Pengtao Xie

Ce Zhou, Qian Li, Chen Li et al. · allen-ai

Pretrained Foundation Models (PFMs) are regarded as the foundation for various downstream tasks with different data modalities. A PFM (e.g., BERT, ChatGPT, and GPT-4) is trained on large-scale data which provides a reasonable parameter initialization for a wide range of downstream applications. BERT learns bidirectional encoder representations from Transformers, which are trained on large datasets as contextual language models. Similarly, the generative pretrained transformer (GPT) method employs Transformers as the feature extractor and is trained using an autoregressive paradigm on large datasets. Recently, ChatGPT shows promising success on large language models, which applies an autoregressive language model with zero shot or few shot prompting. The remarkable achievements of PFM have brought significant breakthroughs to various fields of AI. Numerous studies have proposed different methods, raising the demand for an updated survey. This study provides a comprehensive review of recent research advancements, challenges, and opportunities for PFMs in text, image, graph, as well as other data modalities. The review covers the basic components and existing pretraining methods used in natural language processing, computer vision, and graph learning. Additionally, it explores advanced PFMs used for different data modalities and unified PFMs that consider data quality and quantity. The review also discusses research related to the fundamentals of PFMs, such as model efficiency and compression, security, and privacy. Finally, the study provides key implications, future research directions, challenges, and open problems in the field of PFMs. Overall, this survey aims to shed light on the research of the PFMs on scalability, security, logical reasoning ability, cross-domain learning ability, and the user-friendly interactive ability for artificial general intelligence.

Sang Keun Choe, Willie Neiswanger, Pengtao Xie et al.

Gradient-based multilevel optimization (MLO) has gained attention as a framework for studying numerous problems, ranging from hyperparameter optimization and meta-learning to neural architecture search and reinforcement learning. However, gradients in MLO, which are obtained by composing best-response Jacobians via the chain rule, are notoriously difficult to implement and memory/compute intensive. We take an initial step towards closing this gap by introducing Betty, a software library for large-scale MLO. At its core, we devise a novel dataflow graph for MLO, which allows us to (1) develop efficient automatic differentiation for MLO that reduces the computational complexity from O(d^3) to O(d^2), (2) incorporate systems support such as mixed-precision and data-parallel training for scalability, and (3) facilitate implementation of MLO programs of arbitrary complexity while allowing a modular interface for diverse algorithmic and systems design choices. We empirically demonstrate that Betty can be used to implement an array of MLO programs, while also observing up to 11% increase in test accuracy, 14% decrease in GPU memory usage, and 20% decrease in training wall time over existing implementations on multiple benchmarks. We also showcase that Betty enables scaling MLO to models with hundreds of millions of parameters. We open-source the code at https://github.com/leopard-ai/betty.

Sang Keun Choe, Sanket Vaibhav Mehta, Hwijeen Ahn et al. · deepmind

Despite its flexibility to learn diverse inductive biases in machine learning programs, meta learning (i.e., learning to learn) has long been recognized to suffer from poor scalability due to its tremendous compute/memory costs, training instability, and a lack of efficient distributed training support. In this work, we focus on making scalable meta learning practical by introducing SAMA, which combines advances in both implicit differentiation algorithms and systems. Specifically, SAMA is designed to flexibly support a broad range of adaptive optimizers in the base level of meta learning programs, while reducing computational burden by avoiding explicit computation of second-order gradient information, and exploiting efficient distributed training techniques implemented for first-order gradients. Evaluated on multiple large-scale meta learning benchmarks, SAMA showcases up to 1.7/4.8x increase in throughput and 2.0/3.8x decrease in memory consumption respectively on single-/multi-GPU setups compared to other baseline meta learning algorithms. Furthermore, we show that SAMA-based data optimization leads to consistent improvements in text classification accuracy with BERT and RoBERTa large language models, and achieves state-of-the-art results in both small- and large-scale data pruning on image classification tasks, demonstrating the practical applicability of scalable meta learning across language and vision domains.

Duy M. H. Nguyen, Hoang Nguyen, Nghiem T. Diep et al. · eth-zurich

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

Duy M. H. Nguyen, Hoang Nguyen, Mai T. N. Truong et al. · eth-zurich

Collecting large-scale medical datasets with fully annotated samples for training of deep networks is prohibitively expensive, especially for 3D volume data. Recent breakthroughs in self-supervised learning (SSL) offer the ability to overcome the lack of labeled training samples by learning feature representations from unlabeled data. However, most current SSL techniques in the medical field have been designed for either 2D images or 3D volumes. In practice, this restricts the capability to fully leverage unlabeled data from numerous sources, which may include both 2D and 3D data. Additionally, the use of these pre-trained networks is constrained to downstream tasks with compatible data dimensions. In this paper, we propose a novel framework for unsupervised joint learning on 2D and 3D data modalities. Given a set of 2D images or 2D slices extracted from 3D volumes, we construct an SSL task based on a 2D contrastive clustering problem for distinct classes. The 3D volumes are exploited by computing vectored embedding at each slice and then assembling a holistic feature through deformable self-attention mechanisms in Transformer, allowing incorporating long-range dependencies between slices inside 3D volumes. These holistic features are further utilized to define a novel 3D clustering agreement-based SSL task and masking embedding prediction inspired by pre-trained language models. Experiments on downstream tasks, such as 3D brain segmentation, lung nodule detection, 3D heart structures segmentation, and abnormal chest X-ray detection, demonstrate the effectiveness of our joint 2D and 3D SSL approach. We improve plain 2D Deep-ClusterV2 and SwAV by a significant margin and also surpass various modern 2D and 3D SSL approaches.

Peijia Qin, Qi Cao, Pengtao Xie

Test-time scaling has become a major way to improve large language model reasoning, but its orchestration has remained designer-engineered: a fixed sample budget, a fixed refinement loop, a fixed scoring rule, or a fixed search policy decides how compute is spent, leaving the model in charge of solving but not of orchestration. We introduce ATLAS, an agentic test-time scaling framework in which an LLM orchestrator owns the control loop end-to-end. Through a single action, explore, which dispatches a fresh independent solver on the original problem, the orchestrator decides whether to gather more evidence, when to stop, and how to synthesize the final answer; the action space is extensible, with each explore call optionally specifying solver, reasoning effort, or prompting strategy. We evaluate ATLAS on four benchmarks covering scientific question answering, code generation, and multimodal reasoning under a Claude Sonnet 4.6 backbone, where it reaches 56.00% on HLE-Verified, 82.29% on LiveCodeBench, 85.75% on GPQA-Diamond, and 23.71% on BabyVision while using far fewer API calls than fixed-workflow baselines. A multi-model extension, ATLAS-MM, that exposes solver choice as an additional action dimension further improves HLE-Verified to 60.00% and LiveCodeBench to 85.63%, with consistent gains on GPQA-Diamond and BabyVision. Ablations replacing the orchestrator's direct synthesis with a separate integrator degrade or fail to improve accuracy on three of four benchmarks, consistent with the role of stateful evidence management in producing the gains.

Ruiyi Zhang, Peijia Qin, Qi Cao et al.

AI models underpin data-centric applications from image and text processing to scientific discovery in biology, physics, and chemistry. Yet developing them remains heavily manual, requiring practitioners to design architectures, build training pipelines, and iteratively refine solutions, making it challenging for natural scientists without specialized AI engineering expertise to build the high-performing models their research demands. To reduce this burden and broaden access to AI for scientific discovery, agents that automatically build AI models have been proposed. However, the performance of these agents is largely limited by the parametric knowledge of their underlying large language models, which is static, often outdated, and sparse on practical AI model engineering know-how. To address this limitation, we introduce AIBuildAI-2, a knowledge-enhanced agent with an external, evolving knowledge system for automatically building AI models. The knowledge system of AIBuildAI-2 is hierarchical, organizing curated AI development knowledge into high-level knowledge instructions over topical categories and low-level knowledge documents under each category, from which the agent dynamically loads only the context relevant to its current state and the AI task being solved, grounding each design and implementation decision in concrete, externally verifiable expertise. The system is initialized by collecting and cleaning AI-development-related documents from the web and organizing them into the corresponding categories, and continually evolves from the agent's own experience by distilling each completed run on an AI task into structured takeaways that are written back into the knowledge system. AIBuildAI-2 achieves state-of-the-art results, ranking first on MLE-Bench with a 70.7% medal rate and placing in the top 6.6% among 4,370 human-expert teams in a heart disease prediction competition.

Guiyao Tie, Jiawen Shi, Dingjie Song et al.

Scientific research is being reshaped by AI systems that move beyond isolated assistance toward longer-horizon workflows spanning literature grounding, hypothesis generation, experimentation, validation, reporting, and revision. This shift marks a transition from task-level AI for science to workflow-level research automation. Yet current systems remain fragmented, differing in autonomy, domain scope, execution environment, validation mechanism, and human oversight, while still struggling with evidence preservation, reproducibility, weak-direction rejection, provenance tracking, cross-domain robustness, and accountable scientific closure. This survey examines these developments through AutoResearch, defined as the developmental spectrum of AI-powered scientific workflow automation. Within it, Vibe Research denotes the human-steered region of prompt-based assistance and human-verified execution, whereas emerging AI-led systems coordinate larger portions of the discovery loop without achieving robust autonomy. We analyze how research systems redistribute control, evidence, execution, validation, and accountability across workflows and organize the field around five workflow conditions: literature and research grounding; hypothesis formation and planning; experimentation and tool use; feedback, validation, and review; and reporting and knowledge communication. We further synthesize AI scientist systems, mixed-initiative co-research frameworks, benchmarks, domain deployments, and open-source infrastructures. Finally, we propose five evaluation dimensions--novelty, validity, impact, reliability, and provenance--and show that AutoResearch autonomy is domain-conditioned, being more credible in structured, executable, and rapidly verifiable settings but limited in embodied, delayed, heterogeneous, ethical, or institutionally accountable contexts.

Xin Gao, Ruiyi Zhang, Meixi Du et al.

Despite the success of large language models (LLMs) on general-purpose tasks, their performance in highly specialized domains such as biomedicine remains unsatisfactory. A key limitation is the inability of LLMs to effectively leverage biomedical tools, which clinical experts and biomedical researchers rely on extensively in daily workflows. While recent general-domain tool-calling datasets have substantially improved the capabilities of LLM agents, existing efforts in the biomedical domain largely rely on in-context learning and restrict models to a small set of tools. To address this gap, we introduce BioTool, a comprehensive biomedical tool-calling dataset designed for fine-tuning LLMs. BioTool comprises 34 frequently used tools collected from the NCBI, Ensembl, and UniProt databases, along with 7,040 high-quality, human-verified query-API call pairs spanning variation, genomics, proteomics, evolution, and general biology. Fine-tuning a 4-billion-parameter LLM on BioTool yields substantial improvements in biomedical tool-calling performance, outperforming cutting-edge commercial LLMs such as GPT-5.1. Furthermore, human expert evaluations demonstrate that integrating a BioTool-fine-tuned tool caller significantly improves downstream answer quality compared to the same LLM without tool usage, highlighting the effectiveness of BioTool in enhancing the biomedical capabilities of LLMs. The full dataset and evaluation code are available at https://github.com/gxx27/BioTool

Youwei Liang, Kevin Stone, Ali Shameli et al.

Finding the optimal pass sequence of compilation can lead to a significant reduction in program size and/or improvement in program efficiency. Prior works on compilation pass ordering have two major drawbacks. They either require an excessive budget (in terms of compilation steps) at compile time or fail to generalize to unseen programs. In this paper, for code-size reduction tasks, we propose a novel pipeline to find program-dependent pass sequences within 45 compilation calls. It first identifies a coreset of 50 pass sequences via greedy optimization of a submodular function, and then learns a policy with Graph Neural Network (GNN) to pick the optimal sequence by predicting the normalized values of the pass sequences in the coreset. Despite its simplicity, our pipeline outperforms the default -Oz flag by an average of 4.7% over a large collection (4683) of unseen code repositories from diverse domains across 14 datasets. In comparison, previous approaches like reinforcement learning on the raw pass sequence space may take days to train due to sparse reward, and may not generalize well in held-out ones from different domains. Our results demonstrate that existing human-designed compiler flags can be improved with a simple yet effective technique that transforms the raw action space into a small one with denser rewards.

Li Zhang, Basu Jindal, Ahmed Alaa et al.

Semantic segmentation of medical images is pivotal in applications like disease diagnosis and treatment planning. While deep learning has excelled in automating this task, a major hurdle is the need for numerous annotated segmentation masks, which are resource-intensive to produce due to the required expertise and time. This scenario often leads to ultra low-data regimes, where annotated images are extremely limited, posing significant challenges for the generalization of conventional deep learning methods on test images. To address this, we introduce a generative deep learning framework, which uniquely generates high-quality paired segmentation masks and medical images, serving as auxiliary data for training robust models in data-scarce environments. Unlike traditional generative models that treat data generation and segmentation model training as separate processes, our method employs multi-level optimization for end-to-end data generation. This approach allows segmentation performance to directly influence the data generation process, ensuring that the generated data is specifically tailored to enhance the performance of the segmentation model. Our method demonstrated strong generalization performance across 9 diverse medical image segmentation tasks and on 16 datasets, in ultra-low data regimes, spanning various diseases, organs, and imaging modalities. When applied to various segmentation models, it achieved performance improvements of 10-20\% (absolute), in both same-domain and out-of-domain scenarios. Notably, it requires 8 to 20 times less training data than existing methods to achieve comparable results. This advancement significantly improves the feasibility and cost-effectiveness of applying deep learning in medical imaging, particularly in scenarios with limited data availability.

Qian Li, Jianxin Li, Lihong Wang et al.

Event detection in power systems aims to identify triggers and event types, which helps relevant personnel respond to emergencies promptly and facilitates the optimization of power supply strategies. However, the limited length of short electrical record texts causes severe information sparsity, and numerous domain-specific terminologies of power systems makes it difficult to transfer knowledge from language models pre-trained on general-domain texts. Traditional event detection approaches primarily focus on the general domain and ignore these two problems in the power system domain. To address the above issues, we propose a Multi-Channel graph neural network utilizing Type information for Event Detection in power systems, named MC-TED, leveraging a semantic channel and a topological channel to enrich information interaction from short texts. Concretely, the semantic channel refines textual representations with semantic similarity, building the semantic information interaction among potential event-related words. The topological channel generates a relation-type-aware graph modeling word dependencies, and a word-type-aware graph integrating part-of-speech tags. To further reduce errors worsened by professional terminologies in type analysis, a type learning mechanism is designed for updating the representations of both the word type and relation type in the topological channel. In this way, the information sparsity and professional term occurrence problems can be alleviated by enabling interaction between topological and semantic information. Furthermore, to address the lack of labeled data in power systems, we built a Chinese event detection dataset based on electrical Power Event texts, named PoE. In experiments, our model achieves compelling results not only on the PoE dataset, but on general-domain event detection datasets including ACE 2005 and MAVEN.

Shuhao Zhang, Jiarui Li, Qi Cao et al.

Prompt-injection detectors are heterogeneous: each is strong on a different slice of attacks, and none is always reliable. Yet existing systems still treat detection as a fixed single-detector pipeline, committing every request to one detector's blind spots. We reframe defense as detector allocation: given a heterogeneous pool, decide per request which detectors to run and whether to escalate to an LLM judge. Our framework SCOUT (Scalable and Controllable Outcome-prediction for Uncertainty-aware Triage) makes this decision dynamic by predicting each detector's per-sample reliability and latency from how it behaved on similar past inputs, and exposes a single safety-utility threshold to the operator (where utility bundles benign-pass rate and wall-clock). To evaluate this setting, we build SCOUT-450, a benchmark that captures the structurally complex, agent-facing injections that older prompt-injection sets under-represent. On SCOUT-450, a safety-oriented operating point reduces attack-success rate by 46% and total wall-clock by 40% relative to an always-on GPT-4o judge, at a 5.1-point benign-utility drop. SCOUT also transfers to three external benchmarks (BIPIA, IPI, and IHEval), improving the safety-utility frontier.

Hasan Md Tusfiqur, Duy M. H. Nguyen, Mai T. N. Truong et al.

Diabetic Retinopathy (DR) is a leading cause of vision loss in the world, and early DR detection is necessary to prevent vision loss and support an appropriate treatment. In this work, we leverage interactive machine learning and introduce a joint learning framework, termed DRG-Net, to effectively learn both disease grading and multi-lesion segmentation. Our DRG-Net consists of two modules: (i) DRG-AI-System to classify DR Grading, localize lesion areas, and provide visual explanations; (ii) DRG-Expert-Interaction to receive feedback from user-expert and improve the DRG-AI-System. To deal with sparse data, we utilize transfer learning mechanisms to extract invariant feature representations by using Wasserstein distance and adversarial learning-based entropy minimization. Besides, we propose a novel attention strategy at both low- and high-level features to automatically select the most significant lesion information and provide explainable properties. In terms of human interaction, we further develop DRG-Net as a tool that enables expert users to correct the system's predictions, which may then be used to update the system as a whole. Moreover, thanks to the attention mechanism and loss functions constraint between lesion features and classification features, our approach can be robust given a certain level of noise in the feedback of users. We have benchmarked DRG-Net on the two largest DR datasets, i.e., IDRID and FGADR, and compared it to various state-of-the-art deep learning networks. In addition to outperforming other SOTA approaches, DRG-Net is effectively updated using user feedback, even in a weakly-supervised manner.

Ramtin Hosseini, Li Zhang, Bhanu Garg et al.

The integration of machine learning models in various real-world applications is becoming more prevalent to assist humans in their daily decision-making tasks as a result of recent advancements in this field. However, it has been discovered that there is a tradeoff between the accuracy and fairness of these decision-making tasks. In some cases, these AI systems can be unfair by exhibiting bias or discrimination against certain social groups, which can have severe consequences in real life. Inspired by one of the most well-known human learning skills called grouping, we address this issue by proposing a novel machine learning framework where the ML model learns to group a diverse set of problems into distinct subgroups to solve each subgroup using its specific sub-model. Our proposed framework involves three stages of learning, which are formulated as a three-level optimization problem: (i) learning to group problems into different subgroups; (ii) learning group-specific sub-models for problem-solving; and (iii) updating group assignments of training examples by minimizing the validation loss. These three learning stages are performed end-to-end in a joint manner using gradient descent. To improve fairness and accuracy, we develop an efficient optimization algorithm to solve this three-level optimization problem. To further reduce the risk of overfitting in small datasets, we incorporate domain adaptation techniques in the second stage of training. We further apply our method to neural architecture search. Extensive experiments on various datasets demonstrate our method's effectiveness and performance improvements in both fairness and accuracy. Our proposed Learning by Grouping can reduce overfitting and achieve state-of-the-art performances with fixed human-designed network architectures and searchable network architectures on various datasets.

Duy Minh Ho Nguyen, Tan Ngoc Pham, Nghiem Tuong Diep et al.

Constructing a robust model that can effectively generalize to test samples under distribution shifts remains a significant challenge in the field of medical imaging. The foundational models for vision and language, pre-trained on extensive sets of natural image and text data, have emerged as a promising approach. It showcases impressive learning abilities across different tasks with the need for only a limited amount of annotated samples. While numerous techniques have focused on developing better fine-tuning strategies to adapt these models for specific domains, we instead examine their robustness to domain shifts in the medical image segmentation task. To this end, we compare the generalization performance to unseen domains of various pre-trained models after being fine-tuned on the same in-distribution dataset and show that foundation-based models enjoy better robustness than other architectures. From here, we further developed a new Bayesian uncertainty estimation for frozen models and used them as an indicator to characterize the model's performance on out-of-distribution (OOD) data, proving particularly beneficial for real-world applications. Our experiments not only reveal the limitations of current indicators like accuracy on the line or agreement on the line commonly used in natural image applications but also emphasize the promise of the introduced Bayesian uncertainty. Specifically, lower uncertainty predictions usually tend to higher out-of-distribution (OOD) performance.

Ruiyi Zhang, Peijia Qin, Qi Cao et al.

AI models underpin modern intelligent systems, driving advances across science, medicine, finance, and technology. Yet developing high-performing AI models remains a labor-intensive process that requires expert practitioners to iteratively design architectures, engineer representations, implement training pipelines and refine approaches through empirical evaluation. Existing AutoML methods partially alleviate this burden but remain limited to narrow aspects such as hyperparameter optimization and model selection within predefined search spaces, leaving the full development lifecycle largely dependent on human expertise. To address this gap, we introduce AIBuildAI, an AI agent that automatically builds AI models from a task description and training data. AIBuildAI adopts a hierarchical agent architecture in which a manager agent coordinates three specialized sub-agents: a designer for modeling strategy, a coder for implementation and debugging, and a tuner for training and performance optimization. Each sub-agent is itself a large language model (LLM) based agent capable of multi-step reasoning and tool use, enabling end-to-end automation of the AI model development process that goes beyond the scope of existing AutoML approaches. We evaluate AIBuildAI on MLE-Bench, a benchmark of realistic Kaggle-style AI development tasks spanning visual, textual, time-series and tabular modalities. AIBuildAI ranks first on MLE-Bench with a medal rate of 63.1%, outperforming all existing baseline methods and matching the capability of highly experienced AI engineers. These results demonstrate that hierarchical agent systems can automate the full AI model development process from task specification to deployable model, suggesting a pathway toward broadly accessible AI development with minimal human intervention.

Mingjia Huo, Sai Ashish Somayajula, Youwei Liang et al.

Large language models generate high-quality responses with potential misinformation, underscoring the need for regulation by distinguishing AI-generated and human-written texts. Watermarking is pivotal in this context, which involves embedding hidden markers in texts during the LLM inference phase, which is imperceptible to humans. Achieving both the detectability of inserted watermarks and the semantic quality of generated texts is challenging. While current watermarking algorithms have made promising progress in this direction, there remains significant scope for improvement. To address these challenges, we introduce a novel multi-objective optimization (MOO) approach for watermarking that utilizes lightweight networks to generate token-specific watermarking logits and splitting ratios. By leveraging MOO to optimize for both detection and semantic objective functions, our method simultaneously achieves detectability and semantic integrity. Experimental results show that our method outperforms current watermarking techniques in enhancing the detectability of texts generated by LLMs while maintaining their semantic coherence. Our code is available at https://github.com/mignonjia/TS_watermark.

Kaitong Cai, Jusheng Zhang, Jing Yang et al.

Large vision-language models (VLMs) typically process hundreds or thousands of visual tokens per image or video frame, incurring quadratic attention cost and substantial redundancy. Existing token reduction methods often ignore the textual query or rely on deep attention maps, whose instability under aggressive pruning leads to degraded semantic alignment. We propose FlashVLM, a text guided visual token selection framework that dynamically adapts visual inputs to the query. Instead of relying on noisy attention weights, FlashVLM computes an explicit cross modal similarity between projected image tokens and normalized text embeddings in the language model space. This extrinsic relevance is fused with intrinsic visual saliency using log domain weighting and temperature controlled sharpening. In addition, a diversity preserving partition retains a minimal yet representative set of background tokens to maintain global context. Under identical token budgets and evaluation protocols, FlashVLM achieves beyond lossless compression, slightly surpassing the unpruned baseline while pruning up to 77.8 percent of visual tokens on LLaVA 1.5, and maintaining 92.8 percent accuracy even under 94.4 percent compression. Extensive experiments on 14 image and video benchmarks demonstrate that FlashVLM delivers state of the art efficiency performance trade offs while maintaining strong robustness and generalization across mainstream VLMs.

Peijia Qin, Ruiyi Zhang, Pengtao Xie

Parameter-efficient fine-tuning (PEFT) is a flexible and efficient method for adapting large language models (LLMs) to downstream tasks. Among these methods, weight-decomposed low-rank adaptation (DoRA) is a promising approach that decomposes weight matrices into magnitude and direction components to mimic full fine-tuning (FT) better. However, DoRA's simultaneous optimization of these components makes it over-expressive, increases the risk of overfitting, and creates a coupled updating pattern that limits its learning capacity. To address these issues, we propose Bi-level Optimization-Based Weight-Decomposed Low-Rank Adaptation (BiDoRA), a novel PEFT method based on a bi-level optimization framework. BiDoRA fundamentally differs from DoRA by optimizing the magnitude and direction in two separate, asynchronous loops using distinct training and validation data splits. This decoupled optimization process effectively mitigates overfitting and allows for more flexible updates that align even more closely with FT. For instance, weight decomposition analysis shows BiDoRA achieves a magnitude-direction update correlation of $-8.042$, significantly closer to the FT ideal compared to $-1.784$ for DoRA. Evaluation of BiDoRA on diverse tasks spanning natural language understanding, generation, token classification, and extremely small biomedical datasets reveals that it consistently outperforms DoRA and a wide range of leading PEFT methods. This improvement is statistically significant, as demonstrated on the GLUE benchmark where BiDoRA surpasses DoRA with a p-value of $2.4\times10^{-4}$ in terms of the Wilcoxon signed-rank test. The code for BiDoRA is available at https://github.com/t2ance/BiDoRA.

Ruiyi Zhang, Peijia Qin, Qi Cao et al.

Process Reward Models (PRMs) have become essential for improving Large Language Models (LLMs) via test-time scaling, yet their effectiveness in coding remains limited due to the lack of meaningful step decompositions in code and the noise of Monte-Carlo-generated partial labels. We propose DreamPRM-Code, a coding-focused PRM that treats functions as reasoning steps using a Chain-of-Function prompting strategy to induce modular code generation, enabling PRM training and application analogous to mathematical reasoning tasks. To address label noise, DreamPRM-Code introduces a meta-learning-based correction mechanism that leverages clean final-solution unit-test labels and performs bi-level optimization to refine intermediate labels. Applying on test-time scaling, DreamPRM-Code achieved state-of-the-art performance on LiveCodeBench with 80.9 pass@1 rate, surpassing OpenAI o4-mini.

Qi Cao, Shuhao Zhang, Ruizhe Zhou et al.

Model routing chooses which language model to use for each query. By sending easy queries to cheaper models and hard queries to stronger ones, it can significantly reduce inference cost while maintaining high accuracy. However, most existing routers treat this as a fixed choice among a small set of models, which makes them hard to adapt to new models or changing budget constraints. In this paper, we propose SCOPE (Scalable and Controllable Outcome Performance Estimator), a routing framework that goes beyond model selection by predicting their cost and performance. Trained with reinforcement learning, SCOPE makes reasoning-based predictions by retrieving how models behave on similar problems, rather than relying on fixed model names, enabling it to work with new, unseen models. Moreover, by explicitly predicting how accurate and how expensive a model will be, it turns routing into a dynamic decision problem, allowing users to easily control the trade-off between accuracy and cost. Experiments show that SCOPE is more than just a cost-saving tool. It flexibly adapts to user needs: it can boost accuracy by up to 25.7% when performance is the priority, or cut costs by up to 95.1% when efficiency matters most.

Ruiyi Zhang, Peijia Qin, Qi Cao et al.

Code generation is a core application of large language models (LLMs), yet LLMs still frequently fail on complex programming tasks. Given its success in mathematical reasoning, test-time scaling approaches such as Process Reward Model (PRM)-based Best-of-N selection offer a promising way to improve performance. However, existing PRMs remain ineffective for code generation due to the lack of meaningful step decomposition in code and the noise of Monte Carlo-estimated partial-solution correctness scores (rewards). To address these challenges, we propose FunPRM. FunPRM prompts LLMs to encourage modular code generation organized into functions, with functions treated as PRM reasoning steps. Furthermore, FunPRM introduces a novel meta-learning-based reward correction mechanism that leverages clean final-solution rewards obtained via a unit-test-based evaluation system to purify noisy partial-solution rewards. Experiments on LiveCodeBench and BigCodeBench demonstrate that FunPRM consistently outperforms existing test-time scaling methods across five base LLMs, notably achieving state-of-the-art performance on LiveCodeBench when combined with O4-mini. Furthermore, FunPRM produces code that is more readable and reusable for developers.

Peijia Qin, Ruiyi Zhang, Qi Cao et al.

Test-time scaling for code generation commonly relies on Best-of-N selection, in which multiple candidate solutions are sampled from a base model, and the best one is selected by an LLM judge. However, training reliable LLM judges is challenging due to severe distribution shifts, including imbalances between easy and hard problems, mismatches between training tasks and evaluation benchmarks, and trajectory mismatch arising from training data generated by cheaper models whose behavior differs from that of inference-time models. We propose DAJ, a reasoning-based LLM judge trained with verifiable rewards under a bi-level data-reweighted learning framework. The proposed framework learns data-importance weights (either domain-level or instance-level) to optimize generalization performance on a held-out meta set aligned with target benchmarks. To the best of our knowledge, this is the first application of data reweighting to LLM-as-a-Judge training for test-time scaling. Our approach automatically emphasizes hard problems, in-distribution samples, and trajectory-aligned data, without relying on hand-crafted heuristics. Empirically, DAJ achieves state-of-the-art performance on LiveCodeBench and BigCodeBench, outperforming strong test-time scaling baselines as well as leading proprietary models.

Li Zhang, Shruti Agarwal, John Collomosse et al.

Generative AI models pose a significant challenge to intellectual property (IP), as they can replicate unique artistic styles and concepts without attribution. While watermarking offers a potential solution, existing methods often fail in complex scenarios where multiple concepts (e.g., an object and an artistic style) are composed within a single image. These methods struggle to disentangle and attribute each concept individually. In this work, we introduce TokenTrace, a novel proactive watermarking framework for robust, multi-concept attribution. Our method embeds secret signatures into the semantic domain by simultaneously perturbing the text prompt embedding and the initial latent noise that guide the diffusion model's generation process. For retrieval, we propose a query-based TokenTrace module that takes the generated image and a textual query specifying which concepts need to be retrieved (e.g., a specific object or style) as inputs. This query-based mechanism allows the module to disentangle and independently verify the presence of multiple concepts from a single generated image. Extensive experiments show that our method achieves state-of-the-art performance on both single-concept (object and style) and multi-concept attribution tasks, significantly outperforming existing baselines while maintaining high visual quality and robustness to common transformations.

Qi Cao, Yufan Wang, Peijia Qin et al.

Large language models (LLMs) often expose useful signals of self-monitoring: before solving a problem, they can estimate whether they are likely to succeed, and after solving it, they can judge whether their answer is likely to be correct. However, these signals are typically measured or elicited in isolation, rather than used to control inference. In this work, we ask whether LLMs possess latent metacognitive ability that can be turned into effective test-time control. Inspired by the Nelson--Narens theory from cognitive psychology, we propose a metacognitive harness that separates monitoring from reasoning. For each problem, the model first reports a pre-solve feeling-of-knowing (FOK) signal; after each solve attempt, it reports a post-solve judgment-of-learning (JOL) signal. Rather than treating these signals as passive confidence estimates, the harness turns them into an explicit control interface for reasoning: it decides when to trust the current solution, when to retry with compact metacognitive feedback, and when to pass multiple attempts to a final aggregator. Across text, code, and multimodal reasoning benchmarks, our harness substantially improves a fixed Claude Sonnet-4.6 base model without parameter updates or benchmark-specific fine-tuning. On the evaluated public benchmark snapshots, it raises pooled accuracy from 48.3 to 56.9 and exceeds the strongest listed leaderboard entries on the three primary evaluation settings: HLE-Verified, LiveCodeBench v6, and R-Bench-V. These results suggest that strong LLMs may already possess useful metacognitive ability, but require an explicit control harness to act on it during reasoning.

Li Zhang, Pengtao Xie

The Segment Anything Model has revolutionized image segmentation with its zero-shot capabilities, yet its reliance on manual prompts hinders fully automated deployment. While integrating object detectors as prompt generators offers a pathway to automation, existing pipelines suffer from two fundamental limitations: objective mismatch, where detectors optimized for geometric localization do not correspond to the optimal prompting context required by SAM, and alignment overfitting in standard joint training, where the detector simply memorizes specific prompt adjustments for training samples rather than learning a generalizable policy. To bridge this gap, we introduce BLO-Inst, a unified framework that aligns detection and segmentation objectives by bi-level optimization. We formulate the alignment as a nested optimization problem over disjoint data splits. In the lower level, the SAM is fine-tuned to maximize segmentation fidelity given the current detection proposals on a subset ($D_1$). In the upper level, the detector is updated to generate bounding boxes that explicitly minimize the validation loss of the fine-tuned SAM on a separate subset ($D_2$). This effectively transforms the detector into a segmentation-aware prompt generator, optimizing the bounding boxes not just for localization accuracy, but for downstream mask quality. Extensive experiments demonstrate that BLO-Inst achieves superior performance, outperforming standard baselines on tasks in general and biomedical domains.

Xin Gao, Ruiyi Zhang, Daniel Du et al.

Large Language Models (LLMs) are widely used for temporal prediction, but their reliance on pretraining data raises contamination concerns, as accurate predictions on pre-cutoff test data may reflect memorization rather than reasoning, leading to an overestimation of their generalization capability. With the recent emergence of prompting-based unlearning techniques, a natural question arises: Can LLMs be prompted to simulate an earlier knowledge cutoff? In this work, we investigate the capability of prompting to simulate earlier knowledge cutoff in LLMs. We construct three evaluation datasets to assess the extent to which LLMs can forget (1) direct factual knowledge, (2) semantic shifts, and (3) causally related knowledge. Results demonstrate that while prompt-based simulated knowledge cutoffs show effectiveness when directly queried with the information after that date, they struggle to induce forgetting when the forgotten content is not directly asked but causally related to the query. These findings highlight the need for more rigorous evaluation settings when applying LLMs for temporal prediction tasks. The full dataset and evaluation code are available at https://github.com/gxx27/time_unlearn.

Youwei Liang, Ruiyi Zhang, Li Zhang et al.

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing, reducing the failure rate, and streamlining clinical trials. In this work, we make an initial attempt towards enabling ChatGPT-like capabilities on drug molecule graphs, by developing a prototype system DrugChat. DrugChat works in a similar way as ChatGPT. Users upload a compound molecule graph and ask various questions about this compound. DrugChat will answer these questions in a multi-turn, interactive manner. The DrugChat system consists of a graph neural network (GNN), a large language model (LLM), and an adaptor. The GNN takes a compound molecule graph as input and learns a representation for this graph. The adaptor transforms the graph representation produced by the GNN into another representation that is acceptable to the LLM. The LLM takes the compound representation transformed by the adaptor and users' questions about this compound as inputs and generates answers. All these components are trained end-to-end. To train DrugChat, we collected instruction tuning datasets which contain 10,834 drug compounds and 143,517 question-answer pairs. The code and data is available at \url{https://github.com/UCSD-AI4H/drugchat}

Youwei Liang, Chongjian Ge, Zhan Tong et al.

Vision Transformers (ViTs) take all the image patches as tokens and construct multi-head self-attention (MHSA) among them. Complete leverage of these image tokens brings redundant computations since not all the tokens are attentive in MHSA. Examples include that tokens containing semantically meaningless or distractive image backgrounds do not positively contribute to the ViT predictions. In this work, we propose to reorganize image tokens during the feed-forward process of ViT models, which is integrated into ViT during training. For each forward inference, we identify the attentive image tokens between MHSA and FFN (i.e., feed-forward network) modules, which is guided by the corresponding class token attention. Then, we reorganize image tokens by preserving attentive image tokens and fusing inattentive ones to expedite subsequent MHSA and FFN computations. To this end, our method EViT improves ViTs from two perspectives. First, under the same amount of input image tokens, our method reduces MHSA and FFN computation for efficient inference. For instance, the inference speed of DeiT-S is increased by 50% while its recognition accuracy is decreased by only 0.3% for ImageNet classification. Second, by maintaining the same computational cost, our method empowers ViTs to take more image tokens as input for recognition accuracy improvement, where the image tokens are from higher resolution images. An example is that we improve the recognition accuracy of DeiT-S by 1% for ImageNet classification at the same computational cost of a vanilla DeiT-S. Meanwhile, our method does not introduce more parameters to ViTs. Experiments on the standard benchmarks show the effectiveness of our method. The code is available at https://github.com/youweiliang/evit

Xingyi Yang, Nandiraju Gireesh, Eric Xing et al.

To effectively train medical students to become qualified radiologists, a large number of X-ray images collected from patients with diverse medical conditions are needed. However, due to data privacy concerns, such images are typically difficult to obtain. To address this problem, we develop methods to generate view-consistent, high-fidelity, and high-resolution X-ray images from radiology reports to facilitate radiology training of medical students. This task is presented with several challenges. First, from a single report, images with different views (e.g., frontal, lateral) need to be generated. How to ensure consistency of these images (i.e., make sure they are about the same patient)? Second, X-ray images are required to have high resolution. Otherwise, many details of diseases would be lost. How to generate high-resolutions images? Third, radiology reports are long and have complicated structure. How to effectively understand their semantics to generate high-fidelity images that accurately reflect the contents of the reports? To address these three challenges, we propose an XRayGAN composed of three modules: (1) a view consistency network that maximizes the consistency between generated frontal-view and lateral-view images; (2) a multi-scale conditional GAN that progressively generates a cascade of images with increasing resolution; (3) a hierarchical attentional encoder that learns the latent semantics of a radiology report by capturing its hierarchical linguistic structure and various levels of clinical importance of words and sentences. Experiments on two radiology datasets demonstrate the effectiveness of our methods. To our best knowledge, this work represents the first one generating consistent and high-resolution X-ray images from radiology reports. The code is available at https://github.com/UCSD-AI4H/XRayGAN.

Ishika Singh, Haoyi Zhou, Kunlin Yang et al.

Neural architecture search, which aims to automatically search for architectures (e.g., convolution, max pooling) of neural networks that maximize validation performance, has achieved remarkable progress recently. In many application scenarios, several parties would like to collaboratively search for a shared neural architecture by leveraging data from all parties. However, due to privacy concerns, no party wants its data to be seen by other parties. To address this problem, we propose federated neural architecture search (FNAS), where different parties collectively search for a differentiable architecture by exchanging gradients of architecture variables without exposing their data to other parties. To further preserve privacy, we study differentially-private FNAS (DP-FNAS), which adds random noise to the gradients of architecture variables. We provide theoretical guarantees of DP-FNAS in achieving differential privacy. Experiments show that DP-FNAS can search highly-performant neural architectures while protecting the privacy of individual parties. The code is available at https://github.com/UCSD-AI4H/DP-FNAS

Hongchao Fang, Sicheng Wang, Meng Zhou et al.

Pretrained language models such as BERT, GPT have shown great effectiveness in language understanding. The auxiliary predictive tasks in existing pretraining approaches are mostly defined on tokens, thus may not be able to capture sentence-level semantics very well. To address this issue, we propose CERT: Contrastive self-supervised Encoder Representations from Transformers, which pretrains language representation models using contrastive self-supervised learning at the sentence level. CERT creates augmentations of original sentences using back-translation. Then it finetunes a pretrained language encoder (e.g., BERT) by predicting whether two augmented sentences originate from the same sentence. CERT is simple to use and can be flexibly plugged into any pretraining-finetuning NLP pipeline. We evaluate CERT on 11 natural language understanding tasks in the GLUE benchmark where CERT outperforms BERT on 7 tasks, achieves the same performance as BERT on 2 tasks, and performs worse than BERT on 2 tasks. On the averaged score of the 11 tasks, CERT outperforms BERT. The data and code are available at https://github.com/UCSD-AI4H/CERT

Wenmian Yang, Guangtao Zeng, Bowen Tan et al.

Under the pandemic of COVID-19, people experiencing COVID19-related symptoms or exposed to risk factors have a pressing need to consult doctors. Due to hospital closure, a lot of consulting services have been moved online. Because of the shortage of medical professionals, many people cannot receive online consultations timely. To address this problem, we aim to develop a medical dialogue system that can provide COVID19-related consultations. We collected two dialogue datasets -- CovidDialog -- (in English and Chinese respectively) containing conversations between doctors and patients about COVID-19. On these two datasets, we train several dialogue generation models based on Transformer, GPT, and BERT-GPT. Since the two COVID-19 dialogue datasets are small in size, which bear high risk of overfitting, we leverage transfer learning to mitigate data deficiency. Specifically, we take the pretrained models of Transformer, GPT, and BERT-GPT on dialog datasets and other large-scale texts, then finetune them on our CovidDialog tasks. We perform both automatic and human evaluation of responses generated by these models. The results show that the generated responses are promising in being doctor-like, relevant to the conversation history, and clinically informative. The data and code are available at https://github.com/UCSD-AI4H/COVID-Dialogue.

Xuehai He, Shu Chen, Zeqian Ju et al.

Medical dialogue systems are promising in assisting in telemedicine to increase access to healthcare services, improve the quality of patient care, and reduce medical costs. To facilitate the research and development of medical dialogue systems, we build two large-scale medical dialogue datasets: MedDialog-EN and MedDialog-CN. MedDialog-EN is an English dataset containing 0.3 million conversations between patients and doctors and 0.5 million utterances. MedDialog-CN is an Chinese dataset containing 1.1 million conversations and 4 million utterances. To our best knowledge, MedDialog-(EN,CN) are the largest medical dialogue datasets to date. The dataset is available at https://github.com/UCSD-AI4H/Medical-Dialogue-System

Xingyi Yang, Xuehai He, Jinyu Zhao et al.

During the outbreak time of COVID-19, computed tomography (CT) is a useful manner for diagnosing COVID-19 patients. Due to privacy issues, publicly available COVID-19 CT datasets are highly difficult to obtain, which hinders the research and development of AI-powered diagnosis methods of COVID-19 based on CTs. To address this issue, we build an open-sourced dataset -- COVID-CT, which contains 349 COVID-19 CT images from 216 patients and 463 non-COVID-19 CTs. The utility of this dataset is confirmed by a senior radiologist who has been diagnosing and treating COVID-19 patients since the outbreak of this pandemic. We also perform experimental studies which further demonstrate that this dataset is useful for developing AI-based diagnosis models of COVID-19. Using this dataset, we develop diagnosis methods based on multi-task learning and self-supervised learning, that achieve an F1 of 0.90, an AUC of 0.98, and an accuracy of 0.89. According to the senior radiologist, models with such performance are good enough for clinical usage. The data and code are available at https://github.com/UCSD-AI4H/COVID-CT

Hao Zhang, Zeyu Zheng, Shizhen Xu et al.

Deep learning models can take weeks to train on a single GPU-equipped machine, necessitating scaling out DL training to a GPU-cluster. However, current distributed DL implementations can scale poorly due to substantial parameter synchronization over the network, because the high throughput of GPUs allows more data batches to be processed per unit time than CPUs, leading to more frequent network synchronization. We present Poseidon, an efficient communication architecture for distributed DL on GPUs. Poseidon exploits the layered model structures in DL programs to overlap communication and computation, reducing bursty network communication. Moreover, Poseidon uses a hybrid communication scheme that optimizes the number of bytes required to synchronize each layer, according to layer properties and the number of machines. We show that Poseidon is applicable to different DL frameworks by plugging Poseidon into Caffe and TensorFlow. We show that Poseidon enables Caffe and TensorFlow to achieve 15.5x speed-up on 16 single-GPU machines, even with limited bandwidth (10GbE) and the challenging VGG19-22K network for image classification. Moreover, Poseidon-enabled TensorFlow achieves 31.5x speed-up with 32 single-GPU machines on Inception-V3, a 50% improvement over the open-source TensorFlow (20x speed-up).

Li Zhang, Youwei Liang, Ruiyi Zhang et al.

The Segment Anything Model (SAM), a foundation model pretrained on millions of images and segmentation masks, has significantly advanced semantic segmentation, a fundamental task in computer vision. Despite its strengths, SAM encounters two major challenges. Firstly, it struggles with segmenting specific objects autonomously, as it relies on users to manually input prompts like points or bounding boxes to identify targeted objects. Secondly, SAM faces challenges in excelling at specific downstream tasks, like medical imaging, due to a disparity between the distribution of its pretraining data, which predominantly consists of general-domain images, and the data used in downstream tasks. Current solutions to these problems, which involve finetuning SAM, often lead to overfitting, a notable issue in scenarios with very limited data, like in medical imaging. To overcome these limitations, we introduce BLO-SAM, which finetunes SAM based on bi-level optimization (BLO). Our approach allows for automatic image segmentation without the need for manual prompts, by optimizing a learnable prompt embedding. Furthermore, it significantly reduces the risk of overfitting by training the model's weight parameters and the prompt embedding on two separate subsets of the training dataset, each at a different level of optimization. We apply BLO-SAM to diverse semantic segmentation tasks in general and medical domains. The results demonstrate BLO-SAM's superior performance over various state-of-the-art image semantic segmentation methods.

Ruiyi Zhang, David Sullivan, Kyle Jackson et al.

Large Language Models (LLMs) have emerged as a dominant approach for a wide range of NLP tasks, with their access to external information further enhancing their capabilities. However, this introduces new vulnerabilities, known as prompt injection attacks, where external content embeds malicious instructions that manipulate the LLM's output. Recently, the Base64 defense has been recognized as one of the most effective methods for reducing success rate of prompt injection attacks. Despite its efficacy, this method can degrade LLM performance on certain NLP tasks. To address this challenge, we propose a novel defense mechanism: mixture of encodings, which utilizes multiple character encodings, including Base64. Extensive experimental results show that our method achieves one of the lowest attack success rates under prompt injection attacks, while maintaining high performance across all NLP tasks, outperforming existing character encoding-based defense methods. This underscores the effectiveness of our mixture of encodings strategy for both safety and task performance metrics.

Yuchen Li, Li Zhang, Youwei Liang et al.

Segment Anything Model (SAM) has gained significant recognition in the field of semantic segmentation due to its versatile capabilities and impressive performance. Despite its success, SAM faces two primary limitations: (1) it relies heavily on meticulous human-provided prompts like key points, bounding boxes or text messages, which is labor-intensive; (2) the mask decoder's feature representation is sometimes inaccurate, as it solely employs dot product operations at the end of mask decoder, which inadequately captures the necessary correlations for precise segmentation. Current solutions to these problems such as fine-tuning SAM often require retraining a large number of parameters, which needs huge amount of time and computing resources. To address these limitations, we propose an automated prompting and mask calibration method called AM-SAM based on a bi-level optimization framework. Our approach automatically generates prompts for an input image, eliminating the need for human involvement with a good performance in early training epochs, achieving faster convergence. Additionally, we freeze the main part of SAM, and modify the mask decoder with Low-Rank Adaptation (LoRA), enhancing the mask decoder's feature representation by incorporating advanced techniques that go beyond simple dot product operations to more accurately capture and utilize feature correlations. Our experimental results demonstrate that AM-SAM achieves significantly accurate segmentation, matching or exceeding the effectiveness of human-generated and default prompts. Notably, on the body segmentation dataset, our method yields a 5% higher dice score with a 4-example few-shot training set compared to the SOTA method, underscoring its superiority in semantic segmentation tasks.

Bokai Hu, Sai Ashish Somayajula, Xin Pan et al.

Instruction-fine-tuned large language models (LLMs) under 14B parameters continue to underperform on natural language understanding (NLU) tasks, often trailing smaller models like BERT-base on benchmarks such as GLUE and SuperGLUE. Motivated by the success of reinforcement learning in reasoning tasks (e.g., DeepSeek), we explore Proximal Policy Optimization (PPO) as a framework to improve the NLU capabilities of LLMs. We frame NLU as a reinforcement learning environment, treating token generation as a sequence of actions and optimizing for reward signals based on alignment with ground-truth labels. PPO consistently outperforms supervised fine-tuning, yielding an average improvement of 6.3 points on GLUE, and surpasses zero-shot and few-shot prompting by 38.7 and 26.1 points, respectively. Notably, PPO-tuned models outperform GPT-4o by over 4\% on average across sentiment and natural language inference tasks, including gains of 7.3\% on the Mental Health dataset and 10.9\% on SIGA-nli. This work highlights a promising direction for adapting LLMs to new tasks by reframing them as reinforcement learning problems, enabling learning through simple end-task rewards rather than extensive data curation.

Khai Le-Duc, Duy M. H. Nguyen, Phuong T. H. Trinh et al.

Faithful reasoning in medical vision-language models (VLMs) requires not only accurate predictions but also transparent alignment between textual rationales and visual evidence. While Chain-of-Thought (CoT) prompting has shown promise in medical visual question answering (VQA), no large-scale expert-level dataset has captured stepwise reasoning with precise visual grounding. We introduce S-Chain, the first large-scale dataset of 12,000 expert-annotated medical images with bounding boxes and structured visual CoT (SV-CoT), explicitly linking visual regions to reasoning steps. The dataset further supports 16 languages, totaling over 700k VQA pairs for broad multilingual applicability. Using S-Chain, we benchmark state-of-the-art medical VLMs (ExGra-Med, LLaVA-Med) and general-purpose VLMs (Qwen2.5-VL, InternVL2.5), showing that SV-CoT supervision significantly improves interpretability, grounding fidelity, and robustness. Beyond benchmarking, we study its synergy with retrieval-augmented generation, revealing how domain knowledge and visual grounding interact during autoregressive reasoning. Finally, we propose a new mechanism that strengthens the alignment between visual evidence and reasoning, improving both reliability and efficiency. S-Chain establishes a new benchmark for grounded medical reasoning and paves the way toward more trustworthy and explainable medical VLMs.

Duy M. H. Nguyen, Tuan A. Tran, Duong Nguyen et al.

Recent token merging techniques for Vision Transformers (ViTs) provide substantial speedups by reducing the number of tokens processed by self-attention, often without retraining. However, their direct application to the Segment Anything Model (SAM) family is nontrivial: SAM's image encoder mixes windowed and global attention, and its mask decoder relies on dense, prompt-conditioned features for precise boundary prediction. We systematically evaluate representative token-merging methods on SAM and Medical SAM in a strict off-the-shelf setting, and find that existing destination-selection heuristics can erode boundaries and leak prompt information as merge rates increase. We propose \textbf{StructSAM}, a resolution-preserving merge-unmerge framework tailored to SAM. StructSAM computes a lightweight token-energy score from first-order feature gradients, uses grid-based flatness screening to protect boundary and prompt regions, and merges tokens within flat areas toward low-energy destinations with explicit token recovery. We further provide a spectral graph coarsening view showing that score-guided merging yields bounded Laplacian spectral distortion compared to random or window-restricted baselines. Across eight natural and medical benchmarks, StructSAM reduces encoder FLOPs by 25-30\% (up to 40\%+ with prompt-aware merging) with minor drops in mIoU/Dice, consistently outperforming ToMe, PiToMe, ToMeSD, VidToMe, and ALGM at the same compute.

Eric Xue, Ruiyi Zhang, Zijun Zhang et al.

Transformer models are foundational to natural language processing (NLP) applications, yet remain vulnerable to backdoor attacks introduced through poisoned data, which implant hidden behaviors during training. To strengthen the ability to prevent such compromises, recent research has focused on designing increasingly stealthy attacks to stress-test existing defenses, pairing backdoor behaviors with stylized artifact or token-level perturbation triggers. However, this trend diverts attention from the harder and more realistic case: making the model respond to semantic triggers such as specific names or entities, where a successful backdoor could manipulate outputs tied to real people or events in deployed systems. Motivated by this growing disconnect, we introduce SteganoBackdoor, bringing stealth techniques back into line with practical threat models. Leveraging innocuous properties from natural-language steganography, SteganoBackdoor applies a gradient-guided data optimization process to transform semantic trigger seeds into steganographic carriers that embed a high backdoor payload, remain fluent, and exhibit no representational resemblance to the trigger. Across diverse experimental settings, SteganoBackdoor achieves over 99% attack success at an order-of-magnitude lower data-poisoning rate than prior approaches while maintaining unparalleled evasion against a comprehensive suite of data-level defenses. By revealing this practical and covert attack, SteganoBackdoor highlights an urgent blind spot in current defenses and demands immediate attention to adversarial data defenses and real-world threat modeling.

Qi Cao, Pengtao Xie

Training multimodal process reward models (PRMs) is hard due to (i) distribution shift between training set and test set and (ii) quality imbalance across training data samples. While domain-level reweighting (e.g., DreamPRM) aligns training with test-time objectives, it leaves a clear gap to an oracle upper bound (pass@N), even under a "sanity check" that uses test set data to probe headroom -- pointing to meta-level under-parameterization. We introduce DreamPRM-1.5, an instance-level reweighting framework that assigns an adaptive weight to every training example via bi-level optimization. To realize instance reweighting across scales, we develop two complementary regimes: Instance Table, which learns explicit per-sample weights and excels on small/medium data, and Instance Net, a lightweight neural network that generalizes better and scales to large corpora. A practical, stable training recipe -- time-scale matching between upper/lower updates, cold-start initialization, and bounded-range weights -- prevents divergence. Integrated with test-time scaling, DreamPRM-1.5 attains 84.6 accuracy on the MMMU validation set, 31.3 accuracy on R-Bench-V and, when paired with a leading backbone (e.g., GPT-5-mini), achieves first-place results on public multimodal reasoning leaderboards. Moreover, extensive experiments, including benchmark evaluations, baseline comparisons, and a sanity check, demonstrate that DreamPRM-1.5 closes the gap toward the oracle, achieves leading performance, and trains stably.

Ruiyi Zhang, Sai Ashish Somayajula, Pengtao Xie

Large-scale general domain pretraining followed by downstream-specific finetuning has become a predominant paradigm in machine learning. However, discrepancies between the pretraining and target domains can still lead to performance degradation in certain cases, underscoring the need for task-adaptive continued pretraining (TAP). TAP methods typically involve continued pretraining on task-specific unlabeled datasets or introducing additional unsupervised learning objectives to enhance model capabilities. While many TAP methods perform continued pretraining with multiple pretraining objectives, they often determine the tradeoff parameters between objectives manually, resulting in suboptimal outcomes and higher computational costs. In this paper, we propose TapWeight, a task-adaptive pretraining framework which automatically determines the optimal importance of each pretraining objective based on downstream feedback. TapWeight reweights each pretraining objective by solving a multi-level optimization problem. We applied TapWeight to both molecular property prediction and natural language understanding tasks, significantly surpassing baseline methods. Experimental results validate the effectiveness and generalizability of TapWeight.

Sai Ashish Somayajula, Youwei Liang, Abhishek Singh et al.

Pretrained Language Models (PLMs) have advanced Natural Language Processing (NLP) tasks significantly, but finetuning PLMs on low-resource datasets poses significant challenges such as instability and overfitting. Previous methods tackle these issues by finetuning a strategically chosen subnetwork on a downstream task, while keeping the remaining weights fixed to the pretrained weights. However, they rely on a suboptimal criteria for sub-network selection, leading to suboptimal solutions. To address these limitations, we propose a regularization method based on attention-guided weight mixup for finetuning PLMs. Our approach represents each network weight as a mixup of task-specific weight and pretrained weight, controlled by a learnable attention parameter, providing finer control over sub-network selection. Furthermore, we employ a bi-level optimization (BLO) based framework on two separate splits of the training dataset, improving generalization and combating overfitting. We validate the efficacy of our proposed method through extensive experiments, demonstrating its superiority over previous methods, particularly in the context of finetuning PLMs on low-resource datasets.

Rushi Qiang, Ruiyi Zhang, Pengtao Xie

Low-rank adaptation (LoRA) is a popular method for fine-tuning large-scale pre-trained models in downstream tasks by learning low-rank incremental matrices. Though LoRA and its variants effectively reduce the number of trainable parameters compared to full fine-tuning methods, they often overfit training data, resulting in sub-optimal generalization on test data. To address this problem, we introduce BiLoRA, an overfitting-alleviating fine-tuning approach based on bi-level optimization (BLO). BiLoRA employs pseudo singular value decomposition to parameterize low-rank incremental matrices and splits the training of pseudo singular vectors and values across two different subsets of training data. This division, embedded within separate levels of the BLO framework, mitigates the risk of overfitting to a single dataset. Tested on ten datasets covering natural language understanding and generation tasks and applied to various well-known large pre-trained models, BiLoRA significantly outperforms LoRA methods and other fine-tuning approaches, with similar amounts of trainable parameters.

Ruiyi Zhang, Rushi Qiang, Sai Ashish Somayajula et al.

Large-scale pretraining followed by task-specific finetuning has achieved great success in various NLP tasks. Since finetuning all parameters of large pretrained models poses substantial computational and memory challenges, several efficient finetuning methods have been developed. Among them, low-rank adaptation (LoRA), which finetunes low-rank incremental update matrices on top of frozen pretrained weights, has proven particularly effective. Nonetheless, LoRA's uniform rank assignment across all layers, along with its reliance on an exhaustive search to find the best rank, leads to high computation costs and suboptimal finetuning performance. To address these limitations, we introduce AutoLoRA, a meta learning based framework for automatically identifying the optimal rank of each LoRA layer. AutoLoRA associates each rank-1 matrix in a low-rank update matrix with a selection variable, which determines whether the rank-1 matrix should be discarded. A meta learning based method is developed to learn these selection variables. The optimal rank is determined by thresholding the values of these variables. Our comprehensive experiments on natural language understanding, generation, and sequence labeling demonstrate the effectiveness of AutoLoRA.

Han Guo, Ramtin Hosseini, Ruiyi Zhang et al.

Masked Autoencoder (MAE) is a notable method for self-supervised pretraining in visual representation learning. It operates by randomly masking image patches and reconstructing these masked patches using the unmasked ones. A key limitation of MAE lies in its disregard for the varying informativeness of different patches, as it uniformly selects patches to mask. To overcome this, some approaches propose masking based on patch informativeness. However, these methods often do not consider the specific requirements of downstream tasks, potentially leading to suboptimal representations for these tasks. In response, we introduce the Multi-level Optimized Mask Autoencoder (MLO-MAE), a novel framework that leverages end-to-end feedback from downstream tasks to learn an optimal masking strategy during pretraining. Our experimental findings highlight MLO-MAE's significant advancements in visual representation learning. Compared to existing methods, it demonstrates remarkable improvements across diverse datasets and tasks, showcasing its adaptability and efficiency.