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Mar 25

DiSa: Directional Saliency-Aware Prompt Learning for Generalizable Vision-Language Models

Prompt learning has emerged as a powerful paradigm for adapting vision-language models such as CLIP to downstream tasks. However, existing methods often overfit to seen data, leading to significant performance degradation when generalizing to novel classes or unseen domains. To address this limitation, we propose DiSa, a Directional Saliency-Aware Prompt Learning framework that integrates two complementary regularization strategies to enhance generalization. First, our Cross-Interactive Regularization (CIR) fosters cross-modal alignment by enabling cooperative learning between prompted and frozen encoders. Within CIR, a saliency-aware masking strategy guides the image encoder to prioritize semantically critical image regions, reducing reliance on less informative patches. Second, we introduce a directional regularization strategy that aligns visual embeddings with class-wise prototype features in a directional manner to prioritize consistency in feature orientation over strict proximity. This approach ensures robust generalization by leveraging stable prototype directions derived from class-mean statistics. Extensive evaluations on 11 diverse image classification benchmarks demonstrate that DiSa consistently outperforms state-of-the-art prompt learning methods across various settings, including base-to-novel generalization, cross-dataset transfer, domain generalization, and few-shot learning.

  • 4 authors
·
May 25, 2025

Beyond Degradation Redundancy: Contrastive Prompt Learning for All-in-One Image Restoration

All-in-One Image Restoration (AiOIR), which addresses diverse degradation types with a unified model, presents significant challenges in designing task-aware prompts that effectively guide restoration across multiple degradation scenarios. While adaptive prompt learning enables end-to-end optimization, it often yields overlapping or redundant task representations. Conversely, explicit prompts derived from pretrained classifiers enhance discriminability but discard critical visual information needed for reconstruction. To address these limitations, we introduce Contrastive Prompt Learning (CPL), a framework that aims to improve prompt-task alignment through two complementary components: a Sparse Prompt Module (SPM) that efficiently captures degradation-aware representations while reducing redundancy, and a Contrastive Prompt Regularization (CPR) that explicitly strengthens task boundaries by incorporating negative prompt samples across different degradation types. Unlike previous approaches that focus primarily on degradation classification, CPL directly optimizes the interaction between prompts and the restoration model. Extensive experiments across five benchmarks show that CPL consistently boosts the performance of strong AiOIR baselines across diverse scenarios. Our approach achieves state-of-the-art average performance on these benchmarks, providing a general and robust solution for AiOIR. The code is available at https://github.com/Aitical/CPLIR

  • 5 authors
·
Apr 14, 2025

Geometry-Aware Adaptation for Pretrained Models

Machine learning models -- including prominent zero-shot models -- are often trained on datasets whose labels are only a small proportion of a larger label space. Such spaces are commonly equipped with a metric that relates the labels via distances between them. We propose a simple approach to exploit this information to adapt the trained model to reliably predict new classes -- or, in the case of zero-shot prediction, to improve its performance -- without any additional training. Our technique is a drop-in replacement of the standard prediction rule, swapping argmax with the Fr\'echet mean. We provide a comprehensive theoretical analysis for this approach, studying (i) learning-theoretic results trading off label space diameter, sample complexity, and model dimension, (ii) characterizations of the full range of scenarios in which it is possible to predict any unobserved class, and (iii) an optimal active learning-like next class selection procedure to obtain optimal training classes for when it is not possible to predict the entire range of unobserved classes. Empirically, using easily-available external metrics, our proposed approach, Loki, gains up to 29.7% relative improvement over SimCLR on ImageNet and scales to hundreds of thousands of classes. When no such metric is available, Loki can use self-derived metrics from class embeddings and obtains a 10.5% improvement on pretrained zero-shot models such as CLIP.

  • 7 authors
·
Jul 23, 2023

MMFormalizer: Multimodal Autoformalization in the Wild

Autoformalization, which translates natural language mathematics into formal statements to enable machine reasoning, faces fundamental challenges in the wild due to the multimodal nature of the physical world, where physics requires inferring hidden constraints (e.g., mass or energy) from visual elements. To address this, we propose MMFormalizer, which extends autoformalization beyond text by integrating adaptive grounding with entities from real-world mathematical and physical domains. MMFormalizer recursively constructs formal propositions from perceptually grounded primitives through recursive grounding and axiom composition, with adaptive recursive termination ensuring that every abstraction is supported by visual evidence and anchored in dimensional or axiomatic grounding. We evaluate MMFormalizer on a new benchmark, PhyX-AF, comprising 115 curated samples from MathVerse, PhyX, Synthetic Geometry, and Analytic Geometry, covering diverse multimodal autoformalization tasks. Results show that frontier models such as GPT-5 and Gemini-3-Pro achieve the highest compile and semantic accuracy, with GPT-5 excelling in physical reasoning, while geometry remains the most challenging domain. Overall, MMFormalizer provides a scalable framework for unified multimodal autoformalization, bridging perception and formal reasoning. To the best of our knowledge, this is the first multimodal autoformalization method capable of handling classical mechanics (derived from the Hamiltonian), as well as relativity, quantum mechanics, and thermodynamics. More details are available on our project page: MMFormalizer.github.io

  • 14 authors
·
Jan 6 7

Classification of BCI-EEG based on augmented covariance matrix

Objective: Electroencephalography signals are recorded as a multidimensional dataset. We propose a new framework based on the augmented covariance extracted from an autoregressive model to improve motor imagery classification. Methods: From the autoregressive model can be derived the Yule-Walker equations, which show the emergence of a symmetric positive definite matrix: the augmented covariance matrix. The state-of the art for classifying covariance matrices is based on Riemannian Geometry. A fairly natural idea is therefore to extend the standard approach using these augmented covariance matrices. The methodology for creating the augmented covariance matrix shows a natural connection with the delay embedding theorem proposed by Takens for dynamical systems. Such an embedding method is based on the knowledge of two parameters: the delay and the embedding dimension, respectively related to the lag and the order of the autoregressive model. This approach provides new methods to compute the hyper-parameters in addition to standard grid search. Results: The augmented covariance matrix performed noticeably better than any state-of-the-art methods. We will test our approach on several datasets and several subjects using the MOABB framework, using both within-session and cross-session evaluation. Conclusion: The improvement in results is due to the fact that the augmented covariance matrix incorporates not only spatial but also temporal information, incorporating nonlinear components of the signal through an embedding procedure, which allows the leveraging of dynamical systems algorithms. Significance: These results extend the concepts and the results of the Riemannian distance based classification algorithm.

  • 2 authors
·
Feb 9, 2023

G-ACIL: Analytic Learning for Exemplar-Free Generalized Class Incremental Learning

Class incremental learning (CIL) trains a network on sequential tasks with separated categories but suffers from catastrophic forgetting, where models quickly lose previously learned knowledge when acquiring new tasks. The generalized CIL (GCIL) aims to address the CIL problem in a more real-world scenario, where incoming data have mixed data categories and unknown sample size distribution, leading to intensified forgetting. Existing attempts for the GCIL either have poor performance, or invade data privacy by saving historical exemplars. To address this, in this paper, we propose an exemplar-free generalized analytic class incremental learning (G-ACIL). The G-ACIL adopts analytic learning (a gradient-free training technique), and delivers an analytical solution (i.e., closed-form) to the GCIL scenario. This solution is derived via decomposing the incoming data into exposed and unexposed classes, allowing an equivalence between the incremental learning and its joint training, i.e., the weight-invariant property. Such an equivalence is theoretically validated through matrix analysis tools, and hence contributes interpretability in GCIL. It is also empirically evidenced by experiments on various datasets and settings of GCIL. The results show that the G-ACIL exhibits leading performance with high robustness compared with existing competitive GCIL methods. Codes will be ready at https://github.com/ZHUANGHP/Analytic-continual-learning.

  • 8 authors
·
Mar 22, 2024

Shadow and Light: Digitally Reconstructed Radiographs for Disease Classification

In this paper, we introduce DRR-RATE, a large-scale synthetic chest X-ray dataset derived from the recently released CT-RATE dataset. DRR-RATE comprises of 50,188 frontal Digitally Reconstructed Radiographs (DRRs) from 21,304 unique patients. Each image is paired with a corresponding radiology text report and binary labels for 18 pathology classes. Given the controllable nature of DRR generation, it facilitates the inclusion of lateral view images and images from any desired viewing position. This opens up avenues for research into new and novel multimodal applications involving paired CT, X-ray images from various views, text, and binary labels. We demonstrate the applicability of DRR-RATE alongside existing large-scale chest X-ray resources, notably the CheXpert dataset and CheXnet model. Experiments demonstrate that CheXnet, when trained and tested on the DRR-RATE dataset, achieves sufficient to high AUC scores for the six common pathologies cited in common literature: Atelectasis, Cardiomegaly, Consolidation, Lung Lesion, Lung Opacity, and Pleural Effusion. Additionally, CheXnet trained on the CheXpert dataset can accurately identify several pathologies, even when operating out of distribution. This confirms that the generated DRR images effectively capture the essential pathology features from CT images. The dataset and labels are publicly accessible at https://huggingface.co/datasets/farrell236/DRR-RATE.

  • 6 authors
·
Jun 5, 2024

AnyLoss: Transforming Classification Metrics into Loss Functions

Many evaluation metrics can be used to assess the performance of models in binary classification tasks. However, most of them are derived from a confusion matrix in a non-differentiable form, making it very difficult to generate a differentiable loss function that could directly optimize them. The lack of solutions to bridge this challenge not only hinders our ability to solve difficult tasks, such as imbalanced learning, but also requires the deployment of computationally expensive hyperparameter search processes in model selection. In this paper, we propose a general-purpose approach that transforms any confusion matrix-based metric into a loss function, AnyLoss, that is available in optimization processes. To this end, we use an approximation function to make a confusion matrix represented in a differentiable form, and this approach enables any confusion matrix-based metric to be directly used as a loss function. The mechanism of the approximation function is provided to ensure its operability and the differentiability of our loss functions is proved by suggesting their derivatives. We conduct extensive experiments under diverse neural networks with many datasets, and we demonstrate their general availability to target any confusion matrix-based metrics. Our method, especially, shows outstanding achievements in dealing with imbalanced datasets, and its competitive learning speed, compared to multiple baseline models, underscores its efficiency.

  • 3 authors
·
May 23, 2024

Underwater SONAR Image Classification and Analysis using LIME-based Explainable Artificial Intelligence

Deep learning techniques have revolutionized image classification by mimicking human cognition and automating complex decision-making processes. However, the deployment of AI systems in the wild, especially in high-security domains such as defence, is curbed by the lack of explainability of the model. To this end, eXplainable AI (XAI) is an emerging area of research that is intended to explore the unexplained hidden black box nature of deep neural networks. This paper explores the application of the eXplainable Artificial Intelligence (XAI) tool to interpret the underwater image classification results, one of the first works in the domain to the best of our knowledge. Our study delves into the realm of SONAR image classification using a custom dataset derived from diverse sources, including the Seabed Objects KLSG dataset, the camera SONAR dataset, the mine SONAR images dataset, and the SCTD dataset. An extensive analysis of transfer learning techniques for image classification using benchmark Convolutional Neural Network (CNN) architectures such as VGG16, ResNet50, InceptionV3, DenseNet121, etc. is carried out. On top of this classification model, a post-hoc XAI technique, viz. Local Interpretable Model-Agnostic Explanations (LIME) are incorporated to provide transparent justifications for the model's decisions by perturbing input data locally to see how predictions change. Furthermore, Submodular Picks LIME (SP-LIME) a version of LIME particular to images, that perturbs the image based on the submodular picks is also extensively studied. To this end, two submodular optimization algorithms i.e. Quickshift and Simple Linear Iterative Clustering (SLIC) are leveraged towards submodular picks. The extensive analysis of XAI techniques highlights interpretability of the results in a more human-compliant way, thus boosting our confidence and reliability.

  • 2 authors
·
Aug 23, 2024

Periodical embeddings uncover hidden interdisciplinary patterns in the subject classification scheme of science

Subject classification schemes are foundational to the organization, evaluation, and navigation of scientific knowledge. While expert-curated systems like Scopus provide widely used taxonomies, they often suffer from coarse granularity, subjectivity, and limited adaptability to emerging interdisciplinary fields. Data-driven alternatives based on citation networks show promise but lack rigorous, external validation against the semantic content of scientific literature. Here, we propose a novel quantitative framework that leverages classification tasks to evaluate the effectiveness of journal classification schemes. Using over 23 million paper abstracts, we demonstrate that labels derived from k-means clustering on Periodical2Vec (P2V)--a periodical embedding learned from paper-level citations--yield significantly higher classification performance than both Scopus and other data-driven baselines (e.g., citation, co-citation, and Node2Vec variants). By comparing journal partitions across classification schemes, two structural patterns emerge on the map of science: (1) the reorganization of disciplinary boundaries--splitting overly broad categories (e.g., "Medicine" into "Oncology", "Cardiology", and other specialties) while merging artificially fragmented ones (e.g., "Chemistry" and "Chemical Engineering"); and (2) the identification of coherent interdisciplinary clusters--such as "Biomedical Engineering", "Medical Ethics", and "Information Management"--that are dispersed across multiple categories but unified in citation space. These findings underscore that citation-derived periodical embeddings not only outperform traditional taxonomies in predictive validity but also offer a dynamic, fine-grained map of science that better reflects both the specialization and interdisciplinarity inherent in contemporary research.

  • 2 authors
·
Dec 27, 2025

TestBench: Evaluating Class-Level Test Case Generation Capability of Large Language Models

Software testing is a crucial phase in the software life cycle, helping identify potential risks and reduce maintenance costs. With the advancement of Large Language Models (LLMs), researchers have proposed an increasing number of LLM-based software testing techniques, particularly in the area of test case generation. Despite the growing interest, limited efforts have been made to thoroughly evaluate the actual capabilities of LLMs in this task. In this paper, we introduce TestBench, a benchmark for class-level LLM-based test case generation. We construct a dataset of 108 Java programs from 9 real-world, large-scale projects on GitHub, each representing a different thematic domain. We then design three distinct types of prompts based on context descriptions, including self-contained context, full context, and simple context. Besides, we propose a fine-grained evaluation framework that considers five aspects of test cases: syntactic correctness, compilation correctness, test correctness, code coverage rate, and defect detection rate. Furthermore, we propose a heuristic algorithm to repair erroneous test cases generated by LLMs. We evaluate CodeLlama-13b, GPT-3.5, and GPT-4 on the TestBench, and our experimental results indicate that larger models demonstrate a greater ability to effectively utilize contextual information, thus generating higher-quality test cases. Smaller models may struggle with the noise introduced by the extensive information contained within the full context. However, when using the simplified version, namely the simple context, which is derived from the full context via abstract syntax tree analysis, the performance of these models improves significantly. Our analysis highlights the current progress and pinpoints future directions to further enhance the effectiveness of models by handling contextual information for test case generation.

  • 6 authors
·
Sep 26, 2024

Label-free Node Classification on Graphs with Large Language Models (LLMS)

In recent years, there have been remarkable advancements in node classification achieved by Graph Neural Networks (GNNs). However, they necessitate abundant high-quality labels to ensure promising performance. In contrast, Large Language Models (LLMs) exhibit impressive zero-shot proficiency on text-attributed graphs. Yet, they face challenges in efficiently processing structural data and suffer from high inference costs. In light of these observations, this work introduces a label-free node classification on graphs with LLMs pipeline, LLM-GNN. It amalgamates the strengths of both GNNs and LLMs while mitigating their limitations. Specifically, LLMs are leveraged to annotate a small portion of nodes and then GNNs are trained on LLMs' annotations to make predictions for the remaining large portion of nodes. The implementation of LLM-GNN faces a unique challenge: how can we actively select nodes for LLMs to annotate and consequently enhance the GNN training? How can we leverage LLMs to obtain annotations of high quality, representativeness, and diversity, thereby enhancing GNN performance with less cost? To tackle this challenge, we develop an annotation quality heuristic and leverage the confidence scores derived from LLMs to advanced node selection. Comprehensive experimental results validate the effectiveness of LLM-GNN. In particular, LLM-GNN can achieve an accuracy of 74.9% on a vast-scale dataset \products with a cost less than 1 dollar.

  • 8 authors
·
Oct 6, 2023

Interactive Segmentation as Gaussian Process Classification

Click-based interactive segmentation (IS) aims to extract the target objects under user interaction. For this task, most of the current deep learning (DL)-based methods mainly follow the general pipelines of semantic segmentation. Albeit achieving promising performance, they do not fully and explicitly utilize and propagate the click information, inevitably leading to unsatisfactory segmentation results, even at clicked points. Against this issue, in this paper, we propose to formulate the IS task as a Gaussian process (GP)-based pixel-wise binary classification model on each image. To solve this model, we utilize amortized variational inference to approximate the intractable GP posterior in a data-driven manner and then decouple the approximated GP posterior into double space forms for efficient sampling with linear complexity. Then, we correspondingly construct a GP classification framework, named GPCIS, which is integrated with the deep kernel learning mechanism for more flexibility. The main specificities of the proposed GPCIS lie in: 1) Under the explicit guidance of the derived GP posterior, the information contained in clicks can be finely propagated to the entire image and then boost the segmentation; 2) The accuracy of predictions at clicks has good theoretical support. These merits of GPCIS as well as its good generality and high efficiency are substantiated by comprehensive experiments on several benchmarks, as compared with representative methods both quantitatively and qualitatively.

  • 7 authors
·
Feb 28, 2023

VSFormer: Value and Shape-Aware Transformer with Prior-Enhanced Self-Attention for Multivariate Time Series Classification

Multivariate time series classification is a crucial task in data mining, attracting growing research interest due to its broad applications. While many existing methods focus on discovering discriminative patterns in time series, real-world data does not always present such patterns, and sometimes raw numerical values can also serve as discriminative features. Additionally, the recent success of Transformer models has inspired many studies. However, when applying to time series classification, the self-attention mechanisms in Transformer models could introduce classification-irrelevant features, thereby compromising accuracy. To address these challenges, we propose a novel method, VSFormer, that incorporates both discriminative patterns (shape) and numerical information (value). In addition, we extract class-specific prior information derived from supervised information to enrich the positional encoding and provide classification-oriented self-attention learning, thereby enhancing its effectiveness. Extensive experiments on all 30 UEA archived datasets demonstrate the superior performance of our method compared to SOTA models. Through ablation studies, we demonstrate the effectiveness of the improved encoding layer and the proposed self-attention mechanism. Finally, We provide a case study on a real-world time series dataset without discriminative patterns to interpret our model.

  • 6 authors
·
Dec 21, 2024

CFG-Ctrl: Control-Based Classifier-Free Diffusion Guidance

Classifier-Free Guidance (CFG) has emerged as a central approach for enhancing semantic alignment in flow-based diffusion models. In this paper, we explore a unified framework called CFG-Ctrl, which reinterprets CFG as a control applied to the first-order continuous-time generative flow, using the conditional-unconditional discrepancy as an error signal to adjust the velocity field. From this perspective, we summarize vanilla CFG as a proportional controller (P-control) with fixed gain, and typical follow-up variants develop extended control-law designs derived from it. However, existing methods mainly rely on linear control, inherently leading to instability, overshooting, and degraded semantic fidelity especially on large guidance scales. To address this, we introduce Sliding Mode Control CFG (SMC-CFG), which enforces the generative flow toward a rapidly convergent sliding manifold. Specifically, we define an exponential sliding mode surface over the semantic prediction error and introduce a switching control term to establish nonlinear feedback-guided correction. Moreover, we provide a Lyapunov stability analysis to theoretically support finite-time convergence. Experiments across text-to-image generation models including Stable Diffusion 3.5, Flux, and Qwen-Image demonstrate that SMC-CFG outperforms standard CFG in semantic alignment and enhances robustness across a wide range of guidance scales. Project Page: https://hanyang-21.github.io/CFG-Ctrl

Efficient Distillation of Classifier-Free Guidance using Adapters

While classifier-free guidance (CFG) is essential for conditional diffusion models, it doubles the number of neural function evaluations (NFEs) per inference step. To mitigate this inefficiency, we introduce adapter guidance distillation (AGD), a novel approach that simulates CFG in a single forward pass. AGD leverages lightweight adapters to approximate CFG, effectively doubling the sampling speed while maintaining or even improving sample quality. Unlike prior guidance distillation methods that tune the entire model, AGD keeps the base model frozen and only trains minimal additional parameters (sim2%) to significantly reduce the resource requirement of the distillation phase. Additionally, this approach preserves the original model weights and enables the adapters to be seamlessly combined with other checkpoints derived from the same base model. We also address a key mismatch between training and inference in existing guidance distillation methods by training on CFG-guided trajectories instead of standard diffusion trajectories. Through extensive experiments, we show that AGD achieves comparable or superior FID to CFG across multiple architectures with only half the NFEs. Notably, our method enables the distillation of large models (sim2.6B parameters) on a single consumer GPU with 24 GB of VRAM, making it more accessible than previous approaches that require multiple high-end GPUs. We will publicly release the implementation of our method.

  • 2 authors
·
Mar 10, 2025 1

YouTube-8M: A Large-Scale Video Classification Benchmark

Many recent advancements in Computer Vision are attributed to large datasets. Open-source software packages for Machine Learning and inexpensive commodity hardware have reduced the barrier of entry for exploring novel approaches at scale. It is possible to train models over millions of examples within a few days. Although large-scale datasets exist for image understanding, such as ImageNet, there are no comparable size video classification datasets. In this paper, we introduce YouTube-8M, the largest multi-label video classification dataset, composed of ~8 million videos (500K hours of video), annotated with a vocabulary of 4800 visual entities. To get the videos and their labels, we used a YouTube video annotation system, which labels videos with their main topics. While the labels are machine-generated, they have high-precision and are derived from a variety of human-based signals including metadata and query click signals. We filtered the video labels (Knowledge Graph entities) using both automated and manual curation strategies, including asking human raters if the labels are visually recognizable. Then, we decoded each video at one-frame-per-second, and used a Deep CNN pre-trained on ImageNet to extract the hidden representation immediately prior to the classification layer. Finally, we compressed the frame features and make both the features and video-level labels available for download. We trained various (modest) classification models on the dataset, evaluated them using popular evaluation metrics, and report them as baselines. Despite the size of the dataset, some of our models train to convergence in less than a day on a single machine using TensorFlow. We plan to release code for training a TensorFlow model and for computing metrics.

  • 7 authors
·
Sep 27, 2016

Mitigating Distribution Shift in Graph-Based Android Malware Classification via Function Metadata and LLM Embeddings

Graph-based malware classifiers can achieve over 94% accuracy on standard Android datasets, yet we find they suffer accuracy drops of up to 45% when evaluated on previously unseen malware variants from the same family - a scenario where strong generalization would typically be expected. This highlights a key limitation in existing approaches: both the model architectures and their structure-only representations often fail to capture deeper semantic patterns. In this work, we propose a robust semantic enrichment framework that enhances function call graphs with contextual features, including function-level metadata and, when available, code embeddings derived from large language models. The framework is designed to operate under real-world constraints where feature availability is inconsistent, and supports flexible integration of semantic signals. To evaluate generalization under realistic domain and temporal shifts, we introduce two new benchmarks: MalNet-Tiny-Common and MalNet-Tiny-Distinct, constructed using malware family partitioning to simulate cross-family generalization and evolving threat behavior. Experiments across multiple graph neural network backbones show that our method improves classification performance by up to 8% under distribution shift and consistently enhances robustness when integrated with adaptation-based methods. These results offer a practical path toward building resilient malware detection systems in evolving threat environments.

  • 5 authors
·
Aug 8, 2025

MedBookVQA: A Systematic and Comprehensive Medical Benchmark Derived from Open-Access Book

The accelerating development of general medical artificial intelligence (GMAI), powered by multimodal large language models (MLLMs), offers transformative potential for addressing persistent healthcare challenges, including workforce deficits and escalating costs. The parallel development of systematic evaluation benchmarks emerges as a critical imperative to enable performance assessment and provide technological guidance. Meanwhile, as an invaluable knowledge source, the potential of medical textbooks for benchmark development remains underexploited. Here, we present MedBookVQA, a systematic and comprehensive multimodal benchmark derived from open-access medical textbooks. To curate this benchmark, we propose a standardized pipeline for automated extraction of medical figures while contextually aligning them with corresponding medical narratives. Based on this curated data, we generate 5,000 clinically relevant questions spanning modality recognition, disease classification, anatomical identification, symptom diagnosis, and surgical procedures. A multi-tier annotation system categorizes queries through hierarchical taxonomies encompassing medical imaging modalities (42 categories), body anatomies (125 structures), and clinical specialties (31 departments), enabling nuanced analysis across medical subdomains. We evaluate a wide array of MLLMs, including proprietary, open-sourced, medical, and reasoning models, revealing significant performance disparities across task types and model categories. Our findings highlight critical capability gaps in current GMAI systems while establishing textbook-derived multimodal benchmarks as essential evaluation tools. MedBookVQA establishes textbook-derived benchmarking as a critical paradigm for advancing clinical AI, exposing limitations in GMAI systems while providing anatomically structured performance metrics across specialties.

  • 7 authors
·
Jun 1, 2025

Exploiting Contextual Target Attributes for Target Sentiment Classification

Existing PTLM-based models for TSC can be categorized into two groups: 1) fine-tuning-based models that adopt PTLM as the context encoder; 2) prompting-based models that transfer the classification task to the text/word generation task. In this paper, we present a new perspective of leveraging PTLM for TSC: simultaneously leveraging the merits of both language modeling and explicit target-context interactions via contextual target attributes. Specifically, we design the domain- and target-constrained cloze test, which can leverage the PTLMs' strong language modeling ability to generate the given target's attributes pertaining to the review context. The attributes contain the background and property information of the target, which can help to enrich the semantics of the review context and the target. To exploit the attributes for tackling TSC, we first construct a heterogeneous information graph by treating the attributes as nodes and combining them with (1) the syntax graph automatically produced by the off-the-shelf dependency parser and (2) the semantics graph of the review context, which is derived from the self-attention mechanism. Then we propose a heterogeneous information gated graph convolutional network to model the interactions among the attribute information, the syntactic information, and the contextual information. The experimental results on three benchmark datasets demonstrate the superiority of our model, which achieves new state-of-the-art performance.

  • 2 authors
·
Dec 21, 2023

Pain level and pain-related behaviour classification using GRU-based sparsely-connected RNNs

There is a growing body of studies on applying deep learning to biometrics analysis. Certain circumstances, however, could impair the objective measures and accuracy of the proposed biometric data analysis methods. For instance, people with chronic pain (CP) unconsciously adapt specific body movements to protect themselves from injury or additional pain. Because there is no dedicated benchmark database to analyse this correlation, we considered one of the specific circumstances that potentially influence a person's biometrics during daily activities in this study and classified pain level and pain-related behaviour in the EmoPain database. To achieve this, we proposed a sparsely-connected recurrent neural networks (s-RNNs) ensemble with the gated recurrent unit (GRU) that incorporates multiple autoencoders using a shared training framework. This architecture is fed by multidimensional data collected from inertial measurement unit (IMU) and surface electromyography (sEMG) sensors. Furthermore, to compensate for variations in the temporal dimension that may not be perfectly represented in the latent space of s-RNNs, we fused hand-crafted features derived from information-theoretic approaches with represented features in the shared hidden state. We conducted several experiments which indicate that the proposed method outperforms the state-of-the-art approaches in classifying both pain level and pain-related behaviour.

  • 5 authors
·
Dec 20, 2022

Framework for Machine Evaluation of Reasoning Completeness in Large Language Models For Classification Tasks

The growing adoption of machine learning (ML) in sensitive domains has heightened the demand for transparent and interpretable artificial intelligence. Large Language Models (LLMs) are increasingly capable of producing natural language explanations, yet it remains unclear whether these rationales faithfully capture the predictive signals that underlie decisions. This paper introduces RACE-Reasoning Alignment for Completeness of Explanations, a systematic framework to evaluate the alignment between LLM-generated explanations and interpretable feature importance scores derived from a logistic regression baseline. We analyze four widely used text classification datasets-WIKI ONTOLOGY, AG NEWS, IMDB, and GOEMOTIONS-and compare LLM rationales against top-ranked supporting and contradicting lexical features. To capture alignment at multiple levels of granularity, RACE implements token-aware, exact string, and edit-distance matching techniques. Empirical results reveal a consistent asymmetry: correct predictions exhibit higher coverage of supporting features, while incorrect predictions are associated with elevated coverage of contradicting features. Edit-distance matching further uncovers paraphrastic overlaps, boosting coverage while preserving this asymmetry. These findings demonstrate that LLM rationales combine both surface-level and flexible evidence reuse, yet can also amplify misleading cues in error cases. RACE provides new insights into the faithfulness of LLM explanations and establishes a quantitative basis for evaluating reasoning completeness in neural language models.

  • 1 authors
·
Oct 23, 2025

BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

  • 16 authors
·
Jan 13, 2025 3

Search for dark matter subhalos among unassociated Fermi-LAT sources in presence of dataset shift

We search for dark matter (DM) annihilating subhalos of the Milky Way halo among the Fermi Large Area Telescope (LAT) unassociated sources. We construct, for the first time, a statistical model of the unassociated sources at latitudes above 10 degrees. The latter is built as a combination of both DM annihilation subhalos as well as Galactic and extragalactic astrophysical components. The astrophysical components are constructed based on distributions of associated sources, while the distribution of DM subhalos is derived from Monte Carlo simulations. In this model we take into account the differences in the distributions of associated and unassociated sources including both covariate and prior probability shifts (both being forms of ``dataset shifts''). Previous searches of DM subhalos were based on classify-and-count strategies, while the approach adopted in this work is based on quantification learning, which allows one to determine a well-defined statistical interpretation of the contribution of a population of DM subhalos to the unassociated Fermi-LAT sources. In the bb annihilation channel and for a range of DM masses from 10 GeV to 1 TeV, we don't find a significant contribution from DM subhalos and derive a statistical 95% confidence upper limit on the DM annihilation cross section in this channel. While the derived limits are consistent with previous classify-and-count approaches, our generative statistical model opens new avenues for population studies of Fermi-LAT sources and, more generally, for searches of anomalies on top of backgrounds in presence of statistical and systematic uncertainties.

  • 5 authors
·
Mar 18, 2025

Personality Style Recognition via Machine Learning: Identifying Anaclitic and Introjective Personality Styles from Patients' Speech

In disentangling the heterogeneity observed in psychopathology, personality of the patients is considered crucial. While it has been demonstrated that personality traits are reflected in the language used by a patient, we hypothesize that this enables automatic inference of the personality type directly from speech utterances, potentially more accurately than through a traditional questionnaire-based approach explicitly designed for personality classification. To validate this hypothesis, we adopt natural language processing (NLP) and standard machine learning tools for classification. We test this on a dataset of recorded clinical diagnostic interviews (CDI) on a sample of 79 patients diagnosed with major depressive disorder (MDD) -- a condition for which differentiated treatment based on personality styles has been advocated -- and classified into anaclitic and introjective personality styles. We start by analyzing the interviews to see which linguistic features are associated with each style, in order to gain a better understanding of the styles. Then, we develop automatic classifiers based on (a) standardized questionnaire responses; (b) basic text features, i.e., TF-IDF scores of words and word sequences; (c) more advanced text features, using LIWC (linguistic inquiry and word count) and context-aware features using BERT (bidirectional encoder representations from transformers); (d) audio features. We find that automated classification with language-derived features (i.e., based on LIWC) significantly outperforms questionnaire-based classification models. Furthermore, the best performance is achieved by combining LIWC with the questionnaire features. This suggests that more work should be put into developing linguistically based automated techniques for characterizing personality, however questionnaires still to some extent complement such methods.

  • 6 authors
·
Nov 7, 2023

Benchmarking pre-trained text embedding models in aligning built asset information

Accurate mapping of the built asset information to established data classification systems and taxonomies is crucial for effective asset management, whether for compliance at project handover or ad-hoc data integration scenarios. Due to the complex nature of built asset data, which predominantly comprises technical text elements, this process remains largely manual and reliant on domain expert input. Recent breakthroughs in contextual text representation learning (text embedding), particularly through pre-trained large language models, offer promising approaches that can facilitate the automation of cross-mapping of the built asset data. However, no comprehensive evaluation has yet been conducted to assess these models' ability to effectively represent the complex semantics specific to built asset technical terminology. This study presents a comparative benchmark of state-of-the-art text embedding models to evaluate their effectiveness in aligning built asset information with domain-specific technical concepts. Our proposed datasets are derived from two renowned built asset data classification dictionaries. The results of our benchmarking across six proposed datasets, covering three tasks of clustering, retrieval, and reranking, highlight the need for future research on domain adaptation techniques. The benchmarking resources are published as an open-source library, which will be maintained and extended to support future evaluations in this field.

  • 2 authors
·
Nov 18, 2024

reBEN: Refined BigEarthNet Dataset for Remote Sensing Image Analysis

This paper presents refined BigEarthNet (reBEN) that is a large-scale, multi-modal remote sensing dataset constructed to support deep learning (DL) studies for remote sensing image analysis. The reBEN dataset consists of 549,488 pairs of Sentinel-1 and Sentinel-2 image patches. To construct reBEN, we initially consider the Sentinel-1 and Sentinel-2 tiles used to construct the BigEarthNet dataset and then divide them into patches of size 1200 m x 1200 m. We apply atmospheric correction to the Sentinel-2 patches using the latest version of the sen2cor tool, resulting in higher-quality patches compared to those present in BigEarthNet. Each patch is then associated with a pixel-level reference map and scene-level multi-labels. This makes reBEN suitable for pixel- and scene-based learning tasks. The labels are derived from the most recent CORINE Land Cover (CLC) map of 2018 by utilizing the 19-class nomenclature as in BigEarthNet. The use of the most recent CLC map results in overcoming the label noise present in BigEarthNet. Furthermore, we introduce a new geographical-based split assignment algorithm that significantly reduces the spatial correlation among the train, validation, and test sets with respect to those present in BigEarthNet. This increases the reliability of the evaluation of DL models. To minimize the DL model training time, we introduce software tools that convert the reBEN dataset into a DL-optimized data format. In our experiments, we show the potential of reBEN for multi-modal multi-label image classification problems by considering several state-of-the-art DL models. The pre-trained model weights, associated code, and complete dataset are available at https://bigearth.net.

  • 6 authors
·
Jul 4, 2024

Information-Theoretic Generalization Bounds for Deep Neural Networks

Deep neural networks (DNNs) exhibit an exceptional capacity for generalization in practical applications. This work aims to capture the effect and benefits of depth for supervised learning via information-theoretic generalization bounds. We first derive two hierarchical bounds on the generalization error in terms of the Kullback-Leibler (KL) divergence or the 1-Wasserstein distance between the train and test distributions of the network internal representations. The KL divergence bound shrinks as the layer index increases, while the Wasserstein bound implies the existence of a layer that serves as a generalization funnel, which attains a minimal 1-Wasserstein distance. Analytic expressions for both bounds are derived under the setting of binary Gaussian classification with linear DNNs. To quantify the contraction of the relevant information measures when moving deeper into the network, we analyze the strong data processing inequality (SDPI) coefficient between consecutive layers of three regularized DNN models: Dropout, DropConnect, and Gaussian noise injection. This enables refining our generalization bounds to capture the contraction as a function of the network architecture parameters. Specializing our results to DNNs with a finite parameter space and the Gibbs algorithm reveals that deeper yet narrower network architectures generalize better in those examples, although how broadly this statement applies remains a question.

  • 3 authors
·
Apr 3, 2024

GSEditPro: 3D Gaussian Splatting Editing with Attention-based Progressive Localization

With the emergence of large-scale Text-to-Image(T2I) models and implicit 3D representations like Neural Radiance Fields (NeRF), many text-driven generative editing methods based on NeRF have appeared. However, the implicit encoding of geometric and textural information poses challenges in accurately locating and controlling objects during editing. Recently, significant advancements have been made in the editing methods of 3D Gaussian Splatting, a real-time rendering technology that relies on explicit representation. However, these methods still suffer from issues including inaccurate localization and limited manipulation over editing. To tackle these challenges, we propose GSEditPro, a novel 3D scene editing framework which allows users to perform various creative and precise editing using text prompts only. Leveraging the explicit nature of the 3D Gaussian distribution, we introduce an attention-based progressive localization module to add semantic labels to each Gaussian during rendering. This enables precise localization on editing areas by classifying Gaussians based on their relevance to the editing prompts derived from cross-attention layers of the T2I model. Furthermore, we present an innovative editing optimization method based on 3D Gaussian Splatting, obtaining stable and refined editing results through the guidance of Score Distillation Sampling and pseudo ground truth. We prove the efficacy of our method through extensive experiments.

  • 6 authors
·
Nov 15, 2024

Multimodal Learning Without Labeled Multimodal Data: Guarantees and Applications

In many machine learning systems that jointly learn from multiple modalities, a core research question is to understand the nature of multimodal interactions: the emergence of new task-relevant information during learning from both modalities that was not present in either alone. We study this challenge of interaction quantification in a semi-supervised setting with only labeled unimodal data and naturally co-occurring multimodal data (e.g., unlabeled images and captions, video and corresponding audio) but when labeling them is time-consuming. Using a precise information-theoretic definition of interactions, our key contributions are the derivations of lower and upper bounds to quantify the amount of multimodal interactions in this semi-supervised setting. We propose two lower bounds based on the amount of shared information between modalities and the disagreement between separately trained unimodal classifiers, and derive an upper bound through connections to approximate algorithms for min-entropy couplings. We validate these estimated bounds and show how they accurately track true interactions. Finally, two semi-supervised multimodal applications are explored based on these theoretical results: (1) analyzing the relationship between multimodal performance and estimated interactions, and (2) self-supervised learning that embraces disagreement between modalities beyond agreement as is typically done.

  • 9 authors
·
Jun 7, 2023

Bias Loss for Mobile Neural Networks

Compact convolutional neural networks (CNNs) have witnessed exceptional improvements in performance in recent years. However, they still fail to provide the same predictive power as CNNs with a large number of parameters. The diverse and even abundant features captured by the layers is an important characteristic of these successful CNNs. However, differences in this characteristic between large CNNs and their compact counterparts have rarely been investigated. In compact CNNs, due to the limited number of parameters, abundant features are unlikely to be obtained, and feature diversity becomes an essential characteristic. Diverse features present in the activation maps derived from a data point during model inference may indicate the presence of a set of unique descriptors necessary to distinguish between objects of different classes. In contrast, data points with low feature diversity may not provide a sufficient amount of unique descriptors to make a valid prediction; we refer to them as random predictions. Random predictions can negatively impact the optimization process and harm the final performance. This paper proposes addressing the problem raised by random predictions by reshaping the standard cross-entropy to make it biased toward data points with a limited number of unique descriptive features. Our novel Bias Loss focuses the training on a set of valuable data points and prevents the vast number of samples with poor learning features from misleading the optimization process. Furthermore, to show the importance of diversity, we present a family of SkipNet models whose architectures are brought to boost the number of unique descriptors in the last layers. Our Skipnet-M can achieve 1% higher classification accuracy than MobileNetV3 Large.

  • 4 authors
·
Jul 23, 2021

First observation of the Josephson-Anderson relation in experiments on hydrodynamic drag

We verify a recent prediction (Eq. 3.50 in G. L. Eyink, Phys. Rev. X 11, 031054 (2021)) for the drag on an object moving through a fluid. In this prediction the velocity field is decomposed into a nonvortical (potential) and vortical contribution, and so is the associated drag force. In the Josephson-Anderson relation the vortical contribution of the drag force follows from the flux of vorticity traversing the streamlines of the corresponding potential flow. The potential component is directly determined by the plate acceleration and its added mass. The Josephson-Anderson relation is derived from the quantum description of superfluids, but remarkably applies to the classical fluid in our experiment. In our experiment a flat plate is accelerated through water using a robotic arm. This geometry is simple enough to allow analytic potential flow streamlines. The monitored plate position shows an oscillatory component of the acceleration, which adds an additional test of the Josephson-Anderson relation. The instantaneous velocity field is measured using particle image velocimetry. It enables us to evaluate Eq. 3.50 from [1] and compare its prediction to the measured drag force. We find excellent agreement, and, most remarkably find that the added mass contribution to the drag force still stands out after the flow has turned vortical. We finally comment on the requirements on the experimental techniques for evaluating the Josephson-Anderson relation.

  • 5 authors
·
Aug 27, 2025

Beginning with You: Perceptual-Initialization Improves Vision-Language Representation and Alignment

We introduce Perceptual-Initialization (PI), a paradigm shift in visual representation learning that incorporates human perceptual structure during the initialization phase rather than as a downstream fine-tuning step. By integrating human-derived triplet embeddings from the NIGHTS dataset to initialize a CLIP vision encoder, followed by self-supervised learning on YFCC15M, our approach demonstrates significant zero-shot performance improvements, without any task-specific fine-tuning, across 29 zero shot classification and 2 retrieval benchmarks. On ImageNet-1K, zero-shot gains emerge after approximately 15 epochs of pretraining. Benefits are observed across datasets of various scales, with improvements manifesting at different stages of the pretraining process depending on dataset characteristics. Our approach consistently enhances zero-shot top-1 accuracy, top-5 accuracy, and retrieval recall (e.g., R@1, R@5) across these diverse evaluation tasks, without requiring any adaptation to target domains. These findings challenge the conventional wisdom of using human-perceptual data primarily for fine-tuning and demonstrate that embedding human perceptual structure during early representation learning yields more capable and vision-language aligned systems that generalize immediately to unseen tasks. Our work shows that "beginning with you", starting with human perception, provides a stronger foundation for general-purpose vision-language intelligence.

  • 7 authors
·
May 20, 2025

YOLOE-26: Integrating YOLO26 with YOLOE for Real-Time Open-Vocabulary Instance Segmentation

This paper presents YOLOE-26, a unified framework that integrates the deployment-optimized YOLO26(or YOLOv26) architecture with the open-vocabulary learning paradigm of YOLOE for real-time open-vocabulary instance segmentation. Building on the NMS-free, end-to-end design of YOLOv26, the proposed approach preserves the hallmark efficiency and determinism of the YOLO family while extending its capabilities beyond closed-set recognition. YOLOE-26 employs a convolutional backbone with PAN/FPN-style multi-scale feature aggregation, followed by end-to-end regression and instance segmentation heads. A key architectural contribution is the replacement of fixed class logits with an object embedding head, which formulates classification as similarity matching against prompt embeddings derived from text descriptions, visual examples, or a built-in vocabulary. To enable efficient open-vocabulary reasoning, the framework incorporates Re-Parameterizable Region-Text Alignment (RepRTA) for zero-overhead text prompting, a Semantic-Activated Visual Prompt Encoder (SAVPE) for example-guided segmentation, and Lazy Region Prompt Contrast for prompt-free inference. All prompting modalities operate within a unified object embedding space, allowing seamless switching between text-prompted, visual-prompted, and fully autonomous segmentation. Extensive experiments demonstrate consistent scaling behavior and favorable accuracy-efficiency trade-offs across model sizes in both prompted and prompt-free settings. The training strategy leverages large-scale detection and grounding datasets with multi-task optimization and remains fully compatible with the Ultralytics ecosystem for training, validation, and deployment. Overall, YOLOE-26 provides a practical and scalable solution for real-time open-vocabulary instance segmentation in dynamic, real-world environments.

Limits of Absoluteness of Observed Events in Timelike Scenarios: A No-Go Theorem

Wigner's Friend-type paradoxes challenge the assumption that events are absolute -- that when we measure a system, we obtain a single result, which is not relative to anything or anyone else. These paradoxes highlight the tension between quantum theory and our intuitions about reality being observer-independent. Building on a recent result that developed these paradoxes into a no-go theorem, namely the Local Friendliness Theorem, we introduce the Causal Friendliness Paradox, a time-ordered analogue of it. In this framework, we replace the usual locality assumption with Axiological Time Symmetry (ATS), and show that, when combined with the assumptions of Absoluteness of Observed Events (AOE), No Retrocausality (NRC), and Screening via Pseudo Events (SPE), we obtain a causal inequality. We then show that quantum mechanics violates this inequality and is therefore incompatible with at least one of these assumptions. To probe which assumption might be incompatible, we then examine whether AOE in its entirety is essential for this no-go result. We propose a weaker, operational form of AOE that still leads to inequalities that quantum mechanics violates. This result shows that even under relaxed assumptions, quantum theory resists reconciliation with classical notions of absolute events, reinforcing the foundational significance of Wigner's Friend-type paradoxes in timelike scenarios.

  • 2 authors
·
Oct 30, 2025

Open-Vocabulary Camouflaged Object Segmentation with Cascaded Vision Language Models

Open-Vocabulary Camouflaged Object Segmentation (OVCOS) seeks to segment and classify camouflaged objects from arbitrary categories, presenting unique challenges due to visual ambiguity and unseen categories.Recent approaches typically adopt a two-stage paradigm: first segmenting objects, then classifying the segmented regions using Vision Language Models (VLMs).However, these methods (1) suffer from a domain gap caused by the mismatch between VLMs' full-image training and cropped-region inference, and (2) depend on generic segmentation models optimized for well-delineated objects, making them less effective for camouflaged objects.Without explicit guidance, generic segmentation models often overlook subtle boundaries, leading to imprecise segmentation.In this paper,we introduce a novel VLM-guided cascaded framework to address these issues in OVCOS.For segmentation, we leverage the Segment Anything Model (SAM), guided by the VLM.Our framework uses VLM-derived features as explicit prompts to SAM, effectively directing attention to camouflaged regions and significantly improving localization accuracy.For classification, we avoid the domain gap introduced by hard cropping.Instead, we treat the segmentation output as a soft spatial prior via the alpha channel, which retains the full image context while providing precise spatial guidance, leading to more accurate and context-aware classification of camouflaged objects.The same VLM is shared across both segmentation and classification to ensure efficiency and semantic consistency.Extensive experiments on both OVCOS and conventional camouflaged object segmentation benchmarks demonstrate the clear superiority of our method, highlighting the effectiveness of leveraging rich VLM semantics for both segmentation and classification of camouflaged objects.

  • 7 authors
·
Jun 24, 2025

P-FOLIO: Evaluating and Improving Logical Reasoning with Abundant Human-Written Reasoning Chains

Existing methods on understanding the capabilities of LLMs in logical reasoning rely on binary entailment classification or synthetically derived rationales, which are not sufficient for proper investigation of model's capabilities. We present P-FOLIO, a human-annotated dataset consisting of diverse and complex reasoning chains for a set of realistic logical reasoning stories also written by humans. P-FOLIO is collected with an annotation protocol that facilitates humans to annotate well-structured natural language proofs for first-order logic reasoning problems in a step-by-step manner. The number of reasoning steps in P-FOLIO span from 0 to 20. We further use P-FOLIO to evaluate and improve large-language-model (LLM) reasoning capabilities. We evaluate LLM reasoning capabilities at a fine granularity via single-step inference rule classification, with more diverse inference rules of more diverse and higher levels of complexities than previous works. Given that a single model-generated reasoning chain could take a completely different path than the human-annotated one, we sample multiple reasoning chains from a model and use pass@k metrics for evaluating the quality of model-generated reasoning chains. We show that human-written reasoning chains significantly boost the logical reasoning capabilities of LLMs via many-shot prompting and fine-tuning. Furthermore, fine-tuning Llama3-7B on P-FOLIO improves the model performance by 10% or more on three other out-of-domain logical reasoning datasets. We also conduct detailed analysis to show where most powerful LLMs fall short in reasoning. We will release the dataset and code publicly.

  • 16 authors
·
Oct 11, 2024

Machine learning applications to DNA subsequence and restriction site analysis

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

  • 2 authors
·
Nov 7, 2020

OpenChat: Advancing Open-source Language Models with Mixed-Quality Data

Nowadays, open-source large language models like LLaMA have emerged. Recent developments have incorporated supervised fine-tuning (SFT) and reinforcement learning fine-tuning (RLFT) to align these models with human goals. However, SFT methods treat all training data with mixed quality equally, while RLFT methods require high-quality pairwise or ranking-based preference data. In this study, we present a novel framework, named OpenChat, to advance open-source language models with mixed-quality data. Specifically, we consider the general SFT training data, consisting of a small amount of expert data mixed with a large proportion of sub-optimal data, without any preference labels. We propose the C(onditioned)-RLFT, which regards different data sources as coarse-grained reward labels and learns a class-conditioned policy to leverage complementary data quality information. Interestingly, the optimal policy in C-RLFT can be easily solved through single-stage, RL-free supervised learning, which is lightweight and avoids costly human preference labeling. Through extensive experiments on three standard benchmarks, our openchat-13b fine-tuned with C-RLFT achieves the highest average performance among all 13b open-source language models. Moreover, we use AGIEval to validate the model generalization performance, in which only openchat-13b surpasses the base model. Finally, we conduct a series of analyses to shed light on the effectiveness and robustness of OpenChat. Our code, data, and models are publicly available at https://github.com/imoneoi/openchat.

  • 6 authors
·
Sep 20, 2023 4

Towards Improved Input Masking for Convolutional Neural Networks

The ability to remove features from the input of machine learning models is very important to understand and interpret model predictions. However, this is non-trivial for vision models since masking out parts of the input image typically causes large distribution shifts. This is because the baseline color used for masking (typically grey or black) is out of distribution. Furthermore, the shape of the mask itself can contain unwanted signals which can be used by the model for its predictions. Recently, there has been some progress in mitigating this issue (called missingness bias) in image masking for vision transformers. In this work, we propose a new masking method for CNNs we call layer masking in which the missingness bias caused by masking is reduced to a large extent. Intuitively, layer masking applies a mask to intermediate activation maps so that the model only processes the unmasked input. We show that our method (i) is able to eliminate or minimize the influence of the mask shape or color on the output of the model, and (ii) is much better than replacing the masked region by black or grey for input perturbation based interpretability techniques like LIME. Thus, layer masking is much less affected by missingness bias than other masking strategies. We also demonstrate how the shape of the mask may leak information about the class, thus affecting estimates of model reliance on class-relevant features derived from input masking. Furthermore, we discuss the role of data augmentation techniques for tackling this problem, and argue that they are not sufficient for preventing model reliance on mask shape. The code for this project is publicly available at https://github.com/SriramB-98/layer_masking

  • 2 authors
·
Nov 26, 2022

The Hidden DNA of LLM-Generated JavaScript: Structural Patterns Enable High-Accuracy Authorship Attribution

In this paper, we present the first large-scale study exploring whether JavaScript code generated by Large Language Models (LLMs) can reveal which model produced it, enabling reliable authorship attribution and model fingerprinting. With the rapid rise of AI-generated code, attribution is playing a critical role in detecting vulnerabilities, flagging malicious content, and ensuring accountability. While AI-vs-human detection usually treats AI as a single category we show that individual LLMs leave unique stylistic signatures, even among models belonging to the same family or parameter size. To this end, we introduce LLM-NodeJS, a dataset of 50,000 Node.js back-end programs from 20 large language models. Each has four transformed variants, yielding 250,000 unique JavaScript samples and two additional representations (JSIR and AST) for diverse research applications. Using this dataset, we benchmark traditional machine learning classifiers against fine-tuned Transformer encoders and introduce CodeT5-JSA, a custom architecture derived from the 770M-parameter CodeT5 model with its decoder removed and a modified classification head. It achieves 95.8% accuracy on five-class attribution, 94.6% on ten-class, and 88.5% on twenty-class tasks, surpassing other tested models such as BERT, CodeBERT, and Longformer. We demonstrate that classifiers capture deeper stylistic regularities in program dataflow and structure, rather than relying on surface-level features. As a result, attribution remains effective even after mangling, comment removal, and heavy code transformations. To support open science and reproducibility, we release the LLM-NodeJS dataset, Google Colab training scripts, and all related materials on GitHub: https://github.com/LLM-NodeJS-dataset.

  • 5 authors
·
Oct 12, 2025 2

Advancing Multimodal Medical Capabilities of Gemini

Many clinical tasks require an understanding of specialized data, such as medical images and genomics, which is not typically found in general-purpose large multimodal models. Building upon Gemini's multimodal models, we develop several models within the new Med-Gemini family that inherit core capabilities of Gemini and are optimized for medical use via fine-tuning with 2D and 3D radiology, histopathology, ophthalmology, dermatology and genomic data. Med-Gemini-2D sets a new standard for AI-based chest X-ray (CXR) report generation based on expert evaluation, exceeding previous best results across two separate datasets by an absolute margin of 1% and 12%, where 57% and 96% of AI reports on normal cases, and 43% and 65% on abnormal cases, are evaluated as "equivalent or better" than the original radiologists' reports. We demonstrate the first ever large multimodal model-based report generation for 3D computed tomography (CT) volumes using Med-Gemini-3D, with 53% of AI reports considered clinically acceptable, although additional research is needed to meet expert radiologist reporting quality. Beyond report generation, Med-Gemini-2D surpasses the previous best performance in CXR visual question answering (VQA) and performs well in CXR classification and radiology VQA, exceeding SoTA or baselines on 17 of 20 tasks. In histopathology, ophthalmology, and dermatology image classification, Med-Gemini-2D surpasses baselines across 18 out of 20 tasks and approaches task-specific model performance. Beyond imaging, Med-Gemini-Polygenic outperforms the standard linear polygenic risk score-based approach for disease risk prediction and generalizes to genetically correlated diseases for which it has never been trained. Although further development and evaluation are necessary in the safety-critical medical domain, our results highlight the potential of Med-Gemini across a wide range of medical tasks.

  • 47 authors
·
May 6, 2024

CUPCase: Clinically Uncommon Patient Cases and Diagnoses Dataset

Medical benchmark datasets significantly contribute to developing Large Language Models (LLMs) for medical knowledge extraction, diagnosis, summarization, and other uses. Yet, current benchmarks are mainly derived from exam questions given to medical students or cases described in the medical literature, lacking the complexity of real-world patient cases that deviate from classic textbook abstractions. These include rare diseases, uncommon presentations of common diseases, and unexpected treatment responses. Here, we construct Clinically Uncommon Patient Cases and Diagnosis Dataset (CUPCase) based on 3,562 real-world case reports from BMC, including diagnoses in open-ended textual format and as multiple-choice options with distractors. Using this dataset, we evaluate the ability of state-of-the-art LLMs, including both general-purpose and Clinical LLMs, to identify and correctly diagnose a patient case, and test models' performance when only partial information about cases is available. Our findings show that general-purpose GPT-4o attains the best performance in both the multiple-choice task (average accuracy of 87.9%) and the open-ended task (BERTScore F1 of 0.764), outperforming several LLMs with a focus on the medical domain such as Meditron-70B and MedLM-Large. Moreover, GPT-4o was able to maintain 87% and 88% of its performance with only the first 20% of tokens of the case presentation in multiple-choice and free text, respectively, highlighting the potential of LLMs to aid in early diagnosis in real-world cases. CUPCase expands our ability to evaluate LLMs for clinical decision support in an open and reproducible manner.

  • 4 authors
·
Mar 8, 2025

Rate limits in quantum networks with lossy repeaters

The derivation of ultimate limits to communication over certain quantum repeater networks have provided extremely valuable benchmarks for assessing near-term quantum communication protocols. However, these bounds are usually derived in the limit of ideal devices and leave questions about the performance of practical implementations unanswered. To address this challenge, we quantify how the presence of loss in repeater stations affect the maximum attainable rates for quantum communication over linear repeater chains and more complex quantum networks. Extending the framework of node splitting, we model the loss introduced at the repeater stations and then prove the corresponding limits. In the linear chain scenario we show that, by increasing the number of repeater stations, the maximum rate cannot overcome a quantity which solely depends on the loss of a single station. We introduce a way of adapting the standard machinery for obtaining bounds to this realistic scenario. The difference is that whilst ultimate limits for any strategy can be derived given a fixed channel, when the repeaters introduce additional decoherence, then the effective overall channel is itself a function of the chosen repeater strategy (e.g., one-way versus two-way classical communication). Classes of repeater strategies can be analysed using additional modelling and the subsequent bounds can be interpreted as the optimal rate within that class.

  • 4 authors
·
Oct 19, 2021

The Newspaper Navigator Dataset: Extracting And Analyzing Visual Content from 16 Million Historic Newspaper Pages in Chronicling America

Chronicling America is a product of the National Digital Newspaper Program, a partnership between the Library of Congress and the National Endowment for the Humanities to digitize historic newspapers. Over 16 million pages of historic American newspapers have been digitized for Chronicling America to date, complete with high-resolution images and machine-readable METS/ALTO OCR. Of considerable interest to Chronicling America users is a semantified corpus, complete with extracted visual content and headlines. To accomplish this, we introduce a visual content recognition model trained on bounding box annotations of photographs, illustrations, maps, comics, and editorial cartoons collected as part of the Library of Congress's Beyond Words crowdsourcing initiative and augmented with additional annotations including those of headlines and advertisements. We describe our pipeline that utilizes this deep learning model to extract 7 classes of visual content: headlines, photographs, illustrations, maps, comics, editorial cartoons, and advertisements, complete with textual content such as captions derived from the METS/ALTO OCR, as well as image embeddings for fast image similarity querying. We report the results of running the pipeline on 16.3 million pages from the Chronicling America corpus and describe the resulting Newspaper Navigator dataset, the largest dataset of extracted visual content from historic newspapers ever produced. The Newspaper Navigator dataset, finetuned visual content recognition model, and all source code are placed in the public domain for unrestricted re-use.

  • 9 authors
·
May 4, 2020

Linearized Optimal Transport for Analysis of High-Dimensional Point-Cloud and Single-Cell Data

Single-cell technologies generate high-dimensional point clouds of cells, enabling detailed characterization of complex patient states and treatment responses. Yet each patient is represented by an irregular point cloud rather than a simple vector, making it difficult to directly quantify and compare biological differences between individuals. Nonlinear methods such as kernels and neural networks achieve predictive accuracy but act as black boxes, offering little biological interpretability. To address these limitations, we adapt the Linear Optimal Transport (LOT) framework to this setting, embedding irregular point clouds into a fixed-dimensional Euclidean space while preserving distributional structure. This embedding provides a principled linear representation that preserves optimal transport geometry while enabling downstream analysis. It also forms a registration between any two patients, enabling direct comparison of their cellular distributions. Within this space, LOT enables: (i) accurate and interpretable classification of COVID-19 patient states, where classifier weights map back to specific markers and spatial regions driving predictions; and (ii) synthetic data generation for patient-derived organoids, exploiting the linearity of the LOT embedding. LOT barycenters yield averaged cellular profiles representing combined conditions or samples, supporting drug interaction testing. Together, these results establish LOT as a unified framework that bridges predictive performance, interpretability, and generative modeling. By transforming heterogeneous point clouds into structured embeddings directly traceable to the original data, LOT opens new opportunities for understanding immune variation and treatment effects in high-dimensional biological systems.

  • 5 authors
·
Oct 24, 2025

Adaptive Debiasing Tsallis Entropy for Test-Time Adaptation

Mainstream Test-Time Adaptation (TTA) methods for adapting vision-language models, e.g., CLIP, typically rely on Shannon Entropy (SE) at test time to measure prediction uncertainty and inconsistency. However, since CLIP has a built-in bias from pretraining on highly imbalanced web-crawled data, SE inevitably results in producing biased estimates of uncertainty entropy. To address this issue, we notably find and demonstrate that Tsallis Entropy (TE), a generalized form of SE, is naturally suited for characterizing biased distributions by introducing a non-extensive parameter q, with the performance of SE serving as a lower bound for TE. Building upon this, we generalize TE into Adaptive Debiasing Tsallis Entropy (ADTE) for TTA, customizing a class-specific parameter q^l derived by normalizing the estimated label bias from continuously incoming test instances, for each category. This adaptive approach allows ADTE to accurately select high-confidence views and seamlessly integrate with a label adjustment strategy to enhance adaptation, without introducing distribution-specific hyperparameter tuning. Besides, our investigation reveals that both TE and ADTE can serve as direct, advanced alternatives to SE in TTA, without any other modifications. Experimental results show that ADTE outperforms state-of-the-art methods on ImageNet and its five variants, and achieves the highest average performance on 10 cross-domain benchmarks, regardless of the model architecture or text prompts used. Our code is available at https://github.com/Jinx630/ADTE.

  • 8 authors
·
Feb 12

MVImgNet: A Large-scale Dataset of Multi-view Images

Being data-driven is one of the most iconic properties of deep learning algorithms. The birth of ImageNet drives a remarkable trend of "learning from large-scale data" in computer vision. Pretraining on ImageNet to obtain rich universal representations has been manifested to benefit various 2D visual tasks, and becomes a standard in 2D vision. However, due to the laborious collection of real-world 3D data, there is yet no generic dataset serving as a counterpart of ImageNet in 3D vision, thus how such a dataset can impact the 3D community is unraveled. To remedy this defect, we introduce MVImgNet, a large-scale dataset of multi-view images, which is highly convenient to gain by shooting videos of real-world objects in human daily life. It contains 6.5 million frames from 219,188 videos crossing objects from 238 classes, with rich annotations of object masks, camera parameters, and point clouds. The multi-view attribute endows our dataset with 3D-aware signals, making it a soft bridge between 2D and 3D vision. We conduct pilot studies for probing the potential of MVImgNet on a variety of 3D and 2D visual tasks, including radiance field reconstruction, multi-view stereo, and view-consistent image understanding, where MVImgNet demonstrates promising performance, remaining lots of possibilities for future explorations. Besides, via dense reconstruction on MVImgNet, a 3D object point cloud dataset is derived, called MVPNet, covering 87,200 samples from 150 categories, with the class label on each point cloud. Experiments show that MVPNet can benefit the real-world 3D object classification while posing new challenges to point cloud understanding. MVImgNet and MVPNet will be publicly available, hoping to inspire the broader vision community.

  • 13 authors
·
Mar 10, 2023

HOLa: Zero-Shot HOI Detection with Low-Rank Decomposed VLM Feature Adaptation

Zero-shot human-object interaction (HOI) detection remains a challenging task, particularly in generalizing to unseen actions. Existing methods address this challenge by tapping Vision-Language Models (VLMs) to access knowledge beyond the training data. However, they either struggle to distinguish actions involving the same object or demonstrate limited generalization to unseen classes. In this paper, we introduce HOLa (Zero-Shot HOI Detection with Low-Rank Decomposed VLM Feature Adaptation), a novel approach that both enhances generalization to unseen classes and improves action distinction. In training, HOLa decomposes VLM text features for given HOI classes via low-rank factorization, producing class-shared basis features and adaptable weights. These features and weights form a compact HOI representation that preserves shared information across classes, enhancing generalization to unseen classes. Subsequently, we refine action distinction by adapting weights for each HOI class and introducing human-object tokens to enrich visual interaction representations. To further distinguish unseen actions, we guide the weight adaptation with LLM-derived action regularization. Experimental results show that our method sets a new state-of-the-art across zero-shot HOI settings on HICO-DET, achieving an unseen-class mAP of 27.91 in the unseen-verb setting. Our code is available at https://github.com/ChelsieLei/HOLa.

  • 3 authors
·
Jul 21, 2025

HM-RAG: Hierarchical Multi-Agent Multimodal Retrieval Augmented Generation

While Retrieval-Augmented Generation (RAG) augments Large Language Models (LLMs) with external knowledge, conventional single-agent RAG remains fundamentally limited in resolving complex queries demanding coordinated reasoning across heterogeneous data ecosystems. We present HM-RAG, a novel Hierarchical Multi-agent Multimodal RAG framework that pioneers collaborative intelligence for dynamic knowledge synthesis across structured, unstructured, and graph-based data. The framework is composed of three-tiered architecture with specialized agents: a Decomposition Agent that dissects complex queries into contextually coherent sub-tasks via semantic-aware query rewriting and schema-guided context augmentation; Multi-source Retrieval Agents that carry out parallel, modality-specific retrieval using plug-and-play modules designed for vector, graph, and web-based databases; and a Decision Agent that uses consistency voting to integrate multi-source answers and resolve discrepancies in retrieval results through Expert Model Refinement. This architecture attains comprehensive query understanding by combining textual, graph-relational, and web-derived evidence, resulting in a remarkable 12.95% improvement in answer accuracy and a 3.56% boost in question classification accuracy over baseline RAG systems on the ScienceQA and CrisisMMD benchmarks. Notably, HM-RAG establishes state-of-the-art results in zero-shot settings on both datasets. Its modular architecture ensures seamless integration of new data modalities while maintaining strict data governance, marking a significant advancement in addressing the critical challenges of multimodal reasoning and knowledge synthesis in RAG systems. Code is available at https://github.com/ocean-luna/HMRAG.

  • 7 authors
·
Apr 13, 2025

CLImage: Human-Annotated Datasets for Complementary-Label Learning

Complementary-label learning (CLL) is a weakly-supervised learning paradigm that aims to train a multi-class classifier using only complementary labels, which indicate classes to which an instance does not belong. Despite numerous algorithmic proposals for CLL, their practical applicability remains unverified for two reasons. Firstly, these algorithms often rely on assumptions about the generation of complementary labels, and it is not clear how far the assumptions are from reality. Secondly, their evaluation has been limited to synthetically labeled datasets. To gain insights into the real-world performance of CLL algorithms, we developed a protocol to collect complementary labels from human annotators. Our efforts resulted in the creation of four datasets: CLCIFAR10, CLCIFAR20, CLMicroImageNet10, and CLMicroImageNet20, derived from well-known classification datasets CIFAR10, CIFAR100, and TinyImageNet200. These datasets represent the very first real-world CLL datasets, namely CLImage, which are publicly available at: https://github.com/ntucllab/CLImage\_Dataset. Through extensive benchmark experiments, we discovered a notable decrease in performance when transitioning from synthetically labeled datasets to real-world datasets. We investigated the key factors contributing to the decrease with a thorough dataset-level ablation study. Our analyses highlight annotation noise as the most influential factor in the real-world datasets. In addition, we discover that the biased-nature of human-annotated complementary labels and the difficulty to validate with only complementary labels are two outstanding barriers to practical CLL. These findings suggest that the community focus more research efforts on developing CLL algorithms and validation schemes that are robust to noisy and biased complementary-label distributions.

  • 5 authors
·
May 14, 2023

Learning to Actively Learn: A Robust Approach

This work proposes a procedure for designing algorithms for specific adaptive data collection tasks like active learning and pure-exploration multi-armed bandits. Unlike the design of traditional adaptive algorithms that rely on concentration of measure and careful analysis to justify the correctness and sample complexity of the procedure, our adaptive algorithm is learned via adversarial training over equivalence classes of problems derived from information theoretic lower bounds. In particular, a single adaptive learning algorithm is learned that competes with the best adaptive algorithm learned for each equivalence class. Our procedure takes as input just the available queries, set of hypotheses, loss function, and total query budget. This is in contrast to existing meta-learning work that learns an adaptive algorithm relative to an explicit, user-defined subset or prior distribution over problems which can be challenging to define and be mismatched to the instance encountered at test time. This work is particularly focused on the regime when the total query budget is very small, such as a few dozen, which is much smaller than those budgets typically considered by theoretically derived algorithms. We perform synthetic experiments to justify the stability and effectiveness of the training procedure, and then evaluate the method on tasks derived from real data including a noisy 20 Questions game and a joke recommendation task.

  • 3 authors
·
Oct 29, 2020

RealToxicityPrompts: Evaluating Neural Toxic Degeneration in Language Models

Pretrained neural language models (LMs) are prone to generating racist, sexist, or otherwise toxic language which hinders their safe deployment. We investigate the extent to which pretrained LMs can be prompted to generate toxic language, and the effectiveness of controllable text generation algorithms at preventing such toxic degeneration. We create and release RealToxicityPrompts, a dataset of 100K naturally occurring, sentence-level prompts derived from a large corpus of English web text, paired with toxicity scores from a widely-used toxicity classifier. Using RealToxicityPrompts, we find that pretrained LMs can degenerate into toxic text even from seemingly innocuous prompts. We empirically assess several controllable generation methods, and find that while data- or compute-intensive methods (e.g., adaptive pretraining on non-toxic data) are more effective at steering away from toxicity than simpler solutions (e.g., banning "bad" words), no current method is failsafe against neural toxic degeneration. To pinpoint the potential cause of such persistent toxic degeneration, we analyze two web text corpora used to pretrain several LMs (including GPT-2; Radford et. al, 2019), and find a significant amount of offensive, factually unreliable, and otherwise toxic content. Our work provides a test bed for evaluating toxic generations by LMs and stresses the need for better data selection processes for pretraining.

  • 5 authors
·
Sep 23, 2020