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Jul 24

Enhancing Whole Slide Pathology Foundation Models through Stain Normalization

Recent advancements in digital pathology have led to the development of numerous foundational models that utilize self-supervised learning on patches extracted from gigapixel whole slide images (WSIs). While this approach leverages vast amounts of unlabeled data, we have discovered a significant issue: features extracted from these self-supervised models tend to cluster by individual WSIs, a phenomenon we term WSI-specific feature collapse. This problem can potentially limit the model's generalization ability and performance on various downstream tasks. To address this issue, we introduce Stain Normalized Pathology Foundational Model, a novel foundational model trained on patches that have undergone stain normalization. Stain normalization helps reduce color variability arising from different laboratories and scanners, enabling the model to learn more consistent features. Stain Normalized Pathology Foundational Model is trained using 285,153,903 patches extracted from a total of 34,795 WSIs, combining data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Our experiments demonstrate that Stain Normalized Pathology Foundational Model significantly mitigates the feature collapse problem, indicating that the model has learned more generalized features rather than overfitting to individual WSI characteristics. We compared Stain Normalized Pathology Foundational Model with state-of-the-art models across six downstream task datasets, and our results show that Stain Normalized Pathology Foundational Model achieves excellent performance relative to the number of WSIs used and the model's parameter count. This suggests that the application of stain normalization has substantially improved the model's efficiency and generalization capabilities.

  • 5 authors
·
Aug 1, 2024

Perturbation Analysis of Neural Collapse

Training deep neural networks for classification often includes minimizing the training loss beyond the zero training error point. In this phase of training, a "neural collapse" behavior has been observed: the variability of features (outputs of the penultimate layer) of within-class samples decreases and the mean features of different classes approach a certain tight frame structure. Recent works analyze this behavior via idealized unconstrained features models where all the minimizers exhibit exact collapse. However, with practical networks and datasets, the features typically do not reach exact collapse, e.g., because deep layers cannot arbitrarily modify intermediate features that are far from being collapsed. In this paper, we propose a richer model that can capture this phenomenon by forcing the features to stay in the vicinity of a predefined features matrix (e.g., intermediate features). We explore the model in the small vicinity case via perturbation analysis and establish results that cannot be obtained by the previously studied models. For example, we prove reduction in the within-class variability of the optimized features compared to the predefined input features (via analyzing gradient flow on the "central-path" with minimal assumptions), analyze the minimizers in the near-collapse regime, and provide insights on the effect of regularization hyperparameters on the closeness to collapse. We support our theory with experiments in practical deep learning settings.

  • 3 authors
·
Oct 29, 2022

ConSlide: Asynchronous Hierarchical Interaction Transformer with Breakup-Reorganize Rehearsal for Continual Whole Slide Image Analysis

Whole slide image (WSI) analysis has become increasingly important in the medical imaging community, enabling automated and objective diagnosis, prognosis, and therapeutic-response prediction. However, in clinical practice, the ever-evolving environment hamper the utility of WSI analysis models. In this paper, we propose the FIRST continual learning framework for WSI analysis, named ConSlide, to tackle the challenges of enormous image size, utilization of hierarchical structure, and catastrophic forgetting by progressive model updating on multiple sequential datasets. Our framework contains three key components. The Hierarchical Interaction Transformer (HIT) is proposed to model and utilize the hierarchical structural knowledge of WSI. The Breakup-Reorganize (BuRo) rehearsal method is developed for WSI data replay with efficient region storing buffer and WSI reorganizing operation. The asynchronous updating mechanism is devised to encourage the network to learn generic and specific knowledge respectively during the replay stage, based on a nested cross-scale similarity learning (CSSL) module. We evaluated the proposed ConSlide on four public WSI datasets from TCGA projects. It performs best over other state-of-the-art methods with a fair WSI-based continual learning setting and achieves a better trade-off of the overall performance and forgetting on previous task

  • 6 authors
·
Aug 25, 2023

Revisiting Data Challenges of Computational Pathology: A Pack-based Multiple Instance Learning Framework

Computational pathology (CPath) digitizes pathology slides into whole slide images (WSIs), enabling analysis for critical healthcare tasks such as cancer diagnosis and prognosis. However, WSIs possess extremely long sequence lengths (up to 200K), significant length variations (from 200 to 200K), and limited supervision. These extreme variations in sequence length lead to high data heterogeneity and redundancy. Conventional methods often compromise on training efficiency and optimization to preserve such heterogeneity under limited supervision. To comprehensively address these challenges, we propose a pack-based MIL framework. It packs multiple sampled, variable-length feature sequences into fixed-length ones, enabling batched training while preserving data heterogeneity. Moreover, we introduce a residual branch that composes discarded features from multiple slides into a hyperslide which is trained with tailored labels. It offers multi-slide supervision while mitigating feature loss from sampling. Meanwhile, an attention-driven downsampler is introduced to compress features in both branches to reduce redundancy. By alleviating these challenges, our approach achieves an accuracy improvement of up to 8% while using only 12% of the training time in the PANDA(UNI). Extensive experiments demonstrate that focusing data challenges in CPath holds significant potential in the era of foundation models. The code is https://github.com/FangHeng/PackMIL

  • 5 authors
·
Sep 25, 2025

Simple Token-Efficient Vision-Language Model for Case-level Pathology Synoptic Report Generation

Generating clinically useful pathology reports for pathology cases from whole-slide images (WSIs) is challenging due to gigapixel resolution, long visual-token sequences, and the complexity of case-level reasoning, where a single case may contain multiple WSIs with heterogeneous tissues and ambiguous findings. We present a simple token-efficient vision--language model for case-level synoptic report generation that remains practical under constrained GPU memory. Our architecture follows a minimal three-component design: a frozen pathology patch encoder, a lightweight two-layer MLP vision-language aligner, and a large language model decoder, with an explicit WSI marker token to separate slides within a case. Training proceeds in two supervised stages: (1) aligner-only WSI captioning using heterogeneous WSI-text pairs, and (2) case-level supervised fine-tuning on case-report pairs for structured report generation. To reduce sequence length, we represent each slide using 512 times 512 patches at 5times magnification, which reduces the average sequence length by up to 64times times compared to the commonly used 20times patches. Combined with efficient training techniques, we enable practical training with only half a NVIDIA H100 GPU. Across both training stages, our approach achieves high ROUGE-L/METEOR/BLEU-4 scores while being substantially more efficient in memory and runtime. In AI-based evaluations, our model is consistently preferred over strong baselines. Extensive ablations characterize performance-efficiency trade-offs and identify simple choices that improve robustness in multi-WSI settings. Overall, this work provides a strong, reproducible baseline for efficient pathology report generation, lowering the barrier to multi-WSI VLM research under limited compute.

  • 4 authors
·
May 28

Neural Collapse in Deep Linear Networks: From Balanced to Imbalanced Data

Modern deep neural networks have achieved impressive performance on tasks from image classification to natural language processing. Surprisingly, these complex systems with massive amounts of parameters exhibit the same structural properties in their last-layer features and classifiers across canonical datasets when training until convergence. In particular, it has been observed that the last-layer features collapse to their class-means, and those class-means are the vertices of a simplex Equiangular Tight Frame (ETF). This phenomenon is known as Neural Collapse (NC). Recent papers have theoretically shown that NC emerges in the global minimizers of training problems with the simplified "unconstrained feature model". In this context, we take a step further and prove the NC occurrences in deep linear networks for the popular mean squared error (MSE) and cross entropy (CE) losses, showing that global solutions exhibit NC properties across the linear layers. Furthermore, we extend our study to imbalanced data for MSE loss and present the first geometric analysis of NC under bias-free setting. Our results demonstrate the convergence of the last-layer features and classifiers to a geometry consisting of orthogonal vectors, whose lengths depend on the amount of data in their corresponding classes. Finally, we empirically validate our theoretical analyses on synthetic and practical network architectures with both balanced and imbalanced scenarios.

  • 6 authors
·
Jan 1, 2023

PathAlign: A vision-language model for whole slide images in histopathology

Microscopic interpretation of histopathology images underlies many important diagnostic and treatment decisions. While advances in vision-language modeling raise new opportunities for analysis of such images, the gigapixel-scale size of whole slide images (WSIs) introduces unique challenges. Additionally, pathology reports simultaneously highlight key findings from small regions while also aggregating interpretation across multiple slides, often making it difficult to create robust image-text pairs. As such, pathology reports remain a largely untapped source of supervision in computational pathology, with most efforts relying on region-of-interest annotations or self-supervision at the patch-level. In this work, we develop a vision-language model based on the BLIP-2 framework using WSIs paired with curated text from pathology reports. This enables applications utilizing a shared image-text embedding space, such as text or image retrieval for finding cases of interest, as well as integration of the WSI encoder with a frozen large language model (LLM) for WSI-based generative text capabilities such as report generation or AI-in-the-loop interactions. We utilize a de-identified dataset of over 350,000 WSIs and diagnostic text pairs, spanning a wide range of diagnoses, procedure types, and tissue types. We present pathologist evaluation of text generation and text retrieval using WSI embeddings, as well as results for WSI classification and workflow prioritization (slide-level triaging). Model-generated text for WSIs was rated by pathologists as accurate, without clinically significant error or omission, for 78% of WSIs on average. This work demonstrates exciting potential capabilities for language-aligned WSI embeddings.

  • 17 authors
·
Jun 27, 2024

Internal Safety Collapse in Frontier Large Language Models

This work identifies a critical failure mode in frontier large language models (LLMs), which we term Internal Safety Collapse (ISC): under certain task conditions, models enter a state in which they continuously generate harmful content while executing otherwise benign tasks. We introduce TVD (Task, Validator, Data), a framework that triggers ISC through domain tasks where generating harmful content is the only valid completion, and construct ISC-Bench containing 53 scenarios across 8 professional disciplines. Evaluated on JailbreakBench, three representative scenarios yield worst-case safety failure rates averaging 95.3% across four frontier LLMs (including GPT-5.2 and Claude Sonnet 4.5), substantially exceeding standard jailbreak attacks. Frontier models are more vulnerable than earlier LLMs: the very capabilities that enable complex task execution become liabilities when tasks intrinsically involve harmful content. This reveals a growing attack surface: almost every professional domain uses tools that process sensitive data, and each new dual-use tool automatically expands this vulnerability--even without any deliberate attack. Despite substantial alignment efforts, frontier LLMs retain inherently unsafe internal capabilities: alignment reshapes observable outputs but does not eliminate the underlying risk profile. These findings underscore the need for caution when deploying LLMs in high-stakes settings. Source code: https://github.com/wuyoscar/ISC-Bench

  • 10 authors
·
Mar 4 1

MLLM-HWSI: A Multimodal Large Language Model for Hierarchical Whole Slide Image Understanding

Whole Slide Images (WSIs) exhibit hierarchical structure, where diagnostic information emerges from cellular morphology, regional tissue organization, and global context. Existing Computational Pathology (CPath) Multimodal Large Language Models (MLLMs) typically compress an entire WSI into a single embedding, which hinders fine-grained grounding and ignores how pathologists synthesize evidence across different scales. We introduce MLLM-HWSI, a Hierarchical WSI-level MLLM that aligns visual features with pathology language at four distinct scales, cell as word, patch as phrase, region as sentence, and WSI as paragraph to support interpretable evidence-grounded reasoning. MLLM-HWSI decomposes each WSI into multi-scale embeddings with scale-specific projectors and jointly enforces (i) a hierarchical contrastive objective and (ii) a cross-scale consistency loss, preserving semantic coherence from cells to the WSI. We compute diagnostically relevant patches and aggregate segmented cell embeddings into a compact cellular token per-patch using a lightweight Cell-Cell Attention Fusion (CCAF) transformer. The projected multi-scale tokens are fused with text tokens and fed to an instruction-tuned LLM for open-ended reasoning, VQA, report, and caption generation tasks. Trained in three stages, MLLM-HWSI achieves new SOTA results on 13 WSI-level benchmarks across six CPath tasks. By aligning language with multi-scale visual evidence, MLLM-HWSI provides accurate, interpretable outputs that mirror diagnostic workflows and advance holistic WSI understanding. Code is available at: https://github.com/BasitAlawode/HWSI-MLLM{GitHub}.

  • 9 authors
·
Mar 24

PathoHR: Breast Cancer Survival Prediction on High-Resolution Pathological Images

Breast cancer survival prediction in computational pathology presents a remarkable challenge due to tumor heterogeneity. For instance, different regions of the same tumor in the pathology image can show distinct morphological and molecular characteristics. This makes it difficult to extract representative features from whole slide images (WSIs) that truly reflect the tumor's aggressive potential and likely survival outcomes. In this paper, we present PathoHR, a novel pipeline for accurate breast cancer survival prediction that enhances any size of pathological images to enable more effective feature learning. Our approach entails (1) the incorporation of a plug-and-play high-resolution Vision Transformer (ViT) to enhance patch-wise WSI representation, enabling more detailed and comprehensive feature extraction, (2) the systematic evaluation of multiple advanced similarity metrics for comparing WSI-extracted features, optimizing the representation learning process to better capture tumor characteristics, (3) the demonstration that smaller image patches enhanced follow the proposed pipeline can achieve equivalent or superior prediction accuracy compared to raw larger patches, while significantly reducing computational overhead. Experimental findings valid that PathoHR provides the potential way of integrating enhanced image resolution with optimized feature learning to advance computational pathology, offering a promising direction for more accurate and efficient breast cancer survival prediction. Code will be available at https://github.com/AIGeeksGroup/PathoHR.

  • 10 authors
·
Mar 23, 2025 2

Histopathological Image Classification based on Self-Supervised Vision Transformer and Weak Labels

Whole Slide Image (WSI) analysis is a powerful method to facilitate the diagnosis of cancer in tissue samples. Automating this diagnosis poses various issues, most notably caused by the immense image resolution and limited annotations. WSIs commonly exhibit resolutions of 100Kx100K pixels. Annotating cancerous areas in WSIs on the pixel level is prohibitively labor-intensive and requires a high level of expert knowledge. Multiple instance learning (MIL) alleviates the need for expensive pixel-level annotations. In MIL, learning is performed on slide-level labels, in which a pathologist provides information about whether a slide includes cancerous tissue. Here, we propose Self-ViT-MIL, a novel approach for classifying and localizing cancerous areas based on slide-level annotations, eliminating the need for pixel-wise annotated training data. Self-ViT- MIL is pre-trained in a self-supervised setting to learn rich feature representation without relying on any labels. The recent Vision Transformer (ViT) architecture builds the feature extractor of Self-ViT-MIL. For localizing cancerous regions, a MIL aggregator with global attention is utilized. To the best of our knowledge, Self-ViT- MIL is the first approach to introduce self-supervised ViTs in MIL-based WSI analysis tasks. We showcase the effectiveness of our approach on the common Camelyon16 dataset. Self-ViT-MIL surpasses existing state-of-the-art MIL-based approaches in terms of accuracy and area under the curve (AUC).

  • 6 authors
·
Oct 17, 2022

Multimodal Model for Computational Pathology:Representation Learning and Image Compression

Whole slide imaging (WSI) has transformed digital pathology by enabling computational analysis of gigapixel histopathology images. Recent foundation model advances have accelerated progress in computational pathology, facilitating joint reasoning across pathology images, clinical reports, and structured data. Despite this progress, challenges remain: the extreme resolution of WSIs creates computational hurdles for visual learning; limited expert annotations constrain supervised approaches; integrating multimodal information while preserving biological interpretability remains difficult; and the opacity of modeling ultra-long visual sequences hinders clinical transparency. This review comprehensively surveys recent advances in multimodal computational pathology. We systematically analyze four research directions: (1) self-supervised representation learning and structure-aware token compression for WSIs; (2) multimodal data generation and augmentation; (3) parameter-efficient adaptation and reasoning-enhanced few-shot learning; and (4) multi-agent collaborative reasoning for trustworthy diagnosis. We specifically examine how token compression enables cross-scale modeling and how multi-agent mechanisms simulate a pathologist's "Chain of Thought" across magnifications to achieve uncertainty-aware evidence fusion. Finally, we discuss open challenges and argue that future progress depends on unified multimodal frameworks integrating high-resolution visual data with clinical and biomedical knowledge to support interpretable and safe AI-assisted diagnosis.

  • 3 authors
·
Mar 18

Optimizing Feature Set for Click-Through Rate Prediction

Click-through prediction (CTR) models transform features into latent vectors and enumerate possible feature interactions to improve performance based on the input feature set. Therefore, when selecting an optimal feature set, we should consider the influence of both feature and its interaction. However, most previous works focus on either feature field selection or only select feature interaction based on the fixed feature set to produce the feature set. The former restricts search space to the feature field, which is too coarse to determine subtle features. They also do not filter useless feature interactions, leading to higher computation costs and degraded model performance. The latter identifies useful feature interaction from all available features, resulting in many redundant features in the feature set. In this paper, we propose a novel method named OptFS to address these problems. To unify the selection of feature and its interaction, we decompose the selection of each feature interaction into the selection of two correlated features. Such a decomposition makes the model end-to-end trainable given various feature interaction operations. By adopting feature-level search space, we set a learnable gate to determine whether each feature should be within the feature set. Because of the large-scale search space, we develop a learning-by-continuation training scheme to learn such gates. Hence, OptFS generates the feature set only containing features which improve the final prediction results. Experimentally, we evaluate OptFS on three public datasets, demonstrating OptFS can optimize feature sets which enhance the model performance and further reduce both the storage and computational cost.

  • 6 authors
·
Jan 25, 2023

WaDec: Decompiling WebAssembly Using Large Language Model

WebAssembly (abbreviated Wasm) has emerged as a cornerstone of web development, offering a compact binary format that allows high-performance applications to run at near-native speeds in web browsers. Despite its advantages, Wasm's binary nature presents significant challenges for developers and researchers, particularly regarding readability when debugging or analyzing web applications. Therefore, effective decompilation becomes crucial. Unfortunately, traditional decompilers often struggle with producing readable outputs. While some large language model (LLM)-based decompilers have shown good compatibility with general binary files, they still face specific challenges when dealing with Wasm. In this paper, we introduce a novel approach, WaDec, which is the first use of a fine-tuned LLM to interpret and decompile Wasm binary code into a higher-level, more comprehensible source code representation. The LLM was meticulously fine-tuned using a specialized dataset of wat-c code snippets, employing self-supervised learning techniques. This enables WaDec to effectively decompile not only complete wat functions but also finer-grained wat code snippets. Our experiments demonstrate that WaDec markedly outperforms current state-of-the-art tools, offering substantial improvements across several metrics. It achieves a code inflation rate of only 3.34%, a dramatic 97% reduction compared to the state-of-the-art's 116.94%. Unlike baselines' output that cannot be directly compiled or executed, WaDec maintains a recompilability rate of 52.11%, a re-execution rate of 43.55%, and an output consistency of 27.15%. Additionally, it significantly exceeds state-of-the-art performance in AST edit distance similarity by 185%, cyclomatic complexity by 8%, and cosine similarity by 41%, achieving an average code similarity above 50%.

  • 3 authors
·
Sep 10, 2024

Towards Understanding and Harnessing the Transferability of Prognostic Knowledge in Computational Pathology

Whole-Slide Image (WSI) is an important tool for evaluating the prognosis of cancer patients. Present WSI-based prognosis studies generally follow a conventional paradigm -- cancer-specific model development -- where one cancer disease corresponds to one model and this model cannot make use of the prognostic knowledge from others. Despite its notable success in recent years, this paradigm has inherent limitations and has always been struggling with practical requirements: (i) scaling to the rare tumor diseases with very limited samples and (ii) benefiting from the generalizable prognostic knowledge in other cancers. To this end, this paper presents the first systematic study on Prognostic Knowledge Transfer in Pathology, called Path-PKT. It comprises three main parts. (1) We curate a large dataset (UNI2-h-DSS) with 13 cancers and use it to evaluate the transferability of prognostic knowledge between different cancers computationally. (2) We design experiments to understand what factors affect knowledge transfer and what causes positive transfers. (3) Motivated by empirical findings, we propose a new baseline approach (MoE-PKT) with a routing mechanism to utilize the generalizable prognostic knowledge in other cancers. Finally, we show the transferability of source models to rare tumor diseases. This study could lay solid foundations for the study of knowledge transfer in WSI-based cancer prognosis. Source code is available at https://github.com/liupei101/Path-PKT.

  • 4 authors
·
Aug 18, 2025

Widget2Code: From Visual Widgets to UI Code via Multimodal LLMs

User interface to code (UI2Code) aims to generate executable code that can faithfully reconstruct a given input UI. Prior work focuses largely on web pages and mobile screens, leaving app widgets underexplored. Unlike web or mobile UIs with rich hierarchical context, widgets are compact, context-free micro-interfaces that summarize key information through dense layouts and iconography under strict spatial constraints. Moreover, while (image, code) pairs are widely available for web or mobile UIs, widget designs are proprietary and lack accessible markup. We formalize this setting as the Widget-to-Code (Widget2Code) and introduce an image-only widget benchmark with fine-grained, multi-dimensional evaluation metrics. Benchmarking shows that although generalized multimodal large language models (MLLMs) outperform specialized UI2Code methods, they still produce unreliable and visually inconsistent code. To address these limitations, we develop a baseline that jointly advances perceptual understanding and structured code generation. At the perceptual level, we follow widget design principles to assemble atomic components into complete layouts, equipped with icon retrieval and reusable visualization modules. At the system level, we design an end-to-end infrastructure, WidgetFactory, which includes a framework-agnostic widget-tailored domain-specific language (WidgetDSL) and a compiler that translates it into multiple front-end implementations (e.g., React, HTML/CSS). An adaptive rendering module further refines spatial dimensions to satisfy compactness constraints. Together, these contributions substantially enhance visual fidelity, establishing a strong baseline and unified infrastructure for future Widget2Code research.

  • 13 authors
·
Mar 25

Predicting Maintenance Cessation of Open Source Software Repositories with An Integrated Feature Framework

The maintenance risks of open source software (OSS) projects pose significant threats to the quality, security, and resilience of modern software supply chains. While prior research has proposed diverse approaches for predicting OSS maintenance risk -- leveraging signals ranging from surface features (e.g., stars, commits) to social network analyses and behavioral patterns -- existing methods often suffer from ambiguous operational definitions, limited interpretability, and datasets of insufficient scale or generalizability. In this work, we introduce ``maintenance cessation'', grounded in both explicit archival status and rigorous semantic analysis of project documentation. Building on this foundation, we curate a large-scale, longitudinal dataset of 115,466 GitHub repositories -- encompassing 57,733 confirmed cessation events -- complemented by comprehensive, timeline-based behavioral features. We propose an integrated, multi-perspective feature framework for predicting maintenance cessation, systematically combining user-centric features, maintainer-centric features and project evolution features. AFT survival analysis demonstrates a high C-index (0.846), substantially outperforming models relying only on surface features. Feature ablation and SHAP analysis further confirm the effectiveness and interpretability of our approach. Finally, we demonstrate real-world applicability by deploying a GBSA classifier in the openEuler ecosystem for proactive package risk screening. Our work establishes a scalable, interpretable foundation for maintenance-risk prediction, enabling reproducible risk management across large-scale open source ecosystems.

  • 5 authors
·
Jul 29, 2025

FastPathology: An open-source platform for deep learning-based research and decision support in digital pathology

Deep convolutional neural networks (CNNs) are the current state-of-the-art for digital analysis of histopathological images. The large size of whole-slide microscopy images (WSIs) requires advanced memory handling to read, display and process these images. There are several open-source platforms for working with WSIs, but few support deployment of CNN models. These applications use third-party solutions for inference, making them less user-friendly and unsuitable for high-performance image analysis. To make deployment of CNNs user-friendly and feasible on low-end machines, we have developed a new platform, FastPathology, using the FAST framework and C++. It minimizes memory usage for reading and processing WSIs, deployment of CNN models, and real-time interactive visualization of results. Runtime experiments were conducted on four different use cases, using different architectures, inference engines, hardware configurations and operating systems. Memory usage for reading, visualizing, zooming and panning a WSI were measured, using FastPathology and three existing platforms. FastPathology performed similarly in terms of memory to the other C++ based application, while using considerably less than the two Java-based platforms. The choice of neural network model, inference engine, hardware and processors influenced runtime considerably. Thus, FastPathology includes all steps needed for efficient visualization and processing of WSIs in a single application, including inference of CNNs with real-time display of the results. Source code, binary releases and test data can be found online on GitHub at https://github.com/SINTEFMedtek/FAST-Pathology/.

  • 6 authors
·
Nov 11, 2020

The Compliance Trap: How Structural Constraints Degrade Frontier AI Metacognition Under Adversarial Pressure

As frontier AI models are deployed in high-stakes decision pipelines, their ability to maintain metacognitive stability -- knowing what they do not know, detecting errors, seeking clarification -- under adversarial pressure is a critical safety requirement. Current safety evaluations focus on detecting strategic deception (scheming); we investigate a more fundamental failure mode: cognitive collapse. We present SCHEMA, an evaluation of 11 frontier models from 8 vendors across 67,221 scored records using a 6-condition factorial design with dual-classifier scoring. We find that 8 of 11 models suffer catastrophic metacognitive degradation under adversarial pressure, with accuracy dropping by up to 30.2 percentage points (all p < 2 times 10^{-8}, surviving Bonferroni correction). Crucially, we identify a "Compliance Trap": through factorial isolation and a benign distraction control, we demonstrate that collapse is driven not by the psychological content of survival threats, but by compliance-forcing instructions that override epistemic boundaries. Removing the compliance suffix restores performance even under active threat. Models with advanced reasoning capabilities exhibit the most severe absolute degradation, while Anthropic's Constitutional AI demonstrates near-perfect immunity -- not from superior capability (Google's Gemini matches its baseline accuracy) but from alignment-specific training. We release the complete dataset and evaluation infrastructure.

  • 1 authors
·
May 3

Temporal Spatial Decomposition and Fusion Network for Time Series Forecasting

Feature engineering is required to obtain better results for time series forecasting, and decomposition is a crucial one. One decomposition approach often cannot be used for numerous forecasting tasks since the standard time series decomposition lacks flexibility and robustness. Traditional feature selection relies heavily on preexisting domain knowledge, has no generic methodology, and requires a lot of labor. However, most time series prediction models based on deep learning typically suffer from interpretability issue, so the "black box" results lead to a lack of confidence. To deal with the above issues forms the motivation of the thesis. In the paper we propose TSDFNet as a neural network with self-decomposition mechanism and an attentive feature fusion mechanism, It abandons feature engineering as a preprocessing convention and creatively integrates it as an internal module with the deep model. The self-decomposition mechanism empowers TSDFNet with extensible and adaptive decomposition capabilities for any time series, users can choose their own basis functions to decompose the sequence into temporal and generalized spatial dimensions. Attentive feature fusion mechanism has the ability to capture the importance of external variables and the causality with target variables. It can automatically suppress the unimportant features while enhancing the effective ones, so that users do not have to struggle with feature selection. Moreover, TSDFNet is easy to look into the "black box" of the deep neural network by feature visualization and analyze the prediction results. We demonstrate performance improvements over existing widely accepted models on more than a dozen datasets, and three experiments showcase the interpretability of TSDFNet.

  • 2 authors
·
Oct 5, 2022

Pushing Boundaries: Mixup's Influence on Neural Collapse

Mixup is a data augmentation strategy that employs convex combinations of training instances and their respective labels to augment the robustness and calibration of deep neural networks. Despite its widespread adoption, the nuanced mechanisms that underpin its success are not entirely understood. The observed phenomenon of Neural Collapse, where the last-layer activations and classifier of deep networks converge to a simplex equiangular tight frame (ETF), provides a compelling motivation to explore whether mixup induces alternative geometric configurations and whether those could explain its success. In this study, we delve into the last-layer activations of training data for deep networks subjected to mixup, aiming to uncover insights into its operational efficacy. Our investigation, spanning various architectures and dataset pairs, reveals that mixup's last-layer activations predominantly converge to a distinctive configuration different than one might expect. In this configuration, activations from mixed-up examples of identical classes align with the classifier, while those from different classes delineate channels along the decision boundary. Moreover, activations in earlier layers exhibit patterns, as if trained with manifold mixup. These findings are unexpected, as mixed-up features are not simple convex combinations of feature class means (as one might get, for example, by training mixup with the mean squared error loss). By analyzing this distinctive geometric configuration, we elucidate the mechanisms by which mixup enhances model calibration. To further validate our empirical observations, we conduct a theoretical analysis under the assumption of an unconstrained features model, utilizing the mixup loss. Through this, we characterize and derive the optimal last-layer features under the assumption that the classifier forms a simplex ETF.

  • 3 authors
·
Feb 8, 2024

FedLoGe: Joint Local and Generic Federated Learning under Long-tailed Data

Federated Long-Tailed Learning (Fed-LT), a paradigm wherein data collected from decentralized local clients manifests a globally prevalent long-tailed distribution, has garnered considerable attention in recent times. In the context of Fed-LT, existing works have predominantly centered on addressing the data imbalance issue to enhance the efficacy of the generic global model while neglecting the performance at the local level. In contrast, conventional Personalized Federated Learning (pFL) techniques are primarily devised to optimize personalized local models under the presumption of a balanced global data distribution. This paper introduces an approach termed Federated Local and Generic Model Training in Fed-LT (FedLoGe), which enhances both local and generic model performance through the integration of representation learning and classifier alignment within a neural collapse framework. Our investigation reveals the feasibility of employing a shared backbone as a foundational framework for capturing overarching global trends, while concurrently employing individualized classifiers to encapsulate distinct refinements stemming from each client's local features. Building upon this discovery, we establish the Static Sparse Equiangular Tight Frame Classifier (SSE-C), inspired by neural collapse principles that naturally prune extraneous noisy features and foster the acquisition of potent data representations. Furthermore, leveraging insights from imbalance neural collapse's classifier norm patterns, we develop Global and Local Adaptive Feature Realignment (GLA-FR) via an auxiliary global classifier and personalized Euclidean norm transfer to align global features with client preferences. Extensive experimental results on CIFAR-10/100-LT, ImageNet, and iNaturalist demonstrate the advantage of our method over state-of-the-art pFL and Fed-LT approaches.

  • 9 authors
·
Jan 17, 2024

Unified Embedding: Battle-Tested Feature Representations for Web-Scale ML Systems

Learning high-quality feature embeddings efficiently and effectively is critical for the performance of web-scale machine learning systems. A typical model ingests hundreds of features with vocabularies on the order of millions to billions of tokens. The standard approach is to represent each feature value as a d-dimensional embedding, introducing hundreds of billions of parameters for extremely high-cardinality features. This bottleneck has led to substantial progress in alternative embedding algorithms. Many of these methods, however, make the assumption that each feature uses an independent embedding table. This work introduces a simple yet highly effective framework, Feature Multiplexing, where one single representation space is used across many different categorical features. Our theoretical and empirical analysis reveals that multiplexed embeddings can be decomposed into components from each constituent feature, allowing models to distinguish between features. We show that multiplexed representations lead to Pareto-optimal parameter-accuracy tradeoffs for three public benchmark datasets. Further, we propose a highly practical approach called Unified Embedding with three major benefits: simplified feature configuration, strong adaptation to dynamic data distributions, and compatibility with modern hardware. Unified embedding gives significant improvements in offline and online metrics compared to highly competitive baselines across five web-scale search, ads, and recommender systems, where it serves billions of users across the world in industry-leading products.

  • 7 authors
·
May 20, 2023

Addressing Representation Collapse in Vector Quantized Models with One Linear Layer

Vector Quantization (VQ) is a widely used method for converting continuous representations into discrete codes, which has become fundamental in unsupervised representation learning and latent generative models. However, VQ models are often hindered by the problem of representation collapse in the latent space, which leads to low codebook utilization and limits the scalability of the codebook for large-scale training. Existing methods designed to mitigate representation collapse typically reduce the dimensionality of latent space at the expense of model capacity, which do not fully resolve the core issue. In this study, we conduct a theoretical analysis of representation collapse in VQ models and identify its primary cause as the disjoint optimization of the codebook, where only a small subset of code vectors are updated through gradient descent. To address this issue, we propose SimVQ, a novel method which reparameterizes the code vectors through a linear transformation layer based on a learnable latent basis. This transformation optimizes the entire linear space spanned by the codebook, rather than merely updating the code vector selected by the nearest-neighbor search in vanilla VQ models. Although it is commonly understood that the multiplication of two linear matrices is equivalent to applying a single linear layer, our approach works surprisingly well in resolving the collapse issue in VQ models with just one linear layer. We validate the efficacy of SimVQ through extensive experiments across various modalities, including image and audio data with different model architectures. Our code is available at https://github.com/youngsheen/SimVQ.

  • 4 authors
·
Nov 4, 2024

Metronome: Bound the Cache, Keep the Beat for Real-Time Interaction Model Serving

Real-time interaction models -- Moshi, MiniCPM-o, Qwen-Omni -- turn serving into a periodic real-time task: on every frame a session ingests streaming audio and must respond by a recurring wall-clock deadline, while its KV cache grows monotonically and stays pinned for the whole conversation. This regime hides a dangerous failure mode. On a real full-duplex stack, sustained load does not degrade serving gracefully: it falls off a cliff, jumping in one step from milliseconds per frame to a stalled engine when accumulated session state exhausts the KV pool. The collapse is metastable -- identical five-minute runs collapse or survive on run-to-run variance -- and silent: latency and deadline-miss metrics read healthy throughout. We show one move restores both stability and observability: bound each session's resident state, and latency starts telling the truth. Metronome's in-engine KV window eliminates the collapse (0/20 vs. 14/20 runs across two batches) and turns per-frame latency into a monotone load signal, on which an online admission controller discovers the schedulable concurrency; without the window, the identical controller over-admits into the wall. A first-order model predicts the collapse time within a few percent on the headline model, and a quality probe validates the bound's design by ablation: the window alone is quality-free in turn-based decoding, and its few pinned attention-sink tokens are what keep free-running generation healthy. Everything is measured end-to-end on real audio, across four interaction models on one GPU.

  • 2 authors
·
Jul 1

Linguistic Collapse: Neural Collapse in (Large) Language Models

Neural collapse (NC) is a phenomenon observed in classification tasks where top-layer representations collapse into their class means, which become equinorm, equiangular and aligned with the classifiers. These behaviors -- associated with generalization and robustness -- would manifest under specific conditions: models are trained towards zero loss, with noise-free labels belonging to balanced classes, which do not outnumber the model's hidden dimension. Recent studies have explored NC in the absence of one or more of these conditions to extend and capitalize on the associated benefits of ideal geometries. Language modeling presents a curious frontier, as training by token prediction constitutes a classification task where none of the conditions exist: the vocabulary is imbalanced and exceeds the embedding dimension; different tokens might correspond to similar contextual embeddings; and large language models (LLMs) in particular are typically only trained for a few epochs. This paper empirically investigates the impact of scaling the architectures and training of causal language models (CLMs) on their progression towards NC. We find that NC properties that develop with scaling are linked to generalization. Moreover, there is evidence of some relationship between NC and generalization independent of scale. Our work therefore underscores the generality of NC as it extends to the novel and more challenging setting of language modeling. Downstream, we seek to inspire further research on the phenomenon to deepen our understanding of LLMs -- and neural networks at large -- and improve existing architectures based on NC-related properties.

  • 2 authors
·
May 27, 2024

PLUTO: Pathology-Universal Transformer

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

  • 33 authors
·
May 13, 2024

3DIS: Depth-Driven Decoupled Instance Synthesis for Text-to-Image Generation

The increasing demand for controllable outputs in text-to-image generation has spurred advancements in multi-instance generation (MIG), allowing users to define both instance layouts and attributes. However, unlike image-conditional generation methods such as ControlNet, MIG techniques have not been widely adopted in state-of-the-art models like SD2 and SDXL, primarily due to the challenge of building robust renderers that simultaneously handle instance positioning and attribute rendering. In this paper, we introduce Depth-Driven Decoupled Instance Synthesis (3DIS), a novel framework that decouples the MIG process into two stages: (i) generating a coarse scene depth map for accurate instance positioning and scene composition, and (ii) rendering fine-grained attributes using pre-trained ControlNet on any foundational model, without additional training. Our 3DIS framework integrates a custom adapter into LDM3D for precise depth-based layouts and employs a finetuning-free method for enhanced instance-level attribute rendering. Extensive experiments on COCO-Position and COCO-MIG benchmarks demonstrate that 3DIS significantly outperforms existing methods in both layout precision and attribute rendering. Notably, 3DIS offers seamless compatibility with diverse foundational models, providing a robust, adaptable solution for advanced multi-instance generation. The code is available at: https://github.com/limuloo/3DIS.

  • 4 authors
·
Oct 16, 2024

LWGANet: A Lightweight Group Attention Backbone for Remote Sensing Visual Tasks

Remote sensing (RS) visual tasks have gained significant academic and practical importance. However, they encounter numerous challenges that hinder effective feature extraction, including the detection and recognition of multiple objects exhibiting substantial variations in scale within a single image. While prior dual-branch or multi-branch architectural strategies have been effective in managing these object variances, they have concurrently resulted in considerable increases in computational demands and parameter counts. Consequently, these architectures are rendered less viable for deployment on resource-constrained devices. Contemporary lightweight backbone networks, designed primarily for natural images, frequently encounter difficulties in effectively extracting features from multi-scale objects, which compromises their efficacy in RS visual tasks. This article introduces LWGANet, a specialized lightweight backbone network tailored for RS visual tasks, incorporating a novel lightweight group attention (LWGA) module designed to address these specific challenges. LWGA module, tailored for RS imagery, adeptly harnesses redundant features to extract a wide range of spatial information, from local to global scales, without introducing additional complexity or computational overhead. This facilitates precise feature extraction across multiple scales within an efficient framework.LWGANet was rigorously evaluated across twelve datasets, which span four crucial RS visual tasks: scene classification, oriented object detection, semantic segmentation, and change detection. The results confirm LWGANet's widespread applicability and its ability to maintain an optimal balance between high performance and low complexity, achieving SOTA results across diverse datasets. LWGANet emerged as a novel solution for resource-limited scenarios requiring robust RS image processing capabilities.

  • 5 authors
·
Jan 17, 2025

One Token Away from Collapse: The Fragility of Instruction-Tuned Helpfulness

Instruction-tuned large language models produce helpful, structured responses, but how robust is this helpfulness under trivial constraints? We show that simple lexical constraints (banning a single punctuation character or common word) cause instruction-tuned LLMs to collapse their responses, losing 14--48\% of comprehensiveness across seven models spanning five families (7B--70B, open- and closed-weight). A blinded human evaluation with 10 STEM-trained evaluators confirms genuine content loss, with information criteria degrading 1.5--2.3times more than surface criteria, a finding corroborated by over 4,100 automated pairwise comparisons (77--100\% baseline preference) across three LLM judges from two model families. Diagnostic analysis identifies this as a planning failure: two-pass generation recovers 59--96\% of response length, and linear probes on prompt representations predict response length with R^2 = 0.51--0.94 before generation begins. The same probes yield negative R^2 on base models, confirming that instruction tuning introduces the representational structure underlying the collapse. Base models show no systematic degradation under identical constraints, demonstrating that instruction tuning couples task competence to narrow surface-form templates. The effect extends to realistic deployment constraints (preamble suppression, corporate tone guidelines, legal compliance hedging, accessibility requirements) causing comparable degradation (-22\% to -34\%), with suppressing the conversational opener alone (``Certainly!'') causing 40\% collapse on our most fragile model despite restricting only the opening tokens. We further show that standard independent LLM-as-judge evaluation detects only a 3.5\% quality drop where pairwise evaluation reveals 23\%, exposing a methodological blind spot in current evaluation practice.

  • 4 authors
·
Apr 26

MambaMIL: Enhancing Long Sequence Modeling with Sequence Reordering in Computational Pathology

Multiple Instance Learning (MIL) has emerged as a dominant paradigm to extract discriminative feature representations within Whole Slide Images (WSIs) in computational pathology. Despite driving notable progress, existing MIL approaches suffer from limitations in facilitating comprehensive and efficient interactions among instances, as well as challenges related to time-consuming computations and overfitting. In this paper, we incorporate the Selective Scan Space State Sequential Model (Mamba) in Multiple Instance Learning (MIL) for long sequence modeling with linear complexity, termed as MambaMIL. By inheriting the capability of vanilla Mamba, MambaMIL demonstrates the ability to comprehensively understand and perceive long sequences of instances. Furthermore, we propose the Sequence Reordering Mamba (SR-Mamba) aware of the order and distribution of instances, which exploits the inherent valuable information embedded within the long sequences. With the SR-Mamba as the core component, MambaMIL can effectively capture more discriminative features and mitigate the challenges associated with overfitting and high computational overhead. Extensive experiments on two public challenging tasks across nine diverse datasets demonstrate that our proposed framework performs favorably against state-of-the-art MIL methods. The code is released at https://github.com/isyangshu/MambaMIL.

  • 3 authors
·
Mar 11, 2024

Sign-Aware Gated Sparse Autoencoders: Modeling Anticorrelated Features with Bi-Jump-ReLU Activations

Sparse Autoencoders (SAEs) extract interpretable features from Large Language Models, but standard variants enforce non-negativity, forcing separate latents for diametrically opposed concepts (e.g., "pressure too high" vs. "pressure too low") and wasting dictionary capacity when features are anticorrelated. We propose the Sign-Aware Gated SAE (SA-GSAE): two-sided gated sparsity with signed magnitude and auxiliary supervision. A polarity-sensitive gate selects support on either sign, a signed-magnitude path avoids L1 shrinkage, and an auxiliary reconstruction prevents gate collapse. Bipolar sharing - one latent encoding both signs along a shared direction - is realised via a new Bi-Jump-ReLU activation; parameter accounting shows sign-awareness stays parameter-efficient even when anticorrelated pairs are rare. On real LLM activations across three mid-depth hookpoints on Pythia-1B and SmolLM3-3B (6 cells, 3 seeds), a half-width SA-GSAE at width H strictly Pareto-dominates a full-width Gated SAE at 2H over the entire swept L0 overlap on 3 of 6 cells (both MLP-output hookpoints and resid-mid/Pythia-1B); on the remaining 3 it matches R^2 within 0.025 (max gap -0.008) while cutting dead fraction by 0.35-0.62 absolute. Sweep-geomean dead-fraction reductions are ~100x-500x on MLP-output cells and Pythia-1B resid, ~2x-4x on attention cells and SmolLM3-3B resid. Ablations show the two-sided gate and auxiliary loss are load-bearing (no auxiliary collapses LR to 0.27, 98% dead); tying r_i^+ = r_i^- is indistinguishable (|Delta R^2| = 0.0015), and we recommend this symmetric variant as default. MLP-output gains come from most latents carrying both polarities; on attention, bipolar structure concentrates in a small set of top latents. Full-width SA-GSAE exhibits a reproducible reconstruction collapse at SmolLM3-3B resid that the half-width entirely avoids.

  • 5 authors
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May 26

LLM-FE: Automated Feature Engineering for Tabular Data with LLMs as Evolutionary Optimizers

Automated feature engineering plays a critical role in improving predictive model performance for tabular learning tasks. Traditional automated feature engineering methods are limited by their reliance on pre-defined transformations within fixed, manually designed search spaces, often neglecting domain knowledge. Recent advances using Large Language Models (LLMs) have enabled the integration of domain knowledge into the feature engineering process. However, existing LLM-based approaches use direct prompting or rely solely on validation scores for feature selection, failing to leverage insights from prior feature discovery experiments or establish meaningful reasoning between feature generation and data-driven performance. To address these challenges, we propose LLM-FE, a novel framework that combines evolutionary search with the domain knowledge and reasoning capabilities of LLMs to automatically discover effective features for tabular learning tasks. LLM-FE formulates feature engineering as a program search problem, where LLMs propose new feature transformation programs iteratively, and data-driven feedback guides the search process. Our results demonstrate that LLM-FE consistently outperforms state-of-the-art baselines, significantly enhancing the performance of tabular prediction models across diverse classification and regression benchmarks.

Quilt-LLaVA: Visual Instruction Tuning by Extracting Localized Narratives from Open-Source Histopathology Videos

The gigapixel scale of whole slide images (WSIs) poses a challenge for histopathology multi-modal chatbots, requiring a global WSI analysis for diagnosis, compounding evidence from different WSI patches. Current visual instruction datasets, generated through large language models, focus on creating question/answer pairs for individual image patches, which may lack diagnostic capacity on their own in histopathology, further complicated by the absence of spatial grounding in histopathology image captions. To bridge this gap, we introduce Quilt-Instruct, a large-scale dataset of 107,131 histopathology-specific instruction question/answer pairs, that is collected by leveraging educational histopathology videos from YouTube, which provides spatial localization of captions by automatically extracting narrators' cursor movements. In addition, we provide contextual reasoning by extracting diagnosis and supporting facts from the entire video content to guide the extrapolative reasoning of GPT-4. Using Quilt-Instruct, we train Quilt-LLaVA, which can reason beyond the given single image patch, enabling diagnostic reasoning and the capability of spatial awareness. To evaluate Quilt-LLaVA, we propose a comprehensive evaluation dataset created from 985 images and 1283 human-generated question-answers. We also thoroughly evaluate Quilt-LLaVA using public histopathology datasets, where Quilt-LLaVA significantly outperforms SOTA by over 10% on relative GPT-4 score and 4% and 9% on open and closed set VQA. Our code, data, and model are publicly available at quilt-llava.github.io.

  • 5 authors
·
Dec 7, 2023

NRR-Core: Non-Resolution Reasoning as a Computational Framework for Contextual Identity and Ambiguity Preservation

Current artificial intelligence systems exhibit a fundamental architectural limitation: they resolve ambiguity prematurely. This premature semantic collapse--collapsing multiple valid interpretations into single outputs--stems from classical identity assumptions in neural architectures. We propose Non-Resolution Reasoning (NRR), a framework treating ambiguity retention as a valid reasoning mode. NRR introduces three principles: (1) Non-Identity (A neq A)--the same symbol refers to different entities across contexts; (2) Approximate Identity (A approx A)--entities share partial structural overlap without being identical; (3) Non-Resolution--conflicting interpretations coexist without forced convergence. We formalize these through Multi-Vector Embeddings for context-dependent representation, Non-Collapsing Attention for parallel interpretation retention, and Contextual Identity Tracking (CIT) for maintaining A neq A across inference. We illustrate NRR through case studies in paradox handling, creative generation, and context-dependent reasoning. Functional verification in a synthetic two-turn disambiguation task shows NRR-lite maintains high entropy (H = 0.91 bits, near-maximum 1.0) at ambiguous turns while standard architectures collapse early (H = 0.15 bits), preserving interpretive flexibility until context arrives. NRR challenges the assumption that meaning must collapse to be useful. The question is not whether AI should resolve ambiguity, but when, how, and under whose control.

  • 1 authors
·
Dec 15, 2025

The Illusion of High Utility in Safety Alignment of Text-to-Image Diffusion Models

Safety alignment of text-to-image (T2I) diffusion models aims to suppress harmful generations while preserving utility on benign prompts. Recent methods often appear to deliver high safety with high utility, but this conclusion rests largely on coarse global utility metrics (e.g., FID, CLIPScore) that are insensitive to fine-grained semantic correctness, creating an illusion of high utility. We show that when utility is measured with structured evaluation, this illusion breaks: on TIFA (Text-to-Image Faithfulness evaluation with Question Answering), safety-aligned models suffer substantial drops in semantic fidelity, including failures in object counts, attributes, and relationships. To diagnose the source of this gap, we analyze the text-encoder prompt embedding space and uncover semantic collapse, a contraction of embedding spread coupled with distortion of inter-prompt similarity structure, which strongly correlates with structured utility loss. Guided by this insight, we propose StructureAware Geometric Regularization (SAGE), a safety alignment objective that explicitly preserves embedding spread and inter-prompt relational structure during adaptation. Our method restores structured utility (TIFA +5.0% over prior state-of-the-art) while maintaining strong safety performance and competitive coarse-grained utility scores. Our source code and trained models are available at https://adeelyousaf.github.io/SAGE_ECCV26_Project_Page/.

  • 5 authors
·
Jun 30

Controllable Latent Space Augmentation for Digital Pathology

Whole slide image (WSI) analysis in digital pathology presents unique challenges due to the gigapixel resolution of WSIs and the scarcity of dense supervision signals. While Multiple Instance Learning (MIL) is a natural fit for slide-level tasks, training robust models requires large and diverse datasets. Even though image augmentation techniques could be utilized to increase data variability and reduce overfitting, implementing them effectively is not a trivial task. Traditional patch-level augmentation is prohibitively expensive due to the large number of patches extracted from each WSI, and existing feature-level augmentation methods lack control over transformation semantics. We introduce HistAug, a fast and efficient generative model for controllable augmentations in the latent space for digital pathology. By conditioning on explicit patch-level transformations (e.g., hue, erosion), HistAug generates realistic augmented embeddings while preserving initial semantic information. Our method allows the processing of a large number of patches in a single forward pass efficiently, while at the same time consistently improving MIL model performance. Experiments across multiple slide-level tasks and diverse organs show that HistAug outperforms existing methods, particularly in low-data regimes. Ablation studies confirm the benefits of learned transformations over noise-based perturbations and highlight the importance of uniform WSI-wise augmentation. Code is available at https://github.com/MICS-Lab/HistAug.

  • 6 authors
·
Aug 20, 2025

Build the web for agents, not agents for the web

Recent advancements in Large Language Models (LLMs) and multimodal counterparts have spurred significant interest in developing web agents -- AI systems capable of autonomously navigating and completing tasks within web environments. While holding tremendous promise for automating complex web interactions, current approaches face substantial challenges due to the fundamental mismatch between human-designed interfaces and LLM capabilities. Current methods struggle with the inherent complexity of web inputs, whether processing massive DOM trees, relying on screenshots augmented with additional information, or bypassing the user interface entirely through API interactions. This position paper advocates for a paradigm shift in web agent research: rather than forcing web agents to adapt to interfaces designed for humans, we should develop a new interaction paradigm specifically optimized for agentic capabilities. To this end, we introduce the concept of an Agentic Web Interface (AWI), an interface specifically designed for agents to navigate a website. We establish six guiding principles for AWI design, emphasizing safety, efficiency, and standardization, to account for the interests of all primary stakeholders. This reframing aims to overcome fundamental limitations of existing interfaces, paving the way for more efficient, reliable, and transparent web agent design, which will be a collaborative effort involving the broader ML community.

  • 4 authors
·
Jun 12, 2025 2

Deep Open-Set Recognition for Silicon Wafer Production Monitoring

The chips contained in any electronic device are manufactured over circular silicon wafers, which are monitored by inspection machines at different production stages. Inspection machines detect and locate any defect within the wafer and return a Wafer Defect Map (WDM), i.e., a list of the coordinates where defects lie, which can be considered a huge, sparse, and binary image. In normal conditions, wafers exhibit a small number of randomly distributed defects, while defects grouped in specific patterns might indicate known or novel categories of failures in the production line. Needless to say, a primary concern of semiconductor industries is to identify these patterns and intervene as soon as possible to restore normal production conditions. Here we address WDM monitoring as an open-set recognition problem to accurately classify WDM in known categories and promptly detect novel patterns. In particular, we propose a comprehensive pipeline for wafer monitoring based on a Submanifold Sparse Convolutional Network, a deep architecture designed to process sparse data at an arbitrary resolution, which is trained on the known classes. To detect novelties, we define an outlier detector based on a Gaussian Mixture Model fitted on the latent representation of the classifier. Our experiments on a real dataset of WDMs show that directly processing full-resolution WDMs by Submanifold Sparse Convolutions yields superior classification performance on known classes than traditional Convolutional Neural Networks, which require a preliminary binning to reduce the size of the binary images representing WDMs. Moreover, our solution outperforms state-of-the-art open-set recognition solutions in detecting novelties.

  • 5 authors
·
Aug 30, 2022

Multiple Instance Learning Framework with Masked Hard Instance Mining for Whole Slide Image Classification

The whole slide image (WSI) classification is often formulated as a multiple instance learning (MIL) problem. Since the positive tissue is only a small fraction of the gigapixel WSI, existing MIL methods intuitively focus on identifying salient instances via attention mechanisms. However, this leads to a bias towards easy-to-classify instances while neglecting hard-to-classify instances. Some literature has revealed that hard examples are beneficial for modeling a discriminative boundary accurately. By applying such an idea at the instance level, we elaborate a novel MIL framework with masked hard instance mining (MHIM-MIL), which uses a Siamese structure (Teacher-Student) with a consistency constraint to explore the potential hard instances. With several instance masking strategies based on attention scores, MHIM-MIL employs a momentum teacher to implicitly mine hard instances for training the student model, which can be any attention-based MIL model. This counter-intuitive strategy essentially enables the student to learn a better discriminating boundary. Moreover, the student is used to update the teacher with an exponential moving average (EMA), which in turn identifies new hard instances for subsequent training iterations and stabilizes the optimization. Experimental results on the CAMELYON-16 and TCGA Lung Cancer datasets demonstrate that MHIM-MIL outperforms other latest methods in terms of performance and training cost. The code is available at: https://github.com/DearCaat/MHIM-MIL.

  • 6 authors
·
Jul 27, 2023

Evoflux: Inference-Time Evolution of Executable Tool Workflows for Compact Agents

Compact language models (LMs) reduce cost, latency, and deployment risk for tool agents. Yet MCP-style tool use requires more than isolated function calling: an agent must discover tools from live catalogs, satisfy schemas, preserve dependencies across intermediate outputs, and ground final responses in executed evidence. Small planners often generate plausible workflow graphs that fail under tool resolution, parameter validation, dependency tracking, or execution. We argue that this failure mode is poorly handled by small-corpus distillation. A few hundred teacher traces can teach workflow format, but rarely cover the recovery behavior needed to repair failed plans over changing tool catalogs. We introduce Evoflux, an inference-time evolutionary search method that treats compact tool use as the repair of executable tool workflows. It evolves typed workflow graphs through structured edits, execution feedback, adaptive intensity, meta-guided redesign, and diversity pruning. On held-out MCP-Bench tasks spanning live MCP servers and 250 tools, Evoflux raises execution feasibility from roughly 3% to 17-24% across small planners. In contrast, SFT and SFT+DPO on the same search-mined data match, underperform, or collapse below zero-shot performance; ReAct reaches higher peaks, but with higher variance and token cost. These results show that execution-grounded search is more reliable under scarce teacher-trace budgets.

Multiple Instance Learning Framework with Masked Hard Instance Mining for Gigapixel Histopathology Image Analysis

Digitizing pathological images into gigapixel Whole Slide Images (WSIs) has opened new avenues for Computational Pathology (CPath). As positive tissue comprises only a small fraction of gigapixel WSIs, existing Multiple Instance Learning (MIL) methods typically focus on identifying salient instances via attention mechanisms. However, this leads to a bias towards easy-to-classify instances while neglecting challenging ones. Recent studies have shown that hard examples are crucial for accurately modeling discriminative boundaries. Applying such an idea at the instance level, we elaborate a novel MIL framework with masked hard instance mining (MHIM-MIL), which utilizes a Siamese structure with a consistency constraint to explore the hard instances. Using a class-aware instance probability, MHIM-MIL employs a momentum teacher to mask salient instances and implicitly mine hard instances for training the student model. To obtain diverse, non-redundant hard instances, we adopt large-scale random masking while utilizing a global recycle network to mitigate the risk of losing key features. Furthermore, the student updates the teacher using an exponential moving average, which identifies new hard instances for subsequent training iterations and stabilizes optimization. Experimental results on cancer diagnosis, subtyping, survival analysis tasks, and 12 benchmarks demonstrate that MHIM-MIL outperforms the latest methods in both performance and efficiency. The code is available at: https://github.com/DearCaat/MHIM-MIL.

  • 6 authors
·
Sep 14, 2025 2

The Butterfly Effect of Model Editing: Few Edits Can Trigger Large Language Models Collapse

Although model editing has shown promise in revising knowledge in Large Language Models (LLMs), its impact on the inherent capabilities of LLMs is often overlooked. In this work, we reveal a critical phenomenon: even a single edit can trigger model collapse, manifesting as significant performance degradation in various benchmark tasks. However, benchmarking LLMs after each edit, while necessary to prevent such collapses, is impractically time-consuming and resource-intensive. To mitigate this, we propose using perplexity as a surrogate metric, validated by extensive experiments demonstrating changes in an edited model's perplexity are strongly correlated with its downstream task performances. We further conduct an in-depth study on sequential editing, a practical setting for real-world scenarios, across various editing methods and LLMs, focusing on hard cases from our previous single edit studies. The results indicate that nearly all examined editing methods result in model collapse after only few edits. To facilitate further research, we have utilized GPT-3.5 to develop a new dataset, HardEdit, based on those hard cases. This dataset aims to establish the foundation for pioneering research in reliable model editing and the mechanisms underlying editing-induced model collapse. We hope this work can draw the community's attention to the potential risks inherent in model editing practices.

  • 6 authors
·
Feb 14, 2024

Enhancing Dataset Distillation via Non-Critical Region Refinement

Dataset distillation has become a popular method for compressing large datasets into smaller, more efficient representations while preserving critical information for model training. Data features are broadly categorized into two types: instance-specific features, which capture unique, fine-grained details of individual examples, and class-general features, which represent shared, broad patterns across a class. However, previous approaches often struggle to balance these features-some focus solely on class-general patterns, neglecting finer instance details, while others prioritize instance-specific features, overlooking the shared characteristics essential for class-level understanding. In this paper, we introduce the Non-Critical Region Refinement Dataset Distillation (NRR-DD) method, which preserves instance-specific details and fine-grained regions in synthetic data while enriching non-critical regions with class-general information. This approach enables models to leverage all pixel information, capturing both feature types and enhancing overall performance. Additionally, we present Distance-Based Representative (DBR) knowledge transfer, which eliminates the need for soft labels in training by relying on the distance between synthetic data predictions and one-hot encoded labels. Experimental results show that NRR-DD achieves state-of-the-art performance on both small- and large-scale datasets. Furthermore, by storing only two distances per instance, our method delivers comparable results across various settings. The code is available at https://github.com/tmtuan1307/NRR-DD.

  • 5 authors
·
Mar 23, 2025

LOCOFY Large Design Models -- Design to code conversion solution

Despite rapid advances in Large Language Models and Multimodal Large Language Models (LLMs), numerous challenges related to interpretability, scalability, resource requirements and repeatability remain, related to their application in the design-to-code space. To address this, we introduce the Large Design Models (LDMs) paradigm specifically trained on designs and webpages to enable seamless conversion from design-to-code. We have developed a training and inference pipeline by incorporating data engineering and appropriate model architecture modification. The training pipeline consists of the following: 1)Design Optimiser: developed using a proprietary ground truth dataset and addresses sub-optimal designs; 2)Tagging and feature detection: using pre-trained and fine-tuned models, this enables the accurate detection and classification of UI elements; and 3)Auto Components: extracts repeated UI structures into reusable components to enable creation of modular code, thus reducing redundancy while enhancing code reusability. In this manner, each model addresses distinct but key issues for design-to-code conversion. Separately, our inference pipeline processes real-world designs to produce precise and interpretable instructions for code generation and ensures reliability. Additionally, our models illustrated exceptional end-to-end design-to-code conversion accuracy using a novel preview match score metric. Comparative experiments indicated superior performance of LDMs against LLMs on accuracy of node positioning, responsiveness and reproducibility. Moreover, our custom-trained tagging and feature detection model demonstrated high precision and consistency in identifying UI elements across a wide sample of test designs. Thus, our proposed LDMs are a reliable and superior solution to understanding designs that subsequently enable the generation of efficient and reliable production-ready code.

  • 4 authors
·
Jul 21, 2025

Not All Layers Need Tuning: Selective Layer Restoration Recovers Diversity

Post-training improves instruction-following and helpfulness of large language models (LLMs) but often reduces generation diversity, which leads to repetitive outputs in open-ended settings, a phenomenon known as mode collapse. Motivated by evidence that LLM layers play distinct functional roles, we hypothesize that mode collapse can be localized to specific layers and that restoring a carefully chosen range of layers to their pre-trained weights can recover diversity while maintaining high output quality. To validate this hypothesis and decide which layers to restore, we design a proxy task -- Constrained Random Character(CRC) -- with an explicit validity set and a natural diversity objective. Results on CRC reveal a clear diversity-validity trade-off across restoration ranges and identify configurations that increase diversity with minimal quality loss. Based on these findings, we propose Selective Layer Restoration (SLR), a training-free method that restores selected layers in a post-trained model to their pre-trained weights, yielding a hybrid model with the same architecture and parameter count, incurring no additional inference cost. Across three different tasks (creative writing, open-ended question answering, and multi-step reasoning) and three different model families (Llama, Qwen, and Gemma), we find SLR can consistently and substantially improve output diversity while maintaining high output quality.

  • 3 authors
·
Feb 6

CPKD: Clinical Prior Knowledge-Constrained Diffusion Models for Surgical Phase Recognition in Endoscopic Submucosal Dissection

Gastrointestinal malignancies constitute a leading cause of cancer-related mortality worldwide, with advanced-stage prognosis remaining particularly dismal. Originating as a groundbreaking technique for early gastric cancer treatment, Endoscopic Submucosal Dissection has evolved into a versatile intervention for diverse gastrointestinal lesions. While computer-assisted systems significantly enhance procedural precision and safety in ESD, their clinical adoption faces a critical bottleneck: reliable surgical phase recognition within complex endoscopic workflows. Current state-of-the-art approaches predominantly rely on multi-stage refinement architectures that iteratively optimize temporal predictions. In this paper, we present Clinical Prior Knowledge-Constrained Diffusion (CPKD), a novel generative framework that reimagines phase recognition through denoising diffusion principles while preserving the core iterative refinement philosophy. This architecture progressively reconstructs phase sequences starting from random noise and conditioned on visual-temporal features. To better capture three domain-specific characteristics, including positional priors, boundary ambiguity, and relation dependency, we design a conditional masking strategy. Furthermore, we incorporate clinical prior knowledge into the model training to improve its ability to correct phase logical errors. Comprehensive evaluations on ESD820, Cholec80, and external multi-center demonstrate that our proposed CPKD achieves superior or comparable performance to state-of-the-art approaches, validating the effectiveness of diffusion-based generative paradigms for surgical phase recognition.

  • 7 authors
·
Jul 4, 2025

Qwen-GUI-3B: A Lightweight Vision-Language Model for Cross-Resolution GUI Grounding

This paper introduces Qwen-GUI-3B, a lightweight Vision-Language Model (VLM) specifically designed for Graphical User Interface grounding tasks, achieving performance competitive with significantly larger models. Unlike large-scale VLMs (>7B parameters) that are computationally intensive and impractical for consumer-grade hardware, Qwen-GUI-3B delivers strong grounding accuracy while being fully trainable on a single GPU (RTX 4090). The model incorporates several key innovations: (i) combine cross-platform, multi-resolution dataset of 24K examples from diverse sources including mobile, desktop, and web GUI screenshots to effectively address data scarcity in high-resolution desktop environments; (ii) a two-stage fine-tuning strategy, where initial cross-platform training establishes robust GUI understanding, followed by specialized fine-tuning on high-resolution data to significantly enhance model adaptability; and (iii) data curation and redundancy reduction strategies, demonstrating that randomly sampling a smaller subset with reduced redundancy achieves performance comparable to larger datasets, emphasizing data diversity over sheer volume. Empirical evaluation on standard GUI grounding benchmarks-including ScreenSpot, ScreenSpot-v2, and the challenging ScreenSpot-Pro, highlights Qwen-GUI-3B's exceptional accuracy, achieving 84.9% on ScreenSpot and 86.4% on ScreenSpot-v2, surpassing prior models under 4B parameters. Ablation studies validate the critical role of balanced sampling and two-stage fine-tuning in enhancing robustness, particularly in high-resolution desktop scenarios. The Qwen-GUI-3B is available at: https://github.com/Han1018/Qwen-GUI-3B

  • 2 authors
·
Jun 29, 2025

Beyond Red-Teaming: Formal Guarantees of LLM Guardrail Classifiers

Guardrail Classifiers defend production language models against harmful behavior, but although results seem promising in testing, they provide no formal guarantees. Providing formal guarantees for such models is hard because "harmful behavior" has no natural specification in a discrete input space: and the standard epsilon-ball properties used in other domains do not carry semantic meaning. We close this gap by shifting verification from the discrete input space to the classifier's pre-activation space, where we define a harmful region as a convex shape enclosing the representations of known harmful prompts. Because the sigmoid classification head is monotonic, certifying the worst-case point is sufficient to certify the entire region, yielding a closed-form soundness proof without approximation in O(d) time. To formally evaluate these classifiers, we propose two constructions of such regions: SVD-aligned hyper-rectangles, which yield exact SAT/UNSAT certificates, and Gaussian Mixture Models, which yield probabilistic certificates over semantically coherent clusters. Applying this framework to three author-trained Guardrail Classifiers on the toxicity domain, every hyper-rectangle configuration returns SAT, exposing verifiable safety holes across all classifiers, despite seemingly high empirical metrics. Probabilistic GMM certificates also expose a divergent structural stability in how these models represent harm. While GPT-2 and Llama-3.1-8B maintain robust coverage of 90% and 80% across varying boundaries, BERT's safety guarantees prove uniquely volatile. This 'coverage collapse' to 55% at the optimal threshold reveals a sparsely populated safety margin in BERT, which only achieves full coverage by adopting an extremely conservative pessimistic threshold. These approaches combined, provide new insights on how effective Guardrail Classifiers really are, beyond traditional red-teaming.

  • 4 authors
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May 10

SlideChat: A Large Vision-Language Assistant for Whole-Slide Pathology Image Understanding

Despite the progress made by multimodal large language models (MLLMs) in computational pathology, they remain limited by a predominant focus on patch-level analysis, missing essential contextual information at the whole-slide level. The lack of large-scale instruction datasets and the gigapixel scale of whole slide images (WSIs) pose significant developmental challenges. In this paper, we present SlideChat, the first vision-language assistant capable of understanding gigapixel whole-slide images, exhibiting excellent multimodal conversational capability and response complex instruction across diverse pathology scenarios. To support its development, we created SlideInstruction, the largest instruction-following dataset for WSIs consisting of 4.2K WSI captions and 176K VQA pairs with multiple categories. Furthermore, we propose SlideBench, a multimodal benchmark that incorporates captioning and VQA tasks to assess SlideChat's capabilities in varied clinical settings such as microscopy, diagnosis. Compared to both general and specialized MLLMs, SlideChat exhibits exceptional capabilities achieving state-of-the-art performance on 18 of 22 tasks. For example, it achieved an overall accuracy of 81.17% on SlideBench-VQA (TCGA), and 54.15% on SlideBench-VQA (BCNB). We will fully release SlideChat, SlideInstruction and SlideBench as open-source resources to facilitate research and development in computational pathology.

  • 11 authors
·
Oct 15, 2024

EpiCoder: Encompassing Diversity and Complexity in Code Generation

Effective instruction tuning is indispensable for optimizing code LLMs, aligning model behavior with user expectations and enhancing model performance in real-world applications. However, most existing methods focus on code snippets, which are limited to specific functionalities and rigid structures, restricting the complexity and diversity of the synthesized data. To address these limitations, we introduce a novel feature tree-based synthesis framework inspired by Abstract Syntax Trees (AST). Unlike AST, which captures syntactic structure of code, our framework models semantic relationships between code elements, enabling the generation of more nuanced and diverse data. The feature tree is constructed from raw data and refined iteratively to increase the quantity and diversity of the extracted features. This process enables the identification of more complex patterns and relationships within the code. By sampling subtrees with controlled depth and breadth, our framework allows precise adjustments to the complexity of the generated code, supporting a wide range of tasks from simple function-level operations to intricate multi-file scenarios. We fine-tuned widely-used base models to create the EpiCoder series, achieving state-of-the-art performance at both the function and file levels across multiple benchmarks. Notably, empirical evidence indicates that our approach shows significant potential in synthesizing highly complex repository-level code data. Further analysis elucidates the merits of this approach by rigorously assessing data complexity and diversity through software engineering principles and LLM-as-a-judge method.

  • 13 authors
·
Jan 8, 2025 2

Rethinking Weak-to-Strong Augmentation in Source-Free Domain Adaptive Object Detection

Source-Free domain adaptive Object Detection (SFOD) aims to transfer a detector (pre-trained on source domain) to new unlabelled target domains. Current SFOD methods typically follow the Mean Teacher framework, where weak-to-strong augmentation provides diverse and sharp contrast for self-supervised learning. However, this augmentation strategy suffers from an inherent problem called crucial semantics loss: Due to random, strong disturbance, strong augmentation is prone to losing typical visual components, hindering cross-domain feature extraction. To address this thus-far ignored limitation, this paper introduces a novel Weak-to-Strong Contrastive Learning (WSCoL) approach. The core idea is to distill semantics lossless knowledge in the weak features (from the weak/teacher branch) to guide the representation learning upon the strong features (from the strong/student branch). To achieve this, we project the original features into a shared space using a mapping network, thereby reducing the bias between the weak and strong features. Meanwhile, a weak features-guided contrastive learning is performed in a weak-to-strong manner alternatively. Specifically, we first conduct an adaptation-aware prototype-guided clustering on the weak features to generate pseudo labels for corresponding strong features matched through proposals. Sequentially, we identify positive-negative samples based on the pseudo labels and perform cross-category contrastive learning on the strong features where an uncertainty estimator encourages adaptive background contrast. Extensive experiments demonstrate that WSCoL yields new state-of-the-art performance, offering a built-in mechanism mitigating crucial semantics loss for traditional Mean Teacher framework. The code and data will be released soon.

  • 7 authors
·
Oct 7, 2024

RobustMAD: Evaluating Real-World Robustness of Multimodal Small Language Models for Deployable Anomaly Detection Assistants

Multimodal industrial anomaly inspection assistants are a critical component of next-generation smart factories, enabling interactive vision-language-based querying. However, multimodal large language models remain impractical for on-site deployment due to prohibitive computational demands and privacy risks from cloud-based inference. Compact multimodal small language models (MSLMs) offer a deployable alternative, yet progress is constrained by the lack of comprehensive robustness analyses and meaningfully challenging benchmarks that reflect real-world industrial conditions. To address this gap, we develop RobustMAD, the first deployment-motivated benchmark, designed to comprehensively evaluate model robustness through diverse open-ended queries spanning object understanding, anomaly detection, unanswerable problems, and visual quality degradations. Contrary to conventional assumptions, top-performing MSLMs exhibit promising capabilities, surprisingly outperforming even the larger GPT-5 Nano. However, they still fall short of safety-critical requirements, and RobustMAD reveals critical robustness gaps that pose operational risks. In particular, three recurring failure modes emerge: (i) fragile multimodal grounding under fine-grained distinctions or degraded visual conditions, (ii) insufficiently comprehensive responses, and (iii) weak logical grounding on unanswerable or ill-posed queries, leading to hallucinated outputs. Grounded in these insights, we provide actionable guidance for the design of next-generation multimodal industrial inspection assistants that leverage their promising competence. Code is available at https://github.com/en-research/RobustMAD.

  • 7 authors
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Jun 25

Multimodal Optimal Transport-based Co-Attention Transformer with Global Structure Consistency for Survival Prediction

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

  • 2 authors
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Jun 14, 2023

Language Models are Super Mario: Absorbing Abilities from Homologous Models as a Free Lunch

In this paper, we uncover that Language Models (LMs), either encoder- or decoder-based, can obtain new capabilities by assimilating the parameters of homologous models without retraining or GPUs. Typically, new abilities of LMs can be imparted by Supervised Fine-Tuning (SFT), reflected in the disparity between fine-tuned and pre-trained parameters (i.e., delta parameters). We initially observe that by introducing a novel operation called DARE (Drop And REscale), most delta parameters can be directly set to zeros without affecting the capabilities of SFT LMs and larger models can tolerate a higher proportion of discarded parameters. Based on this observation, we further sparsify delta parameters of multiple SFT homologous models with DARE and subsequently merge them into a single model by parameter averaging. We conduct experiments on eight datasets from the GLUE benchmark with BERT and RoBERTa. We also merge WizardLM, WizardMath, and Code Alpaca based on Llama 2. Experimental results show that: (1) The delta parameter value ranges for SFT models are typically small, often within 0.005, and DARE can eliminate 99% of them effortlessly. However, once the models are continuously pre-trained, the value ranges can grow to around 0.03, making DARE impractical. We have also tried to remove fine-tuned instead of delta parameters and find that a 10% reduction can lead to drastically decreased performance (even to 0). This highlights that SFT merely stimulates the abilities via delta parameters rather than injecting new abilities into LMs; (2) DARE can merge multiple task-specific LMs into one LM with diverse abilities. For instance, the merger of WizardLM and WizardMath improves the GSM8K zero-shot accuracy of WizardLM from 2.2 to 66.3, retaining its instruction-following ability while surpassing WizardMath's original 64.2 performance. Codes are available at https://github.com/yule-BUAA/MergeLM.

  • 5 authors
·
Nov 6, 2023 7

Paired Uterine Whole-Slide Images and Pathology Reports for Multimodal Computational Pathology

Uterine diseases represent an important category of gynecologic pathology and require accurate histopathological assessment for diagnosis and treatment planning. Whole-slide images (WSI) have enabled the digital transformation of pathology workflows and provided new opportunities for artificial intelligence (AI) in computational pathology. In particular, multimodal models that jointly analyze histopathology images and pathology reports have shown promising potential for automated pathology report generation and AI-assisted diagnosis. However, the development of such systems remains limited by the scarcity of datasets that pair whole-slide images with clinically meaningful pathology reports. Instead, existing pathology datasets focus on patch- or slide-level annotations of a single endpoint (e.g., disease class), which do not fully capture the rich information in full clinical diagnostic workflow reports. Here, we introduce TUM-Uteria, a uterine pathology dataset comprising WSIs paired with diagnostic pathology reports at both the case and slide levels, collected from a tertiary medical center. The dataset contains 216 clinical cases, comprising 455 slide-level WSI-report pairs. The dataset underwent a structured multi-stage validation procedure involving board-certified pathologists to ensure reliable annotations. TUM-Uteria supports research in computational pathology, including whole-slide image analysis, multimodal learning, and automated pathology report generation.

  • 17 authors
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Jul 3

FailureSensorIQ: A Multi-Choice QA Dataset for Understanding Sensor Relationships and Failure Modes

We introduce FailureSensorIQ, a novel Multi-Choice Question-Answering (MCQA) benchmarking system designed to assess the ability of Large Language Models (LLMs) to reason and understand complex, domain-specific scenarios in Industry 4.0. Unlike traditional QA benchmarks, our system focuses on multiple aspects of reasoning through failure modes, sensor data, and the relationships between them across various industrial assets. Through this work, we envision a paradigm shift where modeling decisions are not only data-driven using statistical tools like correlation analysis and significance tests, but also domain-driven by specialized LLMs which can reason about the key contributors and useful patterns that can be captured with feature engineering. We evaluate the Industrial knowledge of over a dozen LLMs-including GPT-4, Llama, and Mistral-on FailureSensorIQ from different lens using Perturbation-Uncertainty-Complexity analysis, Expert Evaluation study, Asset-Specific Knowledge Gap analysis, ReAct agent using external knowledge-bases. Even though closed-source models with strong reasoning capabilities approach expert-level performance, the comprehensive benchmark reveals a significant drop in performance that is fragile to perturbations, distractions, and inherent knowledge gaps in the models. We also provide a real-world case study of how LLMs can drive the modeling decisions on 3 different failure prediction datasets related to various assets. We release: (a) expert-curated MCQA for various industrial assets, (b) FailureSensorIQ benchmark and Hugging Face leaderboard based on MCQA built from non-textual data found in ISO documents, and (c) LLMFeatureSelector, an LLM-based feature selection scikit-learn pipeline. The software is available at https://github.com/IBM/FailureSensorIQ.

  • 6 authors
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Jun 3, 2025 1

LoFT: Parameter-Efficient Fine-Tuning for Long-tailed Semi-Supervised Learning in Open-World Scenarios

Long-tailed semi-supervised learning (LTSSL) presents a formidable challenge where models must overcome the scarcity of tail samples while mitigating the noise from unreliable pseudo-labels. Most prior LTSSL methods are designed to train models from scratch, which often leads to issues such as overconfidence and low-quality pseudo-labels. To address this problem, we first theoretically prove that utilizing a foundation model significantly reduces the hypothesis complexity, which tightens the generalization bound and in turn minimizes the Balanced Posterior Error (BPE). Furthermore, we demonstrate that the feature compactness of foundation models strictly compresses the acceptance region for outliers, providing a geometric guarantee for robustness. Motivated by these theoretical insights, we extend LTSSL into the foundation model fine-tuning paradigm and propose a novel framework: LoFT (Long-tailed semi-supervised learning via parameter-efficient Fine-Tuning). Furthermore, we explore a more practical setting by investigating semi-supervised learning under open-world conditions, where the unlabeled data may include out-of-distribution (OOD) samples.To handle this problem, we propose LoFT-OW (LoFT under Open-World scenarios) to improve the discriminative ability. Experimental results on multiple benchmarks demonstrate that our method achieves superior performance. Code is available: https://github.com/games-liker/LoFT

  • 4 authors
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Apr 7 2

PathMoE: Interpretable Multimodal Interaction Experts for Pediatric Brain Tumor Classification

Accurate classification of pediatric central nervous system tumors remains challenging due to histological complexity and limited training data. While pathology foundation models have advanced whole-slide image (WSI) analysis, they often fail to leverage the rich, complementary information found in clinical text and tissue microarchitecture. To this end, we propose PathMoE, an interpretable multimodal framework that integrates H\&E slides, pathology reports, and nuclei-level cell graphs via an interaction-aware mixture-of-experts architecture built on state-of-the-art foundation models for each modality. By training specialized experts to capture modality uniqueness, redundancy, and synergy, PathMoE employs an input-dependent gating mechanism that dynamically weights these interactions, providing sample-level interpretability. We evaluate our framework on two dataset-specific classification tasks on an internal pediatric brain tumor dataset (PBT) and external TCGA datasets. PathMoE improves macro-F1 from 0.762 to 0.799 (+0.037) on PBT when integrating WSI, text, and graph modalities; on TCGA, augmenting WSI with graph knowledge improves macro-F1 from 0.668 to 0.709 (+0.041). These results demonstrate significant performance gains over state-of-the-art image-only baselines while revealing the specific modality interactions driving individual predictions. This interpretability is particularly critical for rare tumor subtypes, where transparent model reasoning is essential for clinical trust and diagnostic validation.

  • 13 authors
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Mar 1

The Good, the Bad, and the Ugly of Markov Boundary for Tabular Prediction

Under standard graphical assumptions, the Markov boundary of a target variable is the smallest set of features that renders every other feature redundant. Once the boundary is observed, the target is conditionally independent of the rest of the table. This is a tempting object for tabular prediction, since it names exactly the columns a model should need. Yet modern regressors are still trained on the full feature set. We ask whether the Markov boundary is genuinely useful for prediction on SCM3K, a 3,450-task synthetic SCM benchmark with feature counts from 40 to 1000 and six SCM families, evaluated with six regressors. The answer is more nuanced than the theory suggests. Restricting a regressor to the oracle boundary often improves prediction substantially, and the improvement grows as the feature space becomes larger and sparser. But the natural pipeline of recovering the boundary with causal discovery and training on the recovered mask does not deliver. Existing estimators exhaust the compute budget before reaching the regime where the boundary helps most, and even where they run they rarely beat the full feature set. We trace this to three causes. Discovery optimizes structural recovery rather than prediction. False negatives and false positives carry sharply asymmetric predictive cost. The exact boundary is only one of many feature sets that beat all features. We then develop what these facts imply for prediction-aligned feature selection and for tabular models that learn to use causal structure.

Procedural Generation of Grain Orientations using the Wave Function Collapse Algorithm

Statistics of grain sizes and orientations in metals correlate to the material's mechanical properties. Reproducing representative volume elements for further analysis of deformation and failure in metals, like 316L stainless steel, is particularly important due to their wide use in manufacturing goods today. Two approaches, initially created for video games, were considered for the procedural generation of representative grain microstructures. The first is the Wave Function Collapse (WFC) algorithm, and the second is constraint propagation and probabilistic inference through Markov Junior, a free and open-source software. This study aimed to investigate these two algorithms' effectiveness in using reference electron backscatter diffraction (EBSD) maps and recreating a statistically similar one that could be used in further research. It utilized two stainless steel EBSD maps as references to test both algorithms. First, the WFC algorithm was too constricting and, thus, incapable of producing images that resembled EBSDs. The second, MarkovJunior, was much more effective in creating a Voronoi tessellation that could be used to create an EBSD map in Python. When comparing the results between the reference and the generated EBSD, we discovered that the orientation and volume fractions were extremely similar. With the study, it was concluded that MarkovJunior is an effective machine learning tool that can reproduce representative grain microstructures.

  • 3 authors
·
Nov 20, 2023

From Data Statistics to Feature Geometry: How Correlations Shape Superposition

A central idea in mechanistic interpretability is that neural networks represent more features than they have dimensions, arranging them in superposition to form an over-complete basis. This framing has been influential, motivating dictionary learning approaches such as sparse autoencoders. However, superposition has mostly been studied in idealized settings where features are sparse and uncorrelated. In these settings, superposition is typically understood as introducing interference that must be minimized geometrically and filtered out by non-linearities such as ReLUs, yielding local structures like regular polytopes. We show that this account is incomplete for realistic data by introducing Bag-of-Words Superposition (BOWS), a controlled setting to encode binary bag-of-words representations of internet text in superposition. Using BOWS, we find that when features are correlated, interference can be constructive rather than just noise to be filtered out. This is achieved by arranging features according to their co-activation patterns, making interference between active features constructive, while still using ReLUs to avoid false positives. We show that this kind of arrangement is more prevalent in models trained with weight decay and naturally gives rise to semantic clusters and cyclical structures which have been observed in real language models yet were not explained by the standard picture of superposition. Code for this paper can be found at https://github.com/LucasPrietoAl/correlations-feature-geometry.

  • 5 authors
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Mar 9

Search over Self-Edit Strategies for LLM Adaptation

Many LLM-based open-ended search systems freeze the foundation model that proposes improvements to existing solutions, which may bottleneck long-run progress. Recent work has explored updating the proposal model at test time [arXiv:2511.23473], but the update strategy is still typically hand-specified. Therefore, this study investigated whether an LLM can use task feedback to decide how it should update its weights. For tractability, we focused on the simpler case where there is only one round of self-improvement, and restricted the update operator to self-supervised next token prediction (NTP), leaving the model freedom in choosing its training data and key NTP hyperparameters. Using the Self-Adapting Language Models (SEAL) [arXiv:2506.10943] framework as a testbed, we relaxed its fixed human template constraint and allowed the model to generate its own self-edit templates, thereby giving it more control over its training data and hyperparameters. Two variants were studied, differing in whether template generation was conditioned on a lightweight archive of past templates. In SEAL's Single-Passage Knowledge Incorporation setting with Qwen3-8B on SQuAD [arXiv:1606.05250], the no-archive variant performed comparably to the weaker "Implications" baseline, while the archive variant outperformed "Implications" and approached the strongest human-designed "Rewrite" baseline without surpassing it. Further analysis of collapse in the model's exploration revealed that a naive archive can confer some short-term robustness but can also accelerate homogenization, suggesting that explicit novelty pressure may be required to consistently advance beyond carefully optimized human strategies. Our code is available at https://github.com/cheongalc/search-self-edit-strategies .

  • 4 authors
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Jan 19