arXiv subjects

Dianbo Liu

Publications and source records attributed to Dianbo Liu.

At least 55 records · Page 3Linked to original sources

arXiv2026

Early Quantization Shrinks Codebook: A Simple Fix for Diversity-Preserving Tokenization

Vector quantization is a technique in machine learning that discretizes continuous representations into a set of discrete vectors. It is widely employed in tokenizing data representations for large language models, diffusion models, and other generative models. Despite its prevalence, the characteristics and behaviors of vector quantization in generative models remain largely underexplored. In this study, we systematically investigate the issue of collapses in vector quantization, where collapsed representations are observed across discrete codebook tokens and continuous latent embeddings. By leveraging both synthetic and real datasets, we identify the severity of each type of collapses and triggering conditions. Our analysis reveals that random initialization and limited encoder capacity result in tokens collapse and embeddings collapse. Building on these findings, we propose potential solutions aimed at mitigating each collapse. To the best of our knowledge, this is the first comprehensive study examining representation collapsing problems in vector quantization.

cs.LG↗

arXiv2026

Mitigating Premature Discretization with Progressive Quantization for Robust Vector Tokenization

Vector Quantization (VQ) has become the cornerstone of tokenization for many multimodal Large Language Models and diffusion synthesis. However, existing VQ paradigms suffer from a fundamental conflict: they enforce discretization before the encoder has captured the underlying data manifold. We term this phenomenon Premature Discretization. To resolve this, we propose Progressive Quantization (ProVQ), which incorporates the dynamics of quantization hardness as a fundamental yet previously overlooked axis in VQ training. By treating quantization as a curriculum that smoothly anneals from a continuous latent space to a discrete one, ProVQ effectively guides the codebook toward the well-expanded manifolds. Extensive experimental results demonstrate the broad effectiveness of ProVQ across diverse modalities. We report improved reconstruction and generative performance on the ImageNet-1K and ImageNet-100 benchmarks, highlighting the ProVQ's boost for generative modeling. Furthermore, ProVQ proves highly effective for modeling complex biological sequences, establishing a new performance ceiling for protein structure tokenization on the StrutTokenBench leaderboard.

cs.LG↗

arXiv2026

FML-bench: Benchmarking Machine Learning Agents for Scientific Research

Large language models (LLMs) have sparked growing interest in machine learning research agents that can autonomously propose ideas and conduct experiments. However, existing benchmarks predominantly adopt an engineering-oriented perspective: they emphasize application-oriented tasks and evaluate primarily on final performance and computational cost, overlooking agents' research processes and limiting assessment of their capabilities in scientific research settings. To more comprehensively evaluate agents in scientific research settings, we introduce FML-bench, a benchmark comprising 8 diverse and fundamental ML research tasks, and further propose complementary metrics, notably Exploration Diversity, which quantifies the variance of proposals across iterations and reveals how exploration patterns influence research outcomes. We evaluate state-of-the-art research agents on FML-bench, showing that agents employing broad exploration strategies exhibit higher exploration diversity and achieve superior performance, and that exploration diversity positively correlates with performance improvements across multiple tasks. We hope these findings and our benchmark inform future agent design and support the community in further investigating agent behavior. Our benchmark is available at https://github.com/qrzou/FML-bench.

cs.CL↗

arXiv2026

Performance Asymmetry in Model-Based Reinforcement Learning

Recently, Model-Based Reinforcement Learning (MBRL) have achieved super-human level performance on the Atari100k benchmark on average. However, we discover that conventional aggregates mask a major problem, Performance Asymmetry: MBRL agents dramatically outperform humans in certain tasks (Agent-Optimal tasks) while drastically underperform humans in other tasks (Human-Optimal tasks). Indeed, despite achieving SOTA in the overall mean Human-Normalized Scores (HNS), the SOTA agent scored the worst among baselines on Human-Optimal tasks, with a striking 21X performance gap between the Human-Optimal and Agent-Optimal subsets. To address this, we partition Atari100k evenly into Human-Optimal and Agent-Optimal subsets, and introduce a more balanced aggregate, Sym-HNS. Furthermore, we trace the striking Performance Asymmetry in the SOTA pixel diffusion world model to the curse of dimensionality and its prowess on high visual detail tasks (e.g. Breakout). To this end, we propose a novel latent end-to-end Joint Embedding DIffusion (JEDI) world model that achieves SOTA results in Sym-HNS, Human-Optimal tasks, and Breakout -- thus reversing the worsening Performance Asymmetry trend while improving computational efficiency and remaining competitive on the full Atari100k.

cs.LG↗

arXiv2026

Improving Discrete Optimisation Via Decoupled Straight-Through Estimator

The Straight-Through Estimator (STE) is the dominant method for training neural networks with discrete variables, enabling gradient-based optimisation by routing gradients through a differentiable surrogate. However, existing STE variants conflate two fundamentally distinct concerns: forward-pass stochasticity, which controls exploration and latent space utilisation, and backward-pass gradient dispersion i.e how learning signals are distributed across categories. We show that these concerns are qualitatively different and that tying them to a single temperature parameter leaves significant performance gains untapped. We propose Decoupled Straight-Through (Decoupled ST), a minimal modification that introduces separate temperatures for the forward pass ($τ_f$) and the backward pass ($τ_b$). This simple change enables independent tuning of exploration and gradient dispersion. Across three diverse tasks (Stochastic Binary Networks, Categorical Autoencoders, and Differentiable Logic Gate Networks), Decoupled ST consistently outperforms Identity STE, Softmax STE, and Straight-Through Gumbel-Softmax. Crucially, optimal $(τ_f, τ_b)$ configurations lie far off the diagonal $τ_f = τ_b$, confirming that the two concerns do require different answers and that single-temperature methods are fundamentally constrained.

cs.LG↗

arXiv2026

Navigating heterogeneous protein landscapes through geometry-aware smoothing

The evolutionary fitness landscape of biological molecules is extremely sparse and heterogeneous, with functional sequences forming isolated dense ``islands'' within a vast combinatorial space of largely non-functional variants. Protein sequences, in particular, exemplify this structure, yet most generative artificial intelligence models implicitly assume a homogeneous data distribution. We show that this assumption fundamentally breaks down in heterogeneous biological sequence spaces: fixed global noise levels impose a destructive trade-off, either oversmoothing dense functional clusters or fragmenting sparse regions and producing non-functional hallucinations. To address this limitation, we introduce \emph{Density-Dependent Smoothing} (DDS), a geometry-aware generative framework that adapts stochastic smoothing to the local density of the underlying sequence landscape. By inversely coupling diffusion noise to estimated sequence density, DDS enables gentle refinement in high-density functional regions while promoting controlled exploration across sparse regions. Implemented as a plug-in mechanism for discrete molecular sampling, DDS consistently outperforms state-of-the-art diffusion and autoregressive models across antibody repertoires, therapeutic antibody design, antimicrobial peptide generation and coronavirus antibody design. Together, these results show that fixed global smoothing assumptions fundamentally limit generative modeling in sparse biological sequence spaces, and that geometry-aware smoothing removes this constraint, enabling reliable exploration and design previously unattainable with fixed-noise generative models.

cs.CE↗

arXiv2026

AI-generated data contamination erodes pathological variability and diagnostic reliability

Generative artificial intelligence (AI) is rapidly populating medical records with synthetic content, creating a feedback loop where future models are increasingly at risk of training on uncurated AI-generated data. However, the clinical consequences of this AI-generated data contamination remain unexplored. Here, we show that in the absence of mandatory human verification, this self-referential cycle drives a rapid erosion of pathological variability and diagnostic reliability. By analysing more than 800,000 synthetic data points across clinical text generation, vision-language reporting, and medical image synthesis, we find that models progressively converge toward generic phenotypes regardless of the model architecture. Specifically, rare but critical findings, including pneumothorax and effusions, vanish from the synthetic content generated by AI models, while demographic representations skew heavily toward middle-aged male phenotypes. Crucially, this degradation is masked by false diagnostic confidence; models continue to issue reassuring reports while failing to detect life-threatening pathology, with false reassurance rates tripling to 40%. Blinded physician evaluation confirms that this decoupling of confidence and accuracy renders AI-generated documentation clinically useless after just two generations. We systematically evaluate three mitigation strategies, finding that while synthetic volume scaling fails to prevent collapse, mixing real data with quality-aware filtering effectively preserves diversity. Ultimately, our results suggest that without policy-mandated human oversight, the deployment of generative AI threatens to degrade the very healthcare data ecosystems it relies upon.

cs.CY↗

arXiv2026

BayesAgent: Bayesian Agentic Reasoning Under Uncertainty via Verbalized Probabilistic Graphical Modeling

Human cognition excels at transcending sensory input and forming latent representations that structure our understanding of the world. While Large Language Model (LLM) agents demonstrate emergent reasoning and decision-making abilities, they lack a principled framework for capturing latent structures and modeling uncertainty. In this work, we explore for the first time how to bridge LLM agents with probabilistic graphical models (PGMs) to address agentic reasoning under uncertainty. To this end, we introduce Verbalized Probabilistic Graphical Modeling (vPGM), a Bayesian agentic framework that (i) guides LLM agents in following key principles of PGMs through natural language and (ii) refines the resulting posterior distributions via numerical Bayesian inference. Unlike many traditional probabilistic methods requiring substantial domain expertise, vPGM bypasses expert-driven model design, making it well-suited for scenarios with limited assumptions. We evaluated our model on several agentic reasoning tasks, both close-ended and open-ended. Our results indicate that the model effectively enhances confidence calibration and text generation quality.

cs.LG↗

arXiv2025

Deconstructing Generative Diversity: An Information Bottleneck Analysis of Discrete Latent Generative Models

Generative diversity varies significantly across discrete latent generative models such as AR, MIM, and Diffusion. We propose a diagnostic framework, grounded in Information Bottleneck (IB) theory, to analyze the underlying strategies resolving this behavior. The framework models generation as a conflict between a 'Compression Pressure' - a drive to minimize overall codebook entropy - and a 'Diversity Pressure' - a drive to maximize conditional entropy given an input. We further decompose this diversity into two primary sources: 'Path Diversity', representing the choice of high-level generative strategies, and 'Execution Diversity', the randomness in executing a chosen strategy. To make this decomposition operational, we introduce three zero-shot, inference-time interventions that directly perturb the latent generative process and reveal how models allocate and express diversity. Application of this probe-based framework to representative AR, MIM, and Diffusion systems reveals three distinct strategies: "Diversity-Prioritized" (MIM), "Compression-Prioritized" (AR), and "Decoupled" (Diffusion). Our analysis provides a principled explanation for their behavioral differences and informs a novel inference-time diversity enhancement technique.

cs.LG↗

arXiv2025

How does My Model Fail? Automatic Identification and Interpretation of Physical Plausibility Failure Modes with Matryoshka Transcoders

Although recent generative models are remarkably capable of producing instruction-following and realistic outputs, they remain prone to notable physical plausibility failures. Though critical in applications, these physical plausibility errors often escape detection by existing evaluation methods. Furthermore, no framework exists for automatically identifying and interpreting specific physical error patterns in natural language, preventing targeted model improvements. We introduce Matryoshka Transcoders, a novel framework for the automatic discovery and interpretation of physical plausibility features in generative models. Our approach extends the Matryoshka representation learning paradigm to transcoder architectures, enabling hierarchical sparse feature learning at multiple granularity levels. By training on intermediate representations from a physical plausibility classifier and leveraging large multimodal models for interpretation, our method identifies diverse physics-related failure modes without manual feature engineering, achieving superior feature relevance and feature accuracy compared to existing approaches. We utilize the discovered visual patterns to establish a benchmark for evaluating physical plausibility in generative models. Our analysis of eight state-of-the-art generative models provides valuable insights into how these models fail to follow physical constraints, paving the way for further model improvements.

cs.LG↗

arXiv2025

Laplacian Score Sharpening for Mitigating Hallucination in Diffusion Models

Diffusion models, though successful, are known to suffer from hallucinations that create incoherent or unrealistic samples. Recent works have attributed this to the phenomenon of mode interpolation and score smoothening, but they lack a method to prevent their generation during sampling. In this paper, we propose a post-hoc adjustment to the score function during inference that leverages the Laplacian (or sharpness) of the score to reduce mode interpolation hallucination in unconditional diffusion models across 1D, 2D, and high-dimensional image data. We derive an efficient Laplacian approximation for higher dimensions using a finite-difference variant of the Hutchinson trace estimator. We show that this correction significantly reduces the rate of hallucinated samples across toy 1D/2D distributions and a high-dimensional image dataset. Furthermore, our analysis explores the relationship between the Laplacian and uncertainty in the score.

cs.CV↗

arXiv2025

LEME: Open Large Language Models for Ophthalmology with Advanced Reasoning and Clinical Validation

The rising prevalence of eye diseases poses a growing public health burden. Large language models (LLMs) offer a promising path to reduce documentation workload and support clinical decision-making. However, few have been tailored for ophthalmology, and most evaluations focus mainly on knowledge-based QA without clinically relevant benchmarks or real-world validation. Here, we present LEME, a suite of open-weight LLMs developed through a two-stage process: (1) instruction tuning on 200,000 samples from clinical guidelines, textbooks, and case reports to enhance reasoning and task-following, and (2) reinforcement learning with ~30,000 preference labels to enhance accuracy and informativeness. LEME was evaluated on five curated zero-shot benchmarks spanning tasks such as patient QA, consultation, and treatment planning. It outperformed all seven baselines (all p < 0.004), exceeding GPT-4o by 3.32% (absolute ROUGE-L gain). It was further evaluated on three downstream tasks using deidentified patient data, reviewed by clinicians. In patient QA, LEME received the highest ratings from attending clinicians in 3 out of 4 criteria, with scores of 4.67 for factuality, 4.77 for specificity, 4.79 for completeness, and 4.88 for safety (1-5 scale). Its completeness score surpassed that of expert-written answers (4.79 vs. 4.56; p = 0.015). In visual acuity extraction, LEME achieved the highest F1, outperforming LLaMA-3 by 14.1% and Eye-LLaMA by 59.0%. In a pilot evaluation on assessment and treatment planning for diabetic retinopathy, AMD, and glaucoma, LEME received scores of 4.36 for factuality, 4.55 for specificity, 4.42 for completeness, and 4.36 for safety, approaching attending-level performance. All models, data, and code will be released to support further development and clinical translation, laying the groundwork for improved efficiency and patient care

cs.CL↗

arXiv2025

Masked Generative Priors Improve World Models Sequence Modelling Capabilities

Deep Reinforcement Learning (RL) has become the leading approach for creating artificial agents in complex environments. Model-based approaches, which are RL methods with world models that predict environment dynamics, are among the most promising directions for improving data efficiency, forming a critical step toward bridging the gap between research and real-world deployment. In particular, world models enhance sample efficiency by learning in imagination, which involves training a generative sequence model of the environment in a self-supervised manner. Recently, Masked Generative Modelling has emerged as a more efficient and superior inductive bias for modelling and generating token sequences. Building on the Efficient Stochastic Transformer-based World Models (STORM) architecture, we replace the traditional MLP prior with a Masked Generative Prior (e.g., MaskGIT Prior) and introduce GIT-STORM. We evaluate our model on two downstream tasks: reinforcement learning and video prediction. GIT-STORM demonstrates substantial performance gains in RL tasks on the Atari 100k benchmark. Moreover, we apply Transformer-based World Models to continuous action environments for the first time, addressing a significant gap in prior research. To achieve this, we employ a state mixer function that integrates latent state representations with actions, enabling our model to handle continuous control tasks. We validate this approach through qualitative and quantitative analyses on the DeepMind Control Suite, showcasing the effectiveness of Transformer-based World Models in this new domain. Our results highlight the versatility and efficacy of the MaskGIT dynamics prior, paving the way for more accurate world models and effective RL policies.

cs.LG↗

arXiv2025

STORI: A Benchmark and Taxonomy for Stochastic Environments

Reinforcement learning (RL) techniques have achieved impressive performance on simulated benchmarks such as Atari100k, yet recent advances remain largely confined to simulation and show limited transfer to real-world domains. A central obstacle is environmental stochasticity, as real systems involve noisy observations, unpredictable dynamics, and non-stationary conditions that undermine the stability of current methods. Existing benchmarks rarely capture these uncertainties and favor simplified settings where algorithms can be tuned to succeed. The absence of a well-defined taxonomy of stochasticity further complicates evaluation, as robustness to one type of stochastic perturbation, such as sticky actions, does not guarantee robustness to other forms of uncertainty. To address this critical gap, we introduce STORI (STOchastic-ataRI), a benchmark that systematically incorporates diverse stochastic effects and enables rigorous evaluation of RL techniques under different forms of uncertainty. We propose a comprehensive five-type taxonomy of environmental stochasticity and demonstrate systematic vulnerabilities in state-of-the-art model-based RL algorithms through targeted evaluation of DreamerV3 and STORM. Our findings reveal that world models dramatically underestimate environmental variance, struggle with action corruption, and exhibit unreliable dynamics under partial observability. We release the code and benchmark publicly at https://github.com/ARY2260/stori, providing a unified framework for developing more robust RL systems.

cs.LG↗

arXiv2025

Attention Schema-based Attention Control (ASAC): A Cognitive-Inspired Approach for Attention Management in Transformers

Attention mechanisms have become integral in AI, significantly enhancing model performance and scalability by drawing inspiration from human cognition. Concurrently, the Attention Schema Theory (AST) in cognitive science posits that individuals manage their attention by creating a model of the attention itself, effectively allocating cognitive resources. Inspired by AST, we introduce ASAC (Attention Schema-based Attention Control), which integrates the attention schema concept into artificial neural networks. Our initial experiments focused on embedding the ASAC module within transformer architectures. This module employs a Vector-Quantized Variational AutoEncoder (VQVAE) as both an attention abstractor and controller, facilitating precise attention management. By explicitly modeling attention allocation, our approach aims to enhance system efficiency. We demonstrate ASAC's effectiveness in both the vision and NLP domains, highlighting its ability to improve classification accuracy and expedite the learning process. Our experiments with vision transformers across various datasets illustrate that the attention controller not only boosts classification accuracy but also accelerates learning. Furthermore, we have demonstrated the model's robustness and generalization capabilities across noisy and out-of-distribution datasets. In addition, we have showcased improved performance in multi-task settings. Quick experiments reveal that the attention schema-based module enhances resilience to adversarial attacks, optimizes attention to improve learning efficiency, and facilitates effective transfer learning and learning from fewer examples. These promising results establish a connection between cognitive science and machine learning, shedding light on the efficient utilization of attention mechanisms in AI systems.

cs.AI↗

arXiv2025

Data-Dependent Smoothing for Protein Discovery with Walk-Jump Sampling

Diffusion models have emerged as a powerful class of generative models by learning to iteratively reverse the noising process. Their ability to generate high-quality samples has extended beyond high-dimensional image data to other complex domains such as proteins, where data distributions are typically sparse and unevenly spread. Importantly, the sparsity itself is uneven. Empirically, we observed that while a small fraction of samples lie in dense clusters, the majority occupy regions of varying sparsity across the data space. Existing approaches largely ignore this data-dependent variability. In this work, we introduce a Data-Dependent Smoothing Walk-Jump framework that employs kernel density estimation (KDE) as a preprocessing step to estimate the noise scale $σ$ for each data point, followed by training a score model with these data-dependent $σ$ values. By incorporating local data geometry into the denoising process, our method accounts for the heterogeneous distribution of protein data. Empirical evaluations demonstrate that our approach yields consistent improvements across multiple metrics, highlighting the importance of data-aware sigma prediction for generative modeling in sparse, high-dimensional settings.

cs.LG↗

arXiv2025

BEnchmarking LLMs for Ophthalmology (BELO) for Ophthalmological Knowledge and Reasoning

Current benchmarks evaluating large language models (LLMs) in ophthalmology are limited in scope and disproportionately prioritise accuracy. We introduce BELO (BEnchmarking LLMs for Ophthalmology), a standardized and comprehensive evaluation benchmark developed through multiple rounds of expert checking by 13 ophthalmologists. BELO assesses ophthalmology-related clinical accuracy and reasoning quality. Using keyword matching and a fine-tuned PubMedBERT model, we curated ophthalmology-specific multiple-choice-questions (MCQs) from diverse medical datasets (BCSC, MedMCQA, MedQA, BioASQ, and PubMedQA). The dataset underwent multiple rounds of expert checking. Duplicate and substandard questions were systematically removed. Ten ophthalmologists refined the explanations of each MCQ's correct answer. This was further adjudicated by three senior ophthalmologists. To illustrate BELO's utility, we evaluated six LLMs (OpenAI o1, o3-mini, GPT-4o, DeepSeek-R1, Llama-3-8B, and Gemini 1.5 Pro) using accuracy, macro-F1, and five text-generation metrics (ROUGE-L, BERTScore, BARTScore, METEOR, and AlignScore). In a further evaluation involving human experts, two ophthalmologists qualitatively reviewed 50 randomly selected outputs for accuracy, comprehensiveness, and completeness. BELO consists of 900 high-quality, expert-reviewed questions aggregated from five sources: BCSC (260), BioASQ (10), MedMCQA (572), MedQA (40), and PubMedQA (18). A public leaderboard has been established to promote transparent evaluation and reporting. Importantly, the BELO dataset will remain a hold-out, evaluation-only benchmark to ensure fair and reproducible comparisons of future models.

cs.CL↗

arXiv2025

Evolution Guided Generative Flow Networks

Generative Flow Networks (GFlowNets) are a family of probabilistic generative models that learn to sample compositional objects proportional to their rewards. One big challenge of GFlowNets is training them effectively when dealing with long time horizons and sparse rewards. To address this, we propose Evolution guided generative flow networks (EGFN), a simple but powerful augmentation to the GFlowNets training using Evolutionary algorithms (EA). Our method can work on top of any GFlowNets training objective, by training a set of agent parameters using EA, storing the resulting trajectories in the prioritized replay buffer, and training the GFlowNets agent using the stored trajectories. We present a thorough investigation over a wide range of toy and real-world benchmark tasks showing the effectiveness of our method in handling long trajectories and sparse rewards. We release the code at http://github.com/zarifikram/egfn.

cs.LG↗