arXiv subjects

Yixin Wang

Publications and source records attributed to Yixin Wang.

At least 73 records · Page 4Linked to original sources

arXiv2025

Streamlining Biomedical Research with Specialized LLMs

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.

cs.CL↗

arXiv2025

Deep Generative Models: Complexity, Dimensionality, and Approximation

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.

cs.LG↗

arXiv2025

Policy Learning with a Natural Language Action Space: A Causal Approach

This paper introduces a novel causal framework for multi-stage decision-making in natural language action spaces where outcomes are only observed after a sequence of actions. While recent approaches like Proximal Policy Optimization (PPO) can handle such delayed-reward settings in high-dimensional action spaces, they typically require multiple models (policy, value, and reward) and substantial training data. Our approach employs Q-learning to estimate Dynamic Treatment Regimes (DTR) through a single model, enabling data-efficient policy learning via gradient ascent on language embeddings. A key technical contribution of our approach is a decoding strategy that translates optimized embeddings back into coherent natural language. We evaluate our approach on mental health intervention, hate speech countering, and sentiment transfer tasks, demonstrating significant improvements over competitive baselines across multiple metrics. Notably, our method achieves superior transfer strength while maintaining content preservation and fluency, as validated through human evaluation. Our work provides a practical foundation for learning optimal policies in complex language tasks where training data is limited.

cs.CL↗

arXiv2025

Deep Ensembles Secretly Perform Empirical Bayes

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.

cs.LG↗

arXiv2025

Exponential Family Attention

The self-attention mechanism is the backbone of the transformer neural network underlying most large language models. It can capture complex word patterns and long-range dependencies in natural language. This paper introduces exponential family attention (EFA), a probabilistic generative model that extends self-attention to handle high-dimensional sequence, spatial, or spatial-temporal data of mixed data types, including both discrete and continuous observations. The key idea of EFA is to model each observation conditional on all other existing observations, called the context, whose relevance is learned in a data-driven way via an attention-based latent factor model. In particular, unlike static latent embeddings, EFA uses the self-attention mechanism to capture dynamic interactions in the context, where the relevance of each context observations depends on other observations. We establish an identifiability result and provide a generalization guarantee on excess loss for EFA. Across real-world and synthetic data sets -- including U.S. city temperatures, Instacart shopping baskets, and MovieLens ratings -- we find that EFA consistently outperforms existing models in capturing complex latent structures and reconstructing held-out data.

stat.ML↗

arXiv2024

Posterior Mean Matching: Generative Modeling through Online Bayesian Inference

This paper introduces posterior mean matching (PMM), a new method for generative modeling that is grounded in Bayesian inference. PMM uses conjugate pairs of distributions to model complex data of various modalities like images and text, offering a flexible alternative to existing methods like diffusion models. PMM models iteratively refine noisy approximations of the target distribution using updates from online Bayesian inference. PMM is flexible because its mechanics are based on general Bayesian models. We demonstrate this flexibility by developing specialized examples: a generative PMM model of real-valued data using the Normal-Normal model, a generative PMM model of count data using a Gamma-Poisson model, and a generative PMM model of discrete data using a Dirichlet-Categorical model. For the Normal-Normal PMM model, we establish a direct connection to diffusion models by showing that its continuous-time formulation converges to a stochastic differential equation (SDE). Additionally, for the Gamma-Poisson PMM, we derive a novel SDE driven by a Cox process, which is a significant departure from traditional Brownian motion-based generative models. PMMs achieve performance that is competitive with generative models for language modeling and image generation.

cs.LG↗

arXiv2024

Faster randomized partial trace estimation

We develop randomized matrix-free algorithms for estimating partial traces, a generalization of the trace arising in quantum physics and chemistry. Our algorithm improves on the typicality-based approach used in [T. Chen and Y-C. Cheng, \emph{Numerical computation of the equilibrium-reduced density matrix for strongly coupled open quantum systems}, J. Chem. Phys. 157, 064106 (2022)] by deflating important subspaces (e.g. corresponding to the low-energy eigenstates) explicitly. This results in a significant variance reduction, leading to several order-of-magnitude speedups over the previous state of the art. We then apply our algorithm to study the thermodynamics of several Heisenberg spin systems, particularly the entanglement spectrum and ergotropy.

math.NA↗

arXiv2024

From Unstructured Data to In-Context Learning: Exploring What Tasks Can Be Learned and When

Large language models (LLMs) like transformers demonstrate impressive in-context learning (ICL) capabilities, allowing them to make predictions for new tasks based on prompt exemplars without parameter updates. While existing ICL theories often assume structured training data resembling ICL tasks (e.g., x-y pairs for linear regression), LLMs are typically trained unsupervised on unstructured text, such as web content, which lacks clear parallels to tasks like word analogy. To address this gap, we examine what enables ICL in models trained on unstructured data, focusing on critical sequence model requirements and training data structure. We find that many ICL capabilities can emerge simply from co-occurrence of semantically related word pairs in unstructured data; word analogy completion, for example, can provably arise purely through co-occurrence modeling, using classical language models like continuous bag of words (CBOW), without needing positional information or attention mechanisms. However, positional information becomes crucial for logic reasoning tasks requiring generalization to unseen tokens. Finally, we identify two cases where ICL fails: one in logic reasoning tasks that require generalizing to new, unseen patterns, and another in analogy completion where relevant word pairs appear only in fixed training positions. These findings suggest that LLMs' ICL abilities depend heavily on the structural elements within their training data.

cs.LG↗

arXiv2024

Optimization-based Causal Estimation from Heterogenous Environments

This paper presents a new optimization approach to causal estimation. Given data that contains covariates and an outcome, which covariates are causes of the outcome, and what is the strength of the causality? In classical machine learning (ML), the goal of optimization is to maximize predictive accuracy. However, some covariates might exhibit a non-causal association with the outcome. Such spurious associations provide predictive power for classical ML, but they prevent us from causally interpreting the result. This paper proposes CoCo, an optimization algorithm that bridges the gap between pure prediction and causal inference. CoCo leverages the recently-proposed idea of environments, datasets of covariates/response where the causal relationships remain invariant but where the distribution of the covariates changes from environment to environment. Given datasets from multiple environments-and ones that exhibit sufficient heterogeneity-CoCo maximizes an objective for which the only solution is the causal solution. We describe the theoretical foundations of this approach and demonstrate its effectiveness on simulated and real datasets. Compared to classical ML and existing methods, CoCo provides more accurate estimates of the causal model and more accurate predictions under interventions.

stat.ME↗

arXiv2024

Instrumental Variable Value Iteration for Causal Offline Reinforcement Learning

In offline reinforcement learning (RL) an optimal policy is learned solely from a priori collected observational data. However, in observational data, actions are often confounded by unobserved variables. Instrumental variables (IVs), in the context of RL, are the variables whose influence on the state variables is all mediated by the action. When a valid instrument is present, we can recover the confounded transition dynamics through observational data. We study a confounded Markov decision process where the transition dynamics admit an additive nonlinear functional form. Using IVs, we derive a conditional moment restriction through which we can identify transition dynamics based on observational data. We propose a provably efficient IV-aided Value Iteration (IVVI) algorithm based on a primal-dual reformulation of the conditional moment restriction. To our knowledge, this is the first provably efficient algorithm for instrument-aided offline RL.

stat.ML↗

arXiv2024

MMedAgent: Learning to Use Medical Tools with Multi-modal Agent

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.

cs.CL↗

arXiv2024

Brain-Cognition Fingerprinting via Graph-GCCA with Contrastive Learning

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.

cs.CV↗

arXiv2024

Random Staircase Generator Matrix Codes: Performance Analysis and Construction

In this paper, we propose a class of codes, referred to as random staircase generator matrix codes (SGMCs), which have staircase-like generator matrices. In the infinite-length region, we prove that the random SGMC is capacity-achieving over binary-input output-symmetric (BIOS) channels. In the finite-length region, we present the representative ordered statistics decoding with local constraints (LC-ROSD) algorithm for the SGMCs. The most distinguished feature of the SGMCs with LC-ROSD is that the staircase-like matrices enable parallel implementation of the Gaussian elimination (GE), avoiding the serial GE of conventional OSD and supporting a potential low decoding latency, as implied from simulations. To analyze the performance of random SGMCs in the finite-length region, we derive the ensemble weight spectrum and invoke the conventional union bound. We also derive a partially random coding union (RCU) bound, which is tighter than the conventional one and is used as a criterion to design the SGMCs. Staircase-like generator matrices allow us to derive a series of (tighter and tighter) lower bounds based on the second-order Bonferroni inequality with the incremental number of codewords. The numerical results show that the decoding performance can match well with the proposed partially RCU bound for different code rates and different profiles. The numerical results also show that the tailored SGMCs with the LC-ROSD algorithm can approach the finite-length performance bound, outperforming the 5G low-density parity-check (LDPC) codes, 5G polar codes, and Reed-Muller (RM) codes.

cs.IT↗

arXiv2024

Valid Inference After Causal Discovery

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.

stat.ME↗

arXiv2024

PharmaGPT: Domain-Specific Large Language Models for Bio-Pharmaceutical and Chemistry

Large language models (LLMs) have revolutionized Natural Language Processing (NLP) by minimizing the need for complex feature engineering. However, the application of LLMs in specialized domains like biopharmaceuticals and chemistry remains largely unexplored. These fields are characterized by intricate terminologies, specialized knowledge, and a high demand for precision areas where general purpose LLMs often fall short. In this study, we introduce PharmaGPT, a suite of domain specilized LLMs with 13 billion and 70 billion parameters, specifically trained on a comprehensive corpus tailored to the Bio-Pharmaceutical and Chemical domains. Our evaluation shows that PharmaGPT surpasses existing general models on specific-domain benchmarks such as NAPLEX, demonstrating its exceptional capability in domain-specific tasks. Remarkably, this performance is achieved with a model that has only a fraction, sometimes just one-tenth-of the parameters of general-purpose large models. This advancement establishes a new benchmark for LLMs in the bio-pharmaceutical and chemical fields, addressing the existing gap in specialized language modeling. It also suggests a promising path for enhanced research and development, paving the way for more precise and effective NLP applications in these areas.

cs.CL↗

arXiv2024

Accuracy on the wrong line: On the pitfalls of noisy data for out-of-distribution generalisation

"Accuracy-on-the-line" is a widely observed phenomenon in machine learning, where a model's accuracy on in-distribution (ID) and out-of-distribution (OOD) data is positively correlated across different hyperparameters and data configurations. But when does this useful relationship break down? In this work, we explore its robustness. The key observation is that noisy data and the presence of nuisance features can be sufficient to shatter the Accuracy-on-the-line phenomenon. In these cases, ID and OOD accuracy can become negatively correlated, leading to "Accuracy-on-the-wrong-line". This phenomenon can also occur in the presence of spurious (shortcut) features, which tend to overshadow the more complex signal (core, non-spurious) features, resulting in a large nuisance feature space. Moreover, scaling to larger datasets does not mitigate this undesirable behavior and may even exacerbate it. We formally prove a lower bound on Out-of-distribution (OOD) error in a linear classification model, characterizing the conditions on the noise and nuisance features for a large OOD error. We finally demonstrate this phenomenon across both synthetic and real datasets with noisy data and nuisance features.

cs.LG↗

arXiv2024

Identifying Nonstationary Causal Structures with High-Order Markov Switching Models

Causal discovery in time series is a rapidly evolving field with a wide variety of applications in other areas such as climate science and neuroscience. Traditional approaches assume a stationary causal graph, which can be adapted to nonstationary time series with time-dependent effects or heterogeneous noise. In this work we address nonstationarity via regime-dependent causal structures. We first establish identifiability for high-order Markov Switching Models, which provide the foundations for identifiable regime-dependent causal discovery. Our empirical studies demonstrate the scalability of our proposed approach for high-order regime-dependent structure estimation, and we illustrate its applicability on brain activity data.

stat.ML↗

arXiv2024

LLMs Are Prone to Fallacies in Causal Inference

Recent work shows that causal facts can be effectively extracted from LLMs through prompting, facilitating the creation of causal graphs for causal inference tasks. However, it is unclear if this success is limited to explicitly-mentioned causal facts in the pretraining data which the model can memorize. Thus, this work investigates: Can LLMs infer causal relations from other relational data in text? To disentangle the role of memorized causal facts vs inferred causal relations, we finetune LLMs on synthetic data containing temporal, spatial and counterfactual relations, and measure whether the LLM can then infer causal relations. We find that: (a) LLMs are susceptible to inferring causal relations from the order of two entity mentions in text (e.g. X mentioned before Y implies X causes Y); (b) if the order is randomized, LLMs still suffer from the post hoc fallacy, i.e. X occurs before Y (temporal relation) implies X causes Y. We also find that while LLMs can correctly deduce the absence of causal relations from temporal and spatial relations, they have difficulty inferring causal relations from counterfactuals, questioning their understanding of causality.

cs.CL↗