efficient, numerically unstable, prone to local minima, and harder to implement. Each concern is shown to be unfounded or addressable, especially when the partially linear structure of the objective is exploited via Variable Projection, enabling unbiased inference on all five loss surface parameters through a two-dimensional optimization that is well-conditioned, analytically differentiable, and amenable to dense, or even exhaustive, grid search. It may serve as a more convenient replacement for Approach 2 or a more scalable alternative for adaptations of Approach 3 to richer scaling law formulations. See https://github.com/Open-Athena/vpnls for details and https://openathena.ai/scaling-law-analysis for other results from this study.

Paula Gradu, Tijana Zrnic, Yixin Wang et al.

Causal discovery and causal effect estimation are two fundamental tasks in causal inference. While many methods have been developed for each task individually, statistical challenges arise when applying these methods jointly: estimating causal effects after running causal discovery algorithms on the same data leads to "double dipping," invalidating the coverage guarantees of classical confidence intervals. To this end, we develop tools for valid post-causal-discovery inference. Across empirical studies, we show that a naive combination of causal discovery and subsequent inference algorithms leads to highly inflated miscoverage rates; on the other hand, applying our method provides reliable coverage while achieving more accurate causal discovery than data splitting.

Kartik Ahuja, Amin Mansouri, Yixin Wang

Causal representation learning has emerged as the center of action in causal machine learning research. In particular, multi-domain datasets present a natural opportunity for showcasing the advantages of causal representation learning over standard unsupervised representation learning. While recent works have taken crucial steps towards learning causal representations, they often lack applicability to multi-domain datasets due to over-simplifying assumptions about the data; e.g. each domain comes from a different single-node perfect intervention. In this work, we relax these assumptions and capitalize on the following observation: there often exists a subset of latents whose certain distributional properties (e.g., support, variance) remain stable across domains; this property holds when, for example, each domain comes from a multi-node imperfect intervention. Leveraging this observation, we show that autoencoders that incorporate such invariances can provably identify the stable set of latents from the rest across different settings.

Yixin Wang, Wei Peng, Yu Zhang et al.

Many longitudinal neuroimaging studies aim to improve the understanding of brain aging and diseases by studying the dynamic interactions between brain function and cognition. Doing so requires accurate encoding of their multidimensional relationship while accounting for individual variability over time. For this purpose, we propose an unsupervised learning model (called \underline{\textbf{Co}}ntrastive Learning-based \underline{\textbf{Gra}}ph Generalized \underline{\textbf{Ca}}nonical Correlation Analysis (CoGraCa)) that encodes their relationship via Graph Attention Networks and generalized Canonical Correlational Analysis. To create brain-cognition fingerprints reflecting unique neural and cognitive phenotype of each person, the model also relies on individualized and multimodal contrastive learning. We apply CoGraCa to longitudinal dataset of healthy individuals consisting of resting-state functional MRI and cognitive measures acquired at multiple visits for each participant. The generated fingerprints effectively capture significant individual differences and outperform current single-modal and CCA-based multimodal models in identifying sex and age. More importantly, our encoding provides interpretable interactions between those two modalities.

Kush Bhatia, Nikki Lijing Kuang, Yi-An Ma et al.

Variational inference has recently emerged as a popular alternative to the classical Markov chain Monte Carlo (MCMC) in large-scale Bayesian inference. The core idea is to trade statistical accuracy for computational efficiency. In this work, we study these statistical and computational trade-offs in variational inference via a case study in inferential model selection. Focusing on Gaussian inferential models (or variational approximating families) with diagonal plus low-rank precision matrices, we initiate a theoretical study of the trade-offs in two aspects, Bayesian posterior inference error and frequentist uncertainty quantification error. From the Bayesian posterior inference perspective, we characterize the error of the variational posterior relative to the exact posterior. We prove that, given a fixed computation budget, a lower-rank inferential model produces variational posteriors with a higher statistical approximation error, but a lower computational error; it reduces variance in stochastic optimization and, in turn, accelerates convergence. From the frequentist uncertainty quantification perspective, we consider the precision matrix of the variational posterior as an uncertainty estimate, which involves an additional statistical error originating from the sampling uncertainty of the data. As a consequence, for small datasets, the inferential model need not be full-rank to achieve optimal estimation error (even with unlimited computation budget).

Ke Xu, Yixin Wang, Zhongcheng Li et al.

Elastic precision quantization enables multi-bit deployment via a single optimization pass, fitting diverse quantization scenarios.Yet, the high storage and optimization costs associated with the Transformer architecture, research on elastic quantization remains limited, particularly for large language models.This paper proposes QuEPT, an efficient post-training scheme that reconstructs block-wise multi-bit errors with one-shot calibration on a small data slice. It can dynamically adapt to various predefined bit-widths by cascading different low-rank adapters, and supports real-time switching between uniform quantization and mixed precision quantization without repeated optimization. To enhance accuracy and robustness, we introduce Multi-Bit Token Merging (MB-ToMe) to dynamically fuse token features across different bit-widths, improving robustness during bit-width switching. Additionally, we propose Multi-Bit Cascaded Low-Rank adapters (MB-CLoRA) to strengthen correlations between bit-width groups, further improve the overall performance of QuEPT. Extensive experiments demonstrate that QuEPT achieves comparable or better performance to existing state-of-the-art post-training quantization methods.Our code is available at https://github.com/xuke225/QuEPT

Yixin Wang, Zihao Lin, Haoyu Dong

Knowledge Graph (KG) plays a crucial role in Medical Report Generation (MRG) because it reveals the relations among diseases and thus can be utilized to guide the generation process. However, constructing a comprehensive KG is labor-intensive and its applications on the MRG process are under-explored. In this study, we establish a complete KG on chest X-ray imaging that includes 137 types of diseases and abnormalities. Based on this KG, we find that the current MRG data sets exhibit a long-tailed problem in disease distribution. To mitigate this problem, we introduce a novel augmentation strategy that enhances the representation of disease types in the tail-end of the distribution. We further design a two-stage MRG approach, where a classifier is first trained to detect whether the input images exhibit any abnormalities. The classified images are then independently fed into two transformer-based generators, namely, ``disease-specific generator" and ``disease-free generator" to generate the corresponding reports. To enhance the clinical evaluation of whether the generated reports correctly describe the diseases appearing in the input image, we propose diverse sensitivity (DS), a new metric that checks whether generated diseases match ground truth and measures the diversity of all generated diseases. Results show that the proposed two-stage generation framework and augmentation strategies improve DS by a considerable margin, indicating a notable reduction in the long-tailed problem associated with under-represented diseases.

Michael I. Jordan, Yixin Wang, Angela Zhou

We study a constructive algorithm that approximates Gateaux derivatives for statistical functionals by finite differencing, with a focus on functionals that arise in causal inference. We study the case where probability distributions are not known a priori but need to be estimated from data. These estimated distributions lead to empirical Gateaux derivatives, and we study the relationships between empirical, numerical, and analytical Gateaux derivatives. Starting with a case study of the interventional mean (average potential outcome), we delineate the relationship between finite differences and the analytical Gateaux derivative. We then derive requirements on the rates of numerical approximation in perturbation and smoothing that preserve the statistical benefits of one-step adjustments, such as rate double robustness. We then study more complicated functionals such as dynamic treatment regimes, the linear-programming formulation for policy optimization in infinite-horizon Markov decision processes, and sensitivity analysis in causal inference. More broadly, we study optimization-based estimators, since this begets a class of estimands where identification via regression adjustment is straightforward but obtaining influence functions under minor variations thereof is not. The ability to approximate bias adjustments in the presence of arbitrary constraints illustrates the usefulness of constructive approaches for Gateaux derivatives. We also find that the statistical structure of the functional (rate double robustness) can permit less conservative rates for finite-difference approximation. This property, however, can be specific to particular functionals; e.g., it occurs for the average potential outcome (hence average treatment effect) but not the infinite-horizon MDP policy value.

Prayag Chatha, Yixin Wang, Zhenke Wu et al.

In medicine, researchers often seek to infer the effects of a given treatment on patients' outcomes. However, the standard methods for causal survival analysis make simplistic assumptions about the data-generating process and cannot capture complex interactions among patient covariates. We introduce the Dynamic Survival Transformer (DynST), a deep survival model that trains on electronic health records (EHRs). Unlike previous transformers used in survival analysis, DynST can make use of time-varying information to predict evolving survival probabilities. We derive a semi-synthetic EHR dataset from MIMIC-III to show that DynST can accurately estimate the causal effect of a treatment intervention on restricted mean survival time (RMST). We demonstrate that DynST achieves better predictive and causal estimation than two alternative models.

Hengrui Cai, Yixin Wang, Michael Jordan et al.

The causal revolution has stimulated interest in understanding complex relationships in various fields. Most of the existing methods aim to discover causal relationships among all variables within a complex large-scale graph. However, in practice, only a small subset of variables in the graph are relevant to the outcomes of interest. Consequently, causal estimation with the full causal graph -- particularly given limited data -- could lead to numerous falsely discovered, spurious variables that exhibit high correlation with, but exert no causal impact on, the target outcome. In this paper, we propose learning a class of necessary and sufficient causal graphs (NSCG) that exclusively comprises causally relevant variables for an outcome of interest, which we term causal features. The key idea is to employ probabilities of causation to systematically evaluate the importance of features in the causal graph, allowing us to identify a subgraph relevant to the outcome of interest. To learn NSCG from data, we develop a necessary and sufficient causal structural learning (NSCSL) algorithm, by establishing theoretical properties and relationships between probabilities of causation and natural causal effects of features. Across empirical studies of simulated and real data, we demonstrate that NSCSL outperforms existing algorithms and can reveal crucial yeast genes for target heritable traits of interest.

Yuanqiao Zhang, Tiantian He, Yuan Gao et al.

In this paper, we present Federated Robust Curvature Optimization (FedRCO), a novel second-order optimization framework designed to improve convergence speed and reduce communication cost in Federated Learning systems under statistical heterogeneity. Existing second-order optimization methods are often computationally expensive and numerically unstable in distributed settings. In contrast, FedRCO addresses these challenges by integrating an efficient approximate curvature optimizer with a provable stability mechanism. Specifically, FedRCO incorporates three key components: (1) a Gradient Anomaly Monitor that detects and mitigates exploding gradients in real-time, (2) a Fail-Safe Resilience protocol that resets optimization states upon numerical instability, and (3) a Curvature-Preserving Adaptive Aggregation strategy that safely integrates global knowledge without erasing the local curvature geometry. Theoretical analysis shows that FedRCO can effectively mitigate instability and prevent unbounded updates while preserving optimization efficiency. Extensive experiments show that FedRCO achieves superior robustness against diverse non-IID scenarios while achieving higher accuracy and faster convergence than both state-of-the-art first-order and second-order methods.

Zhiyu Xu, Jia Liu, Yixin Wang et al.

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 the evaluation of LLMs, we propose the Latency-Response Theory (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.

Yixin Wang, Ting Gao, Jinqiao Duan

We introduce a framework for analyzing topological tipping in time-evolutionary point clouds by extending the recently proposed Topological Optimal Transport (TpOT) distance. While TpOT unifies geometric, homological, and higher-order relations into one metric, its global scalar distance can obscure transient, localized structural reorganizations during dynamic phase transitions. To overcome this limitation, we present a hierarchical dynamic evaluation framework driven by a novel topological and hypergraph reconstruction strategy. Instead of directly interpolating abstract network parameters, our method interpolates the underlying spatial geometry and rigorously recomputes the valid topological structures, ensuring physical fidelity. Along this geodesic, we introduce a set of multi-scale indicators: macroscopic metrics (Topological Distortion and Persistence Entropy) to capture global shifts, and a novel mesoscopic dual-perspective Hypergraph Entropy (node-perspective and edge-perspective) to detect highly sensitive, asynchronous local rewirings. We further propagate the cycle-level entropy change onto individual vertices to form a point-level topological field. Extensive evaluations on physical dynamical systems (Rayleigh-Van der Pol limit cycles, Double-Well cluster fusion), high-dimensional biological aggregation (D'Orsogna model), and longitudinal stroke fMRI data demonstrate the utility of combining transport-based alignment with multi-scale entropy diagnostics for dynamic topological analysis.

Zilong Bai, Ruiji Zhang, Linqing Chen et al.

In recent years, large language models(LLMs) have attracted significant attention due to their exceptional performance across a multitude of natural language process tasks, and have been widely applied in various fields. However, the application of large language models in the Intellectual Property (IP) domain is challenging due to the strong need for specialized knowledge, privacy protection, processing of extremely long text in this field. In this technical report, we present for the first time a low-cost, standardized procedure for training IP-oriented LLMs, meeting the unique requirements of the IP domain. Using this standard process, we have trained the PatentGPT series models based on open-source pretrained models. By evaluating them on the open-source IP-oriented benchmark MOZIP, our domain-specific LLMs outperforms GPT-4, indicating the effectiveness of the proposed training procedure and the expertise of the PatentGPT models in the IP domain. Remarkably, our model surpassed GPT-4 on the 2019 China Patent Agent Qualification Examination, scoring 65 and matching human expert levels. Additionally, the PatentGPT model, which utilizes the SMoE architecture, achieves performance comparable to that of GPT-4 in the IP domain and demonstrates a better cost-performance ratio on long-text tasks, potentially serving as an alternative to GPT-4 within the IP domain.

Weichi Yao, Bianca Dumitrascu, Bryan R. Goldsmith et al.

Active data acquisition is central to many learning and optimization tasks in deep neural networks, yet remains challenging because most approaches rely on predictive uncertainty estimates that are difficult to obtain reliably. To this end, we propose Goal-Oriented Influence- Maximizing Data Acquisition (GOIMDA), an active acquisition algorithm that avoids explicit posterior inference while remaining uncertainty-aware through inverse curvature. GOIMDA selects inputs by maximizing their expected influence on a user-specified goal functional, such as test loss, predictive entropy, or the value of an optimizer-recommended design. Leveraging first-order influence functions, we derive a tractable acquisition rule that combines the goal gradient, training-loss curvature, and candidate sensitivity to model parameters. We show theoretically that, for generalized linear models, GOIMDA approximates predictive-entropy minimization up to a correction term accounting for goal alignment and prediction bias, thereby, yielding uncertainty-aware behavior without maintaining a Bayesian posterior. Empirically, across learning tasks (including image and text classification) and optimization tasks (including noisy global optimization benchmarks and neural-network hyperparameter tuning), GOIMDA consistently reaches target performance with substantially fewer labeled samples or function evaluations than uncertainty-based active learning and Gaussian-process Bayesian optimization baselines.

Shivam Kumar, Yixin Wang, Lizhen Lin

Flow matching has emerged as a simulation-free alternative to diffusion-based generative modeling, producing samples by solving an ODE whose time-dependent velocity field is learned along an interpolation between a simple source distribution (e.g., a standard normal) and a target data distribution. Flow-based methods often exhibit greater training stability and have achieved strong empirical performance in high-dimensional settings where data concentrate near a low-dimensional manifold, such as text-to-image synthesis, video generation, and molecular structure generation. Despite this success, existing theoretical analyses of flow matching assume target distributions with smooth, full-dimensional densities, leaving its effectiveness in manifold-supported settings largely unexplained. To this end, we theoretically analyze flow matching with linear interpolation when the target distribution is supported on a smooth manifold. We establish a non-asymptotic convergence guarantee for the learned velocity field, and then propagate this estimation error through the ODE to obtain statistical consistency of the implicit density estimator induced by the flow-matching objective. The resulting convergence rate is near minimax-optimal, depends only on the intrinsic dimension, and reflects the smoothness of both the manifold and the target distribution. Together, these results provide a principled explanation for how flow matching adapts to intrinsic data geometry and circumvents the curse of dimensionality.

Yang Liu, Yao Zhang, Yixin Wang et al.

Transformer, an attention-based encoder-decoder model, has already revolutionized the field of natural language processing (NLP). Inspired by such significant achievements, some pioneering works have recently been done on employing Transformer-liked architectures in the computer vision (CV) field, which have demonstrated their effectiveness on three fundamental CV tasks (classification, detection, and segmentation) as well as multiple sensory data stream (images, point clouds, and vision-language data). Because of their competitive modeling capabilities, the visual Transformers have achieved impressive performance improvements over multiple benchmarks as compared with modern Convolution Neural Networks (CNNs). In this survey, we have reviewed over one hundred of different visual Transformers comprehensively according to three fundamental CV tasks and different data stream types, where a taxonomy is proposed to organize the representative methods according to their motivations, structures, and application scenarios. Because of their differences on training settings and dedicated vision tasks, we have also evaluated and compared all these existing visual Transformers under different configurations. Furthermore, we have revealed a series of essential but unexploited aspects that may empower such visual Transformers to stand out from numerous architectures, e.g., slack high-level semantic embeddings to bridge the gap between the visual Transformers and the sequential ones. Finally, three promising research directions are suggested for future investment. We will continue to update the latest articles and their released source codes at https://github.com/liuyang-ict/awesome-visual-transformers.

Victor Veitch, Yixin Wang, David M. Blei

We consider causal inference in the presence of unobserved confounding. We study the case where a proxy is available for the unobserved confounding in the form of a network connecting the units. For example, the link structure of a social network carries information about its members. We show how to effectively use the proxy to do causal inference. The main idea is to reduce the causal estimation problem to a semi-supervised prediction of both the treatments and outcomes. Networks admit high-quality embedding models that can be used for this semi-supervised prediction. We show that the method yields valid inferences under suitable (weak) conditions on the quality of the predictive model. We validate the method with experiments on a semi-synthetic social network dataset. Code is available at github.com/vveitch/causal-network-embeddings.

Hao Liu, Xiao-Wen Yang, Atharva Sehgal et al.

Symbolic regression (SR), the task of discovering mathematical expressions that best describe a given dataset, remains a fundamental challenge in scientific discovery. Traditional approaches, primarily based on genetic algorithms and related evolutionary methods, have proven useful but suffer from scalability and expressivity limitations. Recently, large language model (LLM)-based evolutionary search methods have been introduced into SR and show promise. However, existing LLM-based approaches typically rely on scalar evaluation metrics, such as mean squared error, as the sole source of feedback during the search process, thereby overlooking the rich information embedded in the dataset. To address this limitation, we propose a novel LLM-based evolutionary search framework that incorporates programmatic context augmentation. By enabling code-based interactions with the dataset, our method can actively perform data analysis and extract informative signals, beyond aggregated evaluation scores. We evaluate our framework on advanced benchmarks, such as LLM-SRBench, and demonstrate superior efficiency and accuracy compared to strong baselines.

Laura Manduchi, Clara Meister, Kushagra Pandey et al.

The field of deep generative modeling has grown rapidly in the last few years. With the availability of massive amounts of training data coupled with advances in scalable unsupervised learning paradigms, recent large-scale generative models show tremendous promise in synthesizing high-resolution images and text, as well as structured data such as videos and molecules. However, we argue that current large-scale generative AI models exhibit several fundamental shortcomings that hinder their widespread adoption across domains. In this work, our objective is to identify these issues and highlight key unresolved challenges in modern generative AI paradigms that should be addressed to further enhance their capabilities, versatility, and reliability. By identifying these challenges, we aim to provide researchers with insights for exploring fruitful research directions, thus fostering the development of more robust and accessible generative AI solutions.

Kevin Christian Wibisono, Yixin Wang

Bidirectional attention $\unicode{x2013}$ composed of self-attention with positional encodings and the masked language model (MLM) objective $\unicode{x2013}$ has emerged as a key component of modern large language models (LLMs). Despite its empirical success, few studies have examined its statistical underpinnings: What statistical model is bidirectional attention implicitly fitting? What sets it apart from its non-attention predecessors? We explore these questions in this paper. The key observation is that fitting a single-layer single-head bidirectional attention, upon reparameterization, is equivalent to fitting a continuous bag of words (CBOW) model with mixture-of-experts (MoE) weights. Further, bidirectional attention with multiple heads and multiple layers is equivalent to stacked MoEs and a mixture of MoEs, respectively. This statistical viewpoint reveals the distinct use of MoE in bidirectional attention, which aligns with its practical effectiveness in handling heterogeneous data. It also suggests an immediate extension to categorical tabular data, if we view each word location in a sentence as a tabular feature. Across empirical studies, we find that this extension outperforms existing tabular extensions of transformers in out-of-distribution (OOD) generalization. Finally, this statistical perspective of bidirectional attention enables us to theoretically characterize when linear word analogies are present in its word embeddings. These analyses show that bidirectional attention can require much stronger assumptions to exhibit linear word analogies than its non-attention predecessors.

Shuozhi Zuo, Yixin Wang

Out-of-distribution (OOD) prediction is often approached by restricting models to causal or invariant covariates, avoiding non-causal spurious associations that may be unstable across environments. Despite its theoretical appeal, this strategy frequently underperforms empirical risk minimization (ERM) in practice. We investigate the source of this gap and show that such failures naturally arise when only a subset of the true causes of the outcome is observed. In these settings, non-causal spurious covariates can serve as informative proxies for unobserved causes and substantially improve prediction, except under distribution shifts that break these proxy relationships. Consequently, the optimal set of predictive covariates is neither universal nor necessarily exhibits invariant relationships with the outcome across all environments, but instead depends on the specific type of shift encountered. Crucially, we observe that different covariate shifts induce distinct, observable signatures in the covariate distribution itself. Moreover, these signatures can be extracted from unlabeled data in the target OOD environment and used to assess when proxy covariates remain reliable and when they fail. Building on this observation, we propose an environment-adaptive covariate selection (EACS) algorithm that maps environment-level covariate summaries to environment-specific covariate sets, while allowing the incorporation of prior causal knowledge as constraints. Across simulations and applied datasets, EACS consistently outperforms static causal, invariant, and ERM-based predictors under diverse distribution shifts.

Gabriel Loaiza-Ganem, Valentin Villecroze, Yixin Wang

Quantifying uncertainty in neural networks is a highly relevant problem which is essential to many applications. The two predominant paradigms to tackle this task are Bayesian neural networks (BNNs) and deep ensembles. Despite some similarities between these two approaches, they are typically surmised to lack a formal connection and are thus understood as fundamentally different. BNNs are often touted as more principled due to their reliance on the Bayesian paradigm, whereas ensembles are perceived as more ad-hoc; yet, deep ensembles tend to empirically outperform BNNs, with no satisfying explanation as to why this is the case. In this work we bridge this gap by showing that deep ensembles perform exact Bayesian averaging with a posterior obtained with an implicitly learned data-dependent prior. In other words deep ensembles are Bayesian, or more specifically, they implement an empirical Bayes procedure wherein the prior is learned from the data. This perspective offers two main benefits: (i) it theoretically justifies deep ensembles and thus provides an explanation for their strong empirical performance; and (ii) inspection of the learned prior reveals it is given by a mixture of point masses -- the use of such a strong prior helps elucidate observed phenomena about ensembles. Overall, our work delivers a newfound understanding of deep ensembles which is not only of interest in it of itself, but which is also likely to generate future insights that drive empirical improvements for these models.

Zhiwei Xu, Zhiyu Ni, Yixin Wang et al.

''Grokking'' is a phenomenon where a neural network first memorizes training data and generalizes poorly, but then suddenly transitions to near-perfect generalization after prolonged training. While intriguing, this delayed generalization phenomenon compromises predictability and efficiency. Ideally, models should generalize directly without delay. To this end, this paper proposes GrokTransfer, a simple and principled method for accelerating grokking in training neural networks, based on the key observation that data embedding plays a crucial role in determining whether generalization is delayed. GrokTransfer first trains a smaller, weaker model to reach a nontrivial (but far from optimal) test performance. Then, the learned input embedding from this weaker model is extracted and used to initialize the embedding in the target, stronger model. We rigorously prove that, on a synthetic XOR task where delayed generalization always occurs in normal training, GrokTransfer enables the target model to generalize directly without delay. Moreover, we demonstrate that, across empirical studies of different tasks, GrokTransfer effectively reshapes the training dynamics and eliminates delayed generalization, for both fully-connected neural networks and Transformers.

Kevin Wang, Hongqian Niu, Yixin Wang et al.

Generative networks have shown remarkable success in learning complex data distributions, particularly in generating high-dimensional data from lower-dimensional inputs. While this capability is well-documented empirically, its theoretical underpinning remains unclear. One common theoretical explanation appeals to the widely accepted manifold hypothesis, which suggests that many real-world datasets, such as images and signals, often possess intrinsic low-dimensional geometric structures. Under this manifold hypothesis, it is widely believed that to approximate a distribution on a $d$-dimensional Riemannian manifold, the latent dimension needs to be at least $d$ or $d+1$. In this work, we show that this requirement on the latent dimension is not necessary by demonstrating that generative networks can approximate distributions on $d$-dimensional Riemannian manifolds from inputs of any arbitrary dimension, even lower than $d$, taking inspiration from the concept of space-filling curves. This approach, in turn, leads to a super-exponential complexity bound of the deep neural networks through expanded neurons. Our findings thus challenge the conventional belief on the relationship between input dimensionality and the ability of generative networks to model data distributions. This novel insight not only corroborates the practical effectiveness of generative networks in handling complex data structures, but also underscores a critical trade-off between approximation error, dimensionality, and model complexity.

Bohan Zhang, Yixin Wang, Paramveer S. Dhillon

In this paper, we examine the collaborative dynamics between humans and language models (LMs), where the interactions typically involve LMs proposing text segments and humans editing or responding to these proposals. Productive engagement with LMs in such scenarios necessitates that humans discern effective text-based interaction strategies, such as editing and response styles, from historical human-LM interactions. This objective is inherently causal, driven by the counterfactual `what-if' question: how would the outcome of collaboration change if humans employed a different text editing/refinement strategy? A key challenge in answering this causal inference question is formulating an appropriate causal estimand: the conventional average treatment effect (ATE) estimand is inapplicable to text-based treatments due to their high dimensionality. To address this concern, we introduce a new causal estimand -- Incremental Stylistic Effect (ISE) -- which characterizes the average impact of infinitesimally shifting a text towards a specific style, such as increasing formality. We establish the conditions for the non-parametric identification of ISE. Building on this, we develop CausalCollab, an algorithm designed to estimate the ISE of various interaction strategies in dynamic human-LM collaborations. Our empirical investigations across three distinct human-LM collaboration scenarios reveal that CausalCollab effectively reduces confounding and significantly improves counterfactual estimation over a set of competitive baselines.

Linqing Chen, Weilei Wang, Yubin Xia et al.

In this paper, we propose a novel system that integrates state-of-the-art, domain-specific large language models with advanced information retrieval techniques to deliver comprehensive and context-aware responses. Our approach facilitates seamless interaction among diverse components, enabling cross-validation of outputs to produce accurate, high-quality responses enriched with relevant data, images, tables, and other modalities. We demonstrate the system's capability to enhance response precision by leveraging a robust question-answering model, significantly improving the quality of dialogue generation. The system provides an accessible platform for real-time, high-fidelity interactions, allowing users to benefit from efficient human-computer interaction, precise retrieval, and simultaneous access to a wide range of literature and data. This dramatically improves the research efficiency of professionals in the biomedical and pharmaceutical domains and facilitates faster, more informed decision-making throughout the R\&D process. Furthermore, the system proposed in this paper is available at https://synapse-chat.patsnap.com.

Pengwei Sun, Wei Peng, Lun Yu Li et al.

Counterfactual generation offers a principled framework for simulating hypothetical changes in medical imaging, with potential applications in understanding disease mechanisms and generating physiologically plausible data. However, generating realistic structural 3D brain MRIs that respect anatomical and causal constraints remains challenging due to data scarcity, structural complexity, and the lack of standardized evaluation protocols. In this work, we convert six generative models into 3D counterfactual approaches by incorporating an anatomy-guided framework based on a causal graph, in which regional brain volumes serve as direct conditioning inputs. Each model is evaluated with respect to composition, reversibility, realism, effectiveness and minimality on T1-weighted brain MRIs (T1w MRIs) from the Alzheimer's Disease Neuroimaging Initiative (ADNI). In addition, we test the generalizability of each model with respect to T1w MRIs of the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA). Our results indicate that anatomically grounded conditioning successfully modifies the targeted anatomical regions; however, it exhibits limitations in preserving non-targeted structures. Beyond laying the groundwork for more interpretable and clinically relevant generative modeling of brain MRIs, this benchmark highlights the need for novel architectures that more accurately capture anatomical interdependencies.

Luhuan Wu, Mingzhang Yin, Yixin Wang et al.

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.

Piersilvio De Bartolomeis, Julia Kostin, Javier Abad et al. · eth-zurich

Practical and ethical constraints often require the use of observational data for causal inference, particularly in medicine and social sciences. Yet, observational datasets are prone to confounding, potentially compromising the validity of causal conclusions. While it is possible to correct for biases if the underlying causal graph is known, this is rarely a feasible ask in practical scenarios. A common strategy is to adjust for all available covariates, yet this approach can yield biased treatment effect estimates, especially when post-treatment or unobserved variables are present. We propose RAMEN, an algorithm that produces unbiased treatment effect estimates by leveraging the heterogeneity of multiple data sources without the need to know or learn the underlying causal graph. Notably, RAMEN achieves doubly robust identification: it can identify the treatment effect whenever the causal parents of the treatment or those of the outcome are observed, and the node whose parents are observed satisfies an invariance assumption. Empirical evaluations on synthetic and real-world datasets show that our approach outperforms existing methods.

Kevin Zhang, Yixin Wang

While probabilistic graphical models can discover latent structure in data, their effectiveness hinges on choosing well-specified models. Identifying such models is challenging in practice, often requiring iterative checking and revision through trial and error. To this end, we propose meta-probabilistic modeling (MPM), a meta-learning algorithm that learns generative model structure directly from multiple related datasets. MPM uses a hierarchical architecture where global model specifications are shared across datasets while local parameters remain dataset-specific. For learning and inference, we propose a tractable VAE-inspired surrogate objective, and optimize it through bi-level optimization: local variables are updated analytically via coordinate ascent, while global parameters are trained with gradient-based methods. We evaluate MPM on object-centric image modeling and sequential text modeling, demonstrating that it adapts generative models to data while recovering meaningful latent representations.