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Dec 26

Retrieval Augmented Generation (RAG) and Beyond: A Comprehensive Survey on How to Make your LLMs use External Data More Wisely

Large language models (LLMs) augmented with external data have demonstrated remarkable capabilities in completing real-world tasks. Techniques for integrating external data into LLMs, such as Retrieval-Augmented Generation (RAG) and fine-tuning, are gaining increasing attention and widespread application. Nonetheless, the effective deployment of data-augmented LLMs across various specialized fields presents substantial challenges. These challenges encompass a wide range of issues, from retrieving relevant data and accurately interpreting user intent to fully harnessing the reasoning capabilities of LLMs for complex tasks. We believe that there is no one-size-fits-all solution for data-augmented LLM applications. In practice, underperformance often arises from a failure to correctly identify the core focus of a task or because the task inherently requires a blend of multiple capabilities that must be disentangled for better resolution. In this survey, we propose a RAG task categorization method, classifying user queries into four levels based on the type of external data required and primary focus of the task: explicit fact queries, implicit fact queries, interpretable rationale queries, and hidden rationale queries. We define these levels of queries, provide relevant datasets, and summarize the key challenges and most effective techniques for addressing these challenges. Finally, we discuss three main forms of integrating external data into LLMs: context, small model, and fine-tuning, highlighting their respective strengths, limitations, and the types of problems they are suited to solve. This work aims to help readers thoroughly understand and decompose the data requirements and key bottlenecks in building LLM applications, offering solutions to the different challenges and serving as a guide to systematically developing such applications.

  • 6 authors
·
Sep 23, 2024

Adversarial Speaker Disentanglement Using Unannotated External Data for Self-supervised Representation Based Voice Conversion

Nowadays, recognition-synthesis-based methods have been quite popular with voice conversion (VC). By introducing linguistics features with good disentangling characters extracted from an automatic speech recognition (ASR) model, the VC performance achieved considerable breakthroughs. Recently, self-supervised learning (SSL) methods trained with a large-scale unannotated speech corpus have been applied to downstream tasks focusing on the content information, which is suitable for VC tasks. However, a huge amount of speaker information in SSL representations degrades timbre similarity and the quality of converted speech significantly. To address this problem, we proposed a high-similarity any-to-one voice conversion method with the input of SSL representations. We incorporated adversarial training mechanisms in the synthesis module using external unannotated corpora. Two auxiliary discriminators were trained to distinguish whether a sequence of mel-spectrograms has been converted by the acoustic model and whether a sequence of content embeddings contains speaker information from external corpora. Experimental results show that our proposed method achieves comparable similarity and higher naturalness than the supervised method, which needs a huge amount of annotated corpora for training and is applicable to improve similarity for VC methods with other SSL representations as input.

  • 5 authors
·
May 16, 2023

Do Generated Data Always Help Contrastive Learning?

Contrastive Learning (CL) has emerged as one of the most successful paradigms for unsupervised visual representation learning, yet it often depends on intensive manual data augmentations. With the rise of generative models, especially diffusion models, the ability to generate realistic images close to the real data distribution has been well recognized. These generated high-equality images have been successfully applied to enhance contrastive representation learning, a technique termed ``data inflation''. However, we find that the generated data (even from a good diffusion model like DDPM) may sometimes even harm contrastive learning. We investigate the causes behind this failure from the perspective of both data inflation and data augmentation. For the first time, we reveal the complementary roles that stronger data inflation should be accompanied by weaker augmentations, and vice versa. We also provide rigorous theoretical explanations for these phenomena via deriving its generalization bounds under data inflation. Drawing from these insights, we propose Adaptive Inflation (AdaInf), a purely data-centric strategy without introducing any extra computation cost. On benchmark datasets, AdaInf can bring significant improvements for various contrastive learning methods. Notably, without using external data, AdaInf obtains 94.70% linear accuracy on CIFAR-10 with SimCLR, setting a new record that surpasses many sophisticated methods. Code is available at https://github.com/PKU-ML/adainf.

  • 3 authors
·
Mar 19, 2024

American Stories: A Large-Scale Structured Text Dataset of Historical U.S. Newspapers

Existing full text datasets of U.S. public domain newspapers do not recognize the often complex layouts of newspaper scans, and as a result the digitized content scrambles texts from articles, headlines, captions, advertisements, and other layout regions. OCR quality can also be low. This study develops a novel, deep learning pipeline for extracting full article texts from newspaper images and applies it to the nearly 20 million scans in Library of Congress's public domain Chronicling America collection. The pipeline includes layout detection, legibility classification, custom OCR, and association of article texts spanning multiple bounding boxes. To achieve high scalability, it is built with efficient architectures designed for mobile phones. The resulting American Stories dataset provides high quality data that could be used for pre-training a large language model to achieve better understanding of historical English and historical world knowledge. The dataset could also be added to the external database of a retrieval-augmented language model to make historical information - ranging from interpretations of political events to minutiae about the lives of people's ancestors - more widely accessible. Furthermore, structured article texts facilitate using transformer-based methods for popular social science applications like topic classification, detection of reproduced content, and news story clustering. Finally, American Stories provides a massive silver quality dataset for innovating multimodal layout analysis models and other multimodal applications.

  • 10 authors
·
Aug 23, 2023

Absolute Zero: Reinforced Self-play Reasoning with Zero Data

Reinforcement learning with verifiable rewards (RLVR) has shown promise in enhancing the reasoning capabilities of large language models by learning directly from outcome-based rewards. Recent RLVR works that operate under the zero setting avoid supervision in labeling the reasoning process, but still depend on manually curated collections of questions and answers for training. The scarcity of high-quality, human-produced examples raises concerns about the long-term scalability of relying on human supervision, a challenge already evident in the domain of language model pretraining. Furthermore, in a hypothetical future where AI surpasses human intelligence, tasks provided by humans may offer limited learning potential for a superintelligent system. To address these concerns, we propose a new RLVR paradigm called Absolute Zero, in which a single model learns to propose tasks that maximize its own learning progress and improves reasoning by solving them, without relying on any external data. Under this paradigm, we introduce the Absolute Zero Reasoner (AZR), a system that self-evolves its training curriculum and reasoning ability by using a code executor to both validate proposed code reasoning tasks and verify answers, serving as an unified source of verifiable reward to guide open-ended yet grounded learning. Despite being trained entirely without external data, AZR achieves overall SOTA performance on coding and mathematical reasoning tasks, outperforming existing zero-setting models that rely on tens of thousands of in-domain human-curated examples. Furthermore, we demonstrate that AZR can be effectively applied across different model scales and is compatible with various model classes.

BuzzSet v1.0: A Dataset for Pollinator Detection in Field Conditions

Pollinator insects such as honeybees and bumblebees are vital to global food production and ecosystem stability, yet their populations are declining due to increasing anthropogenic and environmental stressors. To support scalable, automated pollinator monitoring, we introduce BuzzSet, a new large-scale dataset of high-resolution pollinator images collected in real agricultural field conditions. BuzzSet contains 7856 manually verified and labeled images, with over 8000 annotated instances across three classes: honeybees, bumblebees, and unidentified insects. Initial annotations were generated using a YOLOv12 model trained on external data and refined via human verification using open-source labeling tools. All images were preprocessed into 256~times~256 tiles to improve the detection of small insects. We provide strong baselines using the RF-DETR transformer-based object detector. The model achieves high F1-scores of 0.94 and 0.92 for honeybee and bumblebee classes, respectively, with confusion matrix results showing minimal misclassification between these categories. The unidentified class remains more challenging due to label ambiguity and lower sample frequency, yet still contributes useful insights for robustness evaluation. Overall detection quality is strong, with a best [email protected] of 0.559. BuzzSet offers a valuable benchmark for small object detection, class separation under label noise, and ecological computer vision.

  • 6 authors
·
Aug 27

Machine Learning Workflow to Explain Black-box Models for Early Alzheimer's Disease Classification Evaluated for Multiple Datasets

Purpose: Hard-to-interpret Black-box Machine Learning (ML) were often used for early Alzheimer's Disease (AD) detection. Methods: To interpret eXtreme Gradient Boosting (XGBoost), Random Forest (RF), and Support Vector Machine (SVM) black-box models a workflow based on Shapley values was developed. All models were trained on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset and evaluated for an independent ADNI test set, as well as the external Australian Imaging and Lifestyle flagship study of Ageing (AIBL), and Open Access Series of Imaging Studies (OASIS) datasets. Shapley values were compared to intuitively interpretable Decision Trees (DTs), and Logistic Regression (LR), as well as natural and permutation feature importances. To avoid the reduction of the explanation validity caused by correlated features, forward selection and aspect consolidation were implemented. Results: Some black-box models outperformed DTs and LR. The forward-selected features correspond to brain areas previously associated with AD. Shapley values identified biologically plausible associations with moderate to strong correlations with feature importances. The most important RF features to predict AD conversion were the volume of the amygdalae, and a cognitive test score. Good cognitive test performances and large brain volumes decreased the AD risk. The models trained using cognitive test scores significantly outperformed brain volumetric models (p<0.05). Cognitive Normal (CN) vs. AD models were successfully transferred to external datasets. Conclusion: In comparison to previous work, improved performances for ADNI and AIBL were achieved for CN vs. Mild Cognitive Impairment (MCI) classification using brain volumes. The Shapley values and the feature importances showed moderate to strong correlations.

  • 2 authors
·
May 12, 2022

Defending Against Prompt Injection with DataFilter

When large language model (LLM) agents are increasingly deployed to automate tasks and interact with untrusted external data, prompt injection emerges as a significant security threat. By injecting malicious instructions into the data that LLMs access, an attacker can arbitrarily override the original user task and redirect the agent toward unintended, potentially harmful actions. Existing defenses either require access to model weights (fine-tuning), incur substantial utility loss (detection-based), or demand non-trivial system redesign (system-level). Motivated by this, we propose DataFilter, a test-time model-agnostic defense that removes malicious instructions from the data before it reaches the backend LLM. DataFilter is trained with supervised fine-tuning on simulated injections and leverages both the user's instruction and the data to selectively strip adversarial content while preserving benign information. Across multiple benchmarks, DataFilter consistently reduces the prompt injection attack success rates to near zero while maintaining the LLMs' utility. DataFilter delivers strong security, high utility, and plug-and-play deployment, making it a strong practical defense to secure black-box commercial LLMs against prompt injection. Our DataFilter model is released at https://huggingface.co/JoyYizhu/DataFilter for immediate use, with the code to reproduce our results at https://github.com/yizhu-joy/DataFilter.

  • 5 authors
·
Oct 21

Improved Robustness for Deep Learning-based Segmentation of Multi-Center Myocardial Perfusion MRI Datasets Using Data Adaptive Uncertainty-guided Space-time Analysis

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

  • 11 authors
·
Aug 8, 2024

Experts' cognition-driven ensemble deep learning for external validation of predicting pathological complete response to neoadjuvant chemotherapy from histological images in breast cancer

In breast cancer imaging, there has been a trend to directly predict pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) from histological images based on deep learning (DL). However, it has been a commonly known problem that the constructed DL-based models numerically have better performances in internal validation than in external validation. The primary reason for this situation lies in that the distribution of the external data for validation is different from the distribution of the training data for the construction of the predictive model. In this paper, we aim to alleviate this situation with a more intrinsic approach. We propose an experts' cognition-driven ensemble deep learning (ECDEDL) approach for external validation of predicting pCR to NAC from histological images in breast cancer. The proposed ECDEDL, which takes the cognition of both pathology and artificial intelligence experts into consideration to improve the generalization of the predictive model to the external validation, more intrinsically approximates the working paradigm of a human being which will refer to his various working experiences to make decisions. The proposed ECDEDL approach was validated with 695 WSIs collected from the same center as the primary dataset to develop the predictive model and perform the internal validation, and 340 WSIs collected from other three centers as the external dataset to perform the external validation. In external validation, the proposed ECDEDL approach improves the AUCs of pCR prediction from 61.52(59.80-63.26) to 67.75(66.74-68.80) and the Accuracies of pCR prediction from 56.09(49.39-62.79) to 71.01(69.44-72.58). The proposed ECDEDL was quite effective for external validation, numerically more approximating the internal validation.

  • 7 authors
·
Jun 19, 2023

Agent0: Unleashing Self-Evolving Agents from Zero Data via Tool-Integrated Reasoning

Large Language Model (LLM) Agents, often trained with Reinforcement Learning (RL), are constrained by a dependency on human-curated data, limiting scalability and tethering AI to human knowledge. Existing self-evolution frameworks offer an alternative but are typically restricted by the model's inherent capabilities and single-round interactions, hindering the development of complex curricula involving tool use or dynamic reasoning. We introduce Agent0, a fully autonomous framework that evolves high-performing agents without external data through multi-step co-evolution and seamless tool integration. Agent0 establishes a symbiotic competition between two agents initialized from the same base LLM: a curriculum agent that proposes increasingly challenging frontier tasks, and an executor agent that learns to solve them. We integrate external tools to enhance the executor's problem-solving capacity; this improvement, in turn, pressures the curriculum agent to construct more complex, tool-aware tasks. Through this iterative process, Agent0 establishes a self-reinforcing cycle that continuously produces high-quality curricula. Empirically, Agent0 substantially boosts reasoning capabilities, improving the Qwen3-8B-Base model by 18% on mathematical reasoning and 24% on general reasoning benchmarks. Code is available at https://github.com/aiming-lab/Agent0.

Flow Map Distillation Without Data

State-of-the-art flow models achieve remarkable quality but require slow, iterative sampling. To accelerate this, flow maps can be distilled from pre-trained teachers, a procedure that conventionally requires sampling from an external dataset. We argue that this data-dependency introduces a fundamental risk of Teacher-Data Mismatch, as a static dataset may provide an incomplete or even misaligned representation of the teacher's full generative capabilities. This leads us to question whether this reliance on data is truly necessary for successful flow map distillation. In this work, we explore a data-free alternative that samples only from the prior distribution, a distribution the teacher is guaranteed to follow by construction, thereby circumventing the mismatch risk entirely. To demonstrate the practical viability of this philosophy, we introduce a principled framework that learns to predict the teacher's sampling path while actively correcting for its own compounding errors to ensure high fidelity. Our approach surpasses all data-based counterparts and establishes a new state-of-the-art by a significant margin. Specifically, distilling from SiT-XL/2+REPA, our method reaches an impressive FID of 1.45 on ImageNet 256x256, and 1.49 on ImageNet 512x512, both with only 1 sampling step. We hope our work establishes a more robust paradigm for accelerating generative models and motivates the broader adoption of flow map distillation without data.

  • 4 authors
·
Nov 24 2

Coping with Information Loss and the Use of Auxiliary Sources of Data: A Report from the NISS Ingram Olkin Forum Series on Unplanned Clinical Trial Disruptions

Clinical trials disruption has always represented a non negligible part of the ending of interventional studies. While the SARS-CoV-2 (COVID-19) pandemic has led to an impressive and unprecedented initiation of clinical research, it has also led to considerable disruption of clinical trials in other disease areas, with around 80% of non-COVID-19 trials stopped or interrupted during the pandemic. In many cases the disrupted trials will not have the planned statistical power necessary to yield interpretable results. This paper describes methods to compensate for the information loss arising from trial disruptions by incorporating additional information available from auxiliary data sources. The methods described include the use of auxiliary data on baseline and early outcome data available from the trial itself and frequentist and Bayesian approaches for the incorporation of information from external data sources. The methods are illustrated by application to the analysis of artificial data based on the Primary care pediatrics Learning Activity Nutrition (PLAN) study, a clinical trial assessing a diet and exercise intervention for overweight children, that was affected by the COVID-19 pandemic. We show how all of the methods proposed lead to an increase in precision relative to use of complete case data only.

  • 12 authors
·
Jun 22, 2022

FMix: Enhancing Mixed Sample Data Augmentation

Mixed Sample Data Augmentation (MSDA) has received increasing attention in recent years, with many successful variants such as MixUp and CutMix. By studying the mutual information between the function learned by a VAE on the original data and on the augmented data we show that MixUp distorts learned functions in a way that CutMix does not. We further demonstrate this by showing that MixUp acts as a form of adversarial training, increasing robustness to attacks such as Deep Fool and Uniform Noise which produce examples similar to those generated by MixUp. We argue that this distortion prevents models from learning about sample specific features in the data, aiding generalisation performance. In contrast, we suggest that CutMix works more like a traditional augmentation, improving performance by preventing memorisation without distorting the data distribution. However, we argue that an MSDA which builds on CutMix to include masks of arbitrary shape, rather than just square, could further prevent memorisation whilst preserving the data distribution in the same way. To this end, we propose FMix, an MSDA that uses random binary masks obtained by applying a threshold to low frequency images sampled from Fourier space. These random masks can take on a wide range of shapes and can be generated for use with one, two, and three dimensional data. FMix improves performance over MixUp and CutMix, without an increase in training time, for a number of models across a range of data sets and problem settings, obtaining a new single model state-of-the-art result on CIFAR-10 without external data. Finally, we show that a consequence of the difference between interpolating MSDA such as MixUp and masking MSDA such as FMix is that the two can be combined to improve performance even further. Code for all experiments is provided at https://github.com/ecs-vlc/FMix .

  • 6 authors
·
Feb 27, 2020

Refining Focus in AI for Lung Cancer: Comparing Lesion-Centric and Chest-Region Models with Performance Insights from Internal and External Validation

Background: AI-based classification models are essential for improving lung cancer diagnosis. However, the relative performance of lesion-level versus chest-region models in internal and external datasets remains unclear. Purpose: This study evaluates the performance of lesion-level and chest-region models for lung cancer classification, comparing their effectiveness across internal Duke Lung Nodule Dataset 2024 (DLND24) and external (LUNA16, NLST) datasets, with a focus on subgroup analyses by demographics, histology, and imaging characteristics. Materials and Methods: Two AI models were trained: one using lesion-centric patches (64,64,64) and the other using chest-region patches (512,512,8). Internal validation was conducted on DLND24, while external validation utilized LUNA16 and NLST datasets. The models performances were assessed using AUC-ROC, with subgroup analyses for demographic, clinical, and imaging factors. Statistical comparisons were performed using DeLongs test. Gradient-based visualizations and probability distribution were further used for analysis. Results: The lesion-level model consistently outperformed the chest-region model across datasets. In internal validation, the lesion-level model achieved an AUC of 0.71(CI: 0.61-0.81), compared to 0.68(0.57-0.77) for the chest-region model. External validation showed similar trends, with AUCs of 0.90(0.87-0.92) and 0.81(0.79-0.82) on LUNA16 and NLST, respectively. Subgroup analyses revealed significant advantages for lesion-level models in certain histological subtypes (adenocarcinoma) and imaging conditions (CT manufacturers). Conclusion: Lesion-level models demonstrate superior classification performance, especially for external datasets and challenging subgroups, suggesting their clinical utility for precision lung cancer diagnostics.

  • 1 authors
·
Nov 25, 2024

AI in Lung Health: Benchmarking Detection and Diagnostic Models Across Multiple CT Scan Datasets

Lung cancer remains the leading cause of cancer-related mortality worldwide, and early detection through low-dose computed tomography (LDCT) has shown significant promise in reducing death rates. With the growing integration of artificial intelligence (AI) into medical imaging, the development and evaluation of robust AI models require access to large, well-annotated datasets. In this study, we introduce the utility of Duke Lung Cancer Screening (DLCS) Dataset, the largest open-access LDCT dataset with over 2,000 scans and 3,000 expert-verified nodules. We benchmark deep learning models for both 3D nodule detection and lung cancer classification across internal and external datasets including LUNA16, LUNA25, and NLST-3D+. For detection, we develop two MONAI-based RetinaNet models (DLCSDmD and LUNA16-mD), evaluated using the Competition Performance Metric (CPM). For classification, we compare five models, including state-of-the-art pretrained models (Models Genesis, Med3D), a selfsupervised foundation model (FMCB), a randomly initialized ResNet50, and proposed a novel Strategic Warm-Start++ (SWS++) model. SWS++ uses curated candidate patches to pretrain a classification backbone within the same detection pipeline, enabling task-relevant feature learning. Our models demonstrated strong generalizability, with SWS++ achieving comparable or superior performance to existing foundational models across multiple datasets (AUC: 0.71 to 0.90). All code, models, and data are publicly released to promote reproducibility and collaboration. This work establishes a standardized benchmarking resource for lung cancer AI research, supporting future efforts in model development, validation, and clinical translation.

  • 7 authors
·
May 7, 2024

Unboxing Occupational Bias: Grounded Debiasing LLMs with U.S. Labor Data

Large Language Models (LLMs) are prone to inheriting and amplifying societal biases embedded within their training data, potentially reinforcing harmful stereotypes related to gender, occupation, and other sensitive categories. This issue becomes particularly problematic as biased LLMs can have far-reaching consequences, leading to unfair practices and exacerbating social inequalities across various domains, such as recruitment, online content moderation, or even the criminal justice system. Although prior research has focused on detecting bias in LLMs using specialized datasets designed to highlight intrinsic biases, there has been a notable lack of investigation into how these findings correlate with authoritative datasets, such as those from the U.S. National Bureau of Labor Statistics (NBLS). To address this gap, we conduct empirical research that evaluates LLMs in a ``bias-out-of-the-box" setting, analyzing how the generated outputs compare with the distributions found in NBLS data. Furthermore, we propose a straightforward yet effective debiasing mechanism that directly incorporates NBLS instances to mitigate bias within LLMs. Our study spans seven different LLMs, including instructable, base, and mixture-of-expert models, and reveals significant levels of bias that are often overlooked by existing bias detection techniques. Importantly, our debiasing method, which does not rely on external datasets, demonstrates a substantial reduction in bias scores, highlighting the efficacy of our approach in creating fairer and more reliable LLMs.

  • 3 authors
·
Aug 20, 2024 4

High-Throughput Precision Phenotyping of Left Ventricular Hypertrophy with Cardiovascular Deep Learning

Left ventricular hypertrophy (LVH) results from chronic remodeling caused by a broad range of systemic and cardiovascular disease including hypertension, aortic stenosis, hypertrophic cardiomyopathy, and cardiac amyloidosis. Early detection and characterization of LVH can significantly impact patient care but is limited by under-recognition of hypertrophy, measurement error and variability, and difficulty differentiating etiologies of LVH. To overcome this challenge, we present EchoNet-LVH - a deep learning workflow that automatically quantifies ventricular hypertrophy with precision equal to human experts and predicts etiology of LVH. Trained on 28,201 echocardiogram videos, our model accurately measures intraventricular wall thickness (mean absolute error [MAE] 1.4mm, 95% CI 1.2-1.5mm), left ventricular diameter (MAE 2.4mm, 95% CI 2.2-2.6mm), and posterior wall thickness (MAE 1.2mm, 95% CI 1.1-1.3mm) and classifies cardiac amyloidosis (area under the curve of 0.83) and hypertrophic cardiomyopathy (AUC 0.98) from other etiologies of LVH. In external datasets from independent domestic and international healthcare systems, EchoNet-LVH accurately quantified ventricular parameters (R2 of 0.96 and 0.90 respectively) and detected cardiac amyloidosis (AUC 0.79) and hypertrophic cardiomyopathy (AUC 0.89) on the domestic external validation site. Leveraging measurements across multiple heart beats, our model can more accurately identify subtle changes in LV geometry and its causal etiologies. Compared to human experts, EchoNet-LVH is fully automated, allowing for reproducible, precise measurements, and lays the foundation for precision diagnosis of cardiac hypertrophy. As a resource to promote further innovation, we also make publicly available a large dataset of 23,212 annotated echocardiogram videos.

  • 18 authors
·
Jun 23, 2021

SelfCheckGPT: Zero-Resource Black-Box Hallucination Detection for Generative Large Language Models

Generative Large Language Models (LLMs) such as GPT-3 are capable of generating highly fluent responses to a wide variety of user prompts. However, LLMs are known to hallucinate facts and make non-factual statements which can undermine trust in their output. Existing fact-checking approaches either require access to token-level output probability distribution (which may not be available for systems such as ChatGPT) or external databases that are interfaced via separate, often complex, modules. In this work, we propose "SelfCheckGPT", a simple sampling-based approach that can be used to fact-check black-box models in a zero-resource fashion, i.e. without an external database. SelfCheckGPT leverages the simple idea that if a LLM has knowledge of a given concept, sampled responses are likely to be similar and contain consistent facts. However, for hallucinated facts, stochastically sampled responses are likely to diverge and contradict one another. We investigate this approach by using GPT-3 to generate passages about individuals from the WikiBio dataset, and manually annotate the factuality of the generated passages. We demonstrate that SelfCheckGPT can: i) detect non-factual and factual sentences; and ii) rank passages in terms of factuality. We compare our approach to several existing baselines and show that in sentence hallucination detection, our approach has AUC-PR scores comparable to grey-box methods, while SelfCheckGPT is best at passage factuality assessment.

  • 3 authors
·
Mar 15, 2023

A Reliable Knowledge Processing Framework for Combustion Science using Foundation Models

This research explores the integration of large language models (LLMs) into scientific data assimilation, focusing on combustion science as a case study. Leveraging foundational models integrated with Retrieval-Augmented Generation (RAG) framework, the study introduces an approach to process diverse combustion research data, spanning experimental studies, simulations, and literature. The multifaceted nature of combustion research emphasizes the critical role of knowledge processing in navigating and extracting valuable information from a vast and diverse pool of sources. The developed approach minimizes computational and economic expenses while optimizing data privacy and accuracy. It incorporates prompt engineering and offline open-source LLMs, offering user autonomy in selecting base models. The study provides a thorough examination of text segmentation strategies, conducts comparative studies between LLMs, and explores various optimized prompts to demonstrate the effectiveness of the framework. By incorporating an external database, the framework outperforms a conventional LLM in generating accurate responses and constructing robust arguments. Additionally, the study delves into the investigation of optimized prompt templates for the purpose of efficient extraction of scientific literature. The research addresses concerns related to hallucinations and false research articles by introducing a custom workflow developed with a detection algorithm to filter out inaccuracies. Despite identified areas for improvement, the framework consistently delivers accurate domain-specific responses with minimal human oversight. The prompt-agnostic approach introduced holds promise for future deliberations. The study underscores the significance of integrating LLMs and knowledge processing techniques in scientific research, providing a foundation for advancements in data assimilation and utilization.

  • 2 authors
·
Dec 31, 2023

Information Extraction from Heterogeneous Documents without Ground Truth Labels using Synthetic Label Generation and Knowledge Distillation

Invoices and receipts submitted by employees are visually rich documents (VRDs) with textual, visual and layout information. To protect against the risk of fraud and abuse, it is crucial for organizations to efficiently extract desired information from submitted receipts. This helps in the assessment of key factors such as appropriateness of the expense claim, adherence to spending and transaction policies, the validity of the receipt, as well as downstream anomaly detection at various levels. These documents are heterogeneous, with multiple formats and languages, uploaded with different image qualities, and often do not contain ground truth labels for the efficient training of models. In this paper we propose Task Aware Instruction-based Labelling (TAIL), a method for synthetic label generation in VRD corpuses without labels, and fine-tune a multimodal Visually Rich Document Understanding Model (VRDU) on TAIL labels using response-based knowledge distillation without using the teacher model's weights or training dataset to conditionally generate annotations in the appropriate format. Using a benchmark external dataset where ground truth labels are available, we demonstrate conditions under which our approach performs at par with Claude 3 Sonnet through empirical studies. We then show that the resulting model performs at par or better on the internal expense documents of a large multinational organization than state-of-the-art LMM (large multimodal model) Claude 3 Sonnet while being 85% less costly and ~5X faster, and outperforms layout-aware baselines by more than 10% in Average Normalized Levenshtein Similarity (ANLS) scores due to its ability to reason and extract information from rare formats. Finally, we illustrate the usage of our approach in overpayment prevention.

  • 2 authors
·
Nov 22, 2024

Vocabulary-free Image Classification and Semantic Segmentation

Large vision-language models revolutionized image classification and semantic segmentation paradigms. However, they typically assume a pre-defined set of categories, or vocabulary, at test time for composing textual prompts. This assumption is impractical in scenarios with unknown or evolving semantic context. Here, we address this issue and introduce the Vocabulary-free Image Classification (VIC) task, which aims to assign a class from an unconstrained language-induced semantic space to an input image without needing a known vocabulary. VIC is challenging due to the vastness of the semantic space, which contains millions of concepts, including fine-grained categories. To address VIC, we propose Category Search from External Databases (CaSED), a training-free method that leverages a pre-trained vision-language model and an external database. CaSED first extracts the set of candidate categories from the most semantically similar captions in the database and then assigns the image to the best-matching candidate category according to the same vision-language model. Furthermore, we demonstrate that CaSED can be applied locally to generate a coarse segmentation mask that classifies image regions, introducing the task of Vocabulary-free Semantic Segmentation. CaSED and its variants outperform other more complex vision-language models, on classification and semantic segmentation benchmarks, while using much fewer parameters.

  • 6 authors
·
Apr 16, 2024

RAG vs Fine-tuning: Pipelines, Tradeoffs, and a Case Study on Agriculture

There are two common ways in which developers are incorporating proprietary and domain-specific data when building applications of Large Language Models (LLMs): Retrieval-Augmented Generation (RAG) and Fine-Tuning. RAG augments the prompt with the external data, while fine-Tuning incorporates the additional knowledge into the model itself. However, the pros and cons of both approaches are not well understood. In this paper, we propose a pipeline for fine-tuning and RAG, and present the tradeoffs of both for multiple popular LLMs, including Llama2-13B, GPT-3.5, and GPT-4. Our pipeline consists of multiple stages, including extracting information from PDFs, generating questions and answers, using them for fine-tuning, and leveraging GPT-4 for evaluating the results. We propose metrics to assess the performance of different stages of the RAG and fine-Tuning pipeline. We conduct an in-depth study on an agricultural dataset. Agriculture as an industry has not seen much penetration of AI, and we study a potentially disruptive application - what if we could provide location-specific insights to a farmer? Our results show the effectiveness of our dataset generation pipeline in capturing geographic-specific knowledge, and the quantitative and qualitative benefits of RAG and fine-tuning. We see an accuracy increase of over 6 p.p. when fine-tuning the model and this is cumulative with RAG, which increases accuracy by 5 p.p. further. In one particular experiment, we also demonstrate that the fine-tuned model leverages information from across geographies to answer specific questions, increasing answer similarity from 47% to 72%. Overall, the results point to how systems built using LLMs can be adapted to respond and incorporate knowledge across a dimension that is critical for a specific industry, paving the way for further applications of LLMs in other industrial domains.

  • 22 authors
·
Jan 16, 2024 1

Towards Lifelong Learning of Large Language Models: A Survey

As the applications of large language models (LLMs) expand across diverse fields, the ability of these models to adapt to ongoing changes in data, tasks, and user preferences becomes crucial. Traditional training methods, relying on static datasets, are increasingly inadequate for coping with the dynamic nature of real-world information. Lifelong learning, also known as continual or incremental learning, addresses this challenge by enabling LLMs to learn continuously and adaptively over their operational lifetime, integrating new knowledge while retaining previously learned information and preventing catastrophic forgetting. This survey delves into the sophisticated landscape of lifelong learning, categorizing strategies into two primary groups: Internal Knowledge and External Knowledge. Internal Knowledge includes continual pretraining and continual finetuning, each enhancing the adaptability of LLMs in various scenarios. External Knowledge encompasses retrieval-based and tool-based lifelong learning, leveraging external data sources and computational tools to extend the model's capabilities without modifying core parameters. The key contributions of our survey are: (1) Introducing a novel taxonomy categorizing the extensive literature of lifelong learning into 12 scenarios; (2) Identifying common techniques across all lifelong learning scenarios and classifying existing literature into various technique groups within each scenario; (3) Highlighting emerging techniques such as model expansion and data selection, which were less explored in the pre-LLM era. Through a detailed examination of these groups and their respective categories, this survey aims to enhance the adaptability, reliability, and overall performance of LLMs in real-world applications.

  • 4 authors
·
Jun 10, 2024

UniBiomed: A Universal Foundation Model for Grounded Biomedical Image Interpretation

Multi-modal interpretation of biomedical images opens up novel opportunities in biomedical image analysis. Conventional AI approaches typically rely on disjointed training, i.e., Large Language Models (LLMs) for clinical text generation and segmentation models for target extraction, which results in inflexible real-world deployment and a failure to leverage holistic biomedical information. To this end, we introduce UniBiomed, the first universal foundation model for grounded biomedical image interpretation. UniBiomed is based on a novel integration of Multi-modal Large Language Model (MLLM) and Segment Anything Model (SAM), which effectively unifies the generation of clinical texts and the segmentation of corresponding biomedical objects for grounded interpretation. In this way, UniBiomed is capable of tackling a wide range of biomedical tasks across ten diverse biomedical imaging modalities. To develop UniBiomed, we curate a large-scale dataset comprising over 27 million triplets of images, annotations, and text descriptions across ten imaging modalities. Extensive validation on 84 internal and external datasets demonstrated that UniBiomed achieves state-of-the-art performance in segmentation, disease recognition, region-aware diagnosis, visual question answering, and report generation. Moreover, unlike previous models that rely on clinical experts to pre-diagnose images and manually craft precise textual or visual prompts, UniBiomed can provide automated and end-to-end grounded interpretation for biomedical image analysis. This represents a novel paradigm shift in clinical workflows, which will significantly improve diagnostic efficiency. In summary, UniBiomed represents a novel breakthrough in biomedical AI, unlocking powerful grounded interpretation capabilities for more accurate and efficient biomedical image analysis.

  • 5 authors
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Apr 30 4

Audiobox TTA-RAG: Improving Zero-Shot and Few-Shot Text-To-Audio with Retrieval-Augmented Generation

Current leading Text-To-Audio (TTA) generation models suffer from degraded performance on zero-shot and few-shot settings. It is often challenging to generate high-quality audio for audio events that are unseen or uncommon in the training set. Inspired by the success of Retrieval-Augmented Generation (RAG) in Large Language Model (LLM)-based knowledge-intensive tasks, we extend the TTA process with additional conditioning contexts. We propose Audiobox TTA-RAG, a novel retrieval-augmented TTA approach based on Audiobox, a conditional flow-matching audio generation model. Unlike the vanilla Audiobox TTA solution which generates audio conditioned on text, we augmented the conditioning input with retrieved audio samples that provide additional acoustic information to generate the target audio. Our retrieval method does not require the external database to have labeled audio, offering more practical use cases. To evaluate our proposed method, we curated test sets in zero-shot and few-shot settings. Our empirical results show that the proposed model can effectively leverage the retrieved audio samples and significantly improve zero-shot and few-shot TTA performance, with large margins on multiple evaluation metrics, while maintaining the ability to generate semantically aligned audio for the in-domain setting. In addition, we investigate the effect of different retrieval methods and data sources.

  • 5 authors
·
Nov 7, 2024

A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES'22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model achieved superior ischemic lesion detection and segmentation accuracy on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm's segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model's generalizability. The algorithm's outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm (https://github.com/Tabrisrei/ISLES22_Ensemble) that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)radiologists. Second, we show the potential for biomedical challenge outputs to extend beyond the challenge's initial objectives, demonstrating their real-world clinical applicability.

  • 58 authors
·
Mar 28, 2024

Vocabulary-free Image Classification

Recent advances in large vision-language models have revolutionized the image classification paradigm. Despite showing impressive zero-shot capabilities, a pre-defined set of categories, a.k.a. the vocabulary, is assumed at test time for composing the textual prompts. However, such assumption can be impractical when the semantic context is unknown and evolving. We thus formalize a novel task, termed as Vocabulary-free Image Classification (VIC), where we aim to assign to an input image a class that resides in an unconstrained language-induced semantic space, without the prerequisite of a known vocabulary. VIC is a challenging task as the semantic space is extremely large, containing millions of concepts, with hard-to-discriminate fine-grained categories. In this work, we first empirically verify that representing this semantic space by means of an external vision-language database is the most effective way to obtain semantically relevant content for classifying the image. We then propose Category Search from External Databases (CaSED), a method that exploits a pre-trained vision-language model and an external vision-language database to address VIC in a training-free manner. CaSED first extracts a set of candidate categories from captions retrieved from the database based on their semantic similarity to the image, and then assigns to the image the best matching candidate category according to the same vision-language model. Experiments on benchmark datasets validate that CaSED outperforms other complex vision-language frameworks, while being efficient with much fewer parameters, paving the way for future research in this direction.

  • 6 authors
·
Jun 1, 2023

Rewiring Experts on the Fly:Continuous Rerouting for Better Online Adaptation in Mixture-of-Expert models

Mixture-of-Experts (MoE) models achieve efficient scaling through sparse expert activation, but often suffer from suboptimal routing decisions due to distribution shifts in deployment. While existing test-time adaptation methods could potentially address these issues, they primarily focus on dense models and require access to external data, limiting their practical applicability to MoE architectures. However, we find that, instead of relying on reference data, we can optimize MoE expert selection on-the-fly based only on input context. As such, we propose a data-free, online test-time framework that continuously adapts MoE routing decisions during text generation without external supervision or data. Our method cycles between two phases: During the prefill stage, and later in regular intervals, we optimize the routing decisions of the model using self-supervision based on the already generated sequence. Then, we generate text as normal, maintaining the modified router until the next adaption. We implement this through lightweight additive vectors that only update router logits in selected layers, maintaining computational efficiency while preventing over-adaptation. The experimental results show consistent performance gains on challenging reasoning tasks while maintaining robustness to context shifts. For example, our method achieves a 5.5\% improvement on HumanEval with OLMoE. Furthermore, owing to its plug-and-play property, our method naturally complements existing test-time scaling techniques, e.g., achieving 6\% average gains when incorporated with self-consistency on DeepSeek-V2-Lite.

  • 6 authors
·
Oct 16 3

MMKB-RAG: A Multi-Modal Knowledge-Based Retrieval-Augmented Generation Framework

Recent advancements in large language models (LLMs) and multi-modal LLMs have been remarkable. However, these models still rely solely on their parametric knowledge, which limits their ability to generate up-to-date information and increases the risk of producing erroneous content. Retrieval-Augmented Generation (RAG) partially mitigates these challenges by incorporating external data sources, yet the reliance on databases and retrieval systems can introduce irrelevant or inaccurate documents, ultimately undermining both performance and reasoning quality. In this paper, we propose Multi-Modal Knowledge-Based Retrieval-Augmented Generation (MMKB-RAG), a novel multi-modal RAG framework that leverages the inherent knowledge boundaries of models to dynamically generate semantic tags for the retrieval process. This strategy enables the joint filtering of retrieved documents, retaining only the most relevant and accurate references. Extensive experiments on knowledge-based visual question-answering tasks demonstrate the efficacy of our approach: on the E-VQA dataset, our method improves performance by +4.2% on the Single-Hop subset and +0.4% on the full dataset, while on the InfoSeek dataset, it achieves gains of +7.8% on the Unseen-Q subset, +8.2% on the Unseen-E subset, and +8.1% on the full dataset. These results highlight significant enhancements in both accuracy and robustness over the current state-of-the-art MLLM and RAG frameworks.

  • 8 authors
·
Apr 14

MemoRAG: Moving towards Next-Gen RAG Via Memory-Inspired Knowledge Discovery

Retrieval-Augmented Generation (RAG) leverages retrieval tools to access external databases, thereby enhancing the generation quality of large language models (LLMs) through optimized context. However, the existing retrieval methods are constrained inherently, as they can only perform relevance matching between explicitly stated queries and well-formed knowledge, but unable to handle tasks involving ambiguous information needs or unstructured knowledge. Consequently, existing RAG systems are primarily effective for straightforward question-answering tasks. In this work, we propose MemoRAG, a novel retrieval-augmented generation paradigm empowered by long-term memory. MemoRAG adopts a dual-system architecture. On the one hand, it employs a light but long-range LLM to form the global memory of database. Once a task is presented, it generates draft answers, cluing the retrieval tools to locate useful information within the database. On the other hand, it leverages an expensive but expressive LLM, which generates the ultimate answer based on the retrieved information. Building on this general framework, we further optimize MemoRAG's performance by enhancing its cluing mechanism and memorization capacity. In our experiment, MemoRAG achieves superior performance across a variety of evaluation tasks, including both complex ones where conventional RAG fails and straightforward ones where RAG is commonly applied.

  • 5 authors
·
Sep 9, 2024 4

Semi-Parametric Neural Image Synthesis

Novel architectures have recently improved generative image synthesis leading to excellent visual quality in various tasks. Much of this success is due to the scalability of these architectures and hence caused by a dramatic increase in model complexity and in the computational resources invested in training these models. Our work questions the underlying paradigm of compressing large training data into ever growing parametric representations. We rather present an orthogonal, semi-parametric approach. We complement comparably small diffusion or autoregressive models with a separate image database and a retrieval strategy. During training we retrieve a set of nearest neighbors from this external database for each training instance and condition the generative model on these informative samples. While the retrieval approach is providing the (local) content, the model is focusing on learning the composition of scenes based on this content. As demonstrated by our experiments, simply swapping the database for one with different contents transfers a trained model post-hoc to a novel domain. The evaluation shows competitive performance on tasks which the generative model has not been trained on, such as class-conditional synthesis, zero-shot stylization or text-to-image synthesis without requiring paired text-image data. With negligible memory and computational overhead for the external database and retrieval we can significantly reduce the parameter count of the generative model and still outperform the state-of-the-art.

  • 5 authors
·
Apr 25, 2022

DESI 2024 V: Full-Shape Galaxy Clustering from Galaxies and Quasars

We present the measurements and cosmological implications of the galaxy two-point clustering using over 4.7 million unique galaxy and quasar redshifts in the range 0.1<z<2.1 divided into six redshift bins over a sim 7,500 square degree footprint, from the first year of observations with the Dark Energy Spectroscopic Instrument (DESI Data Release 1). By fitting the full power spectrum, we extend previous DESI DR1 baryon acoustic oscillation (BAO) measurements to include redshift-space distortions and signals from the matter-radiation equality scale. For the first time, this Full-Shape analysis is blinded at the catalogue-level to avoid confirmation bias and the systematic errors are accounted for at the two-point clustering level, which automatically propagates them into any cosmological parameter. When analysing the data in terms of compressed model-agnostic variables, we obtain a combined precision of 4.7\% on the amplitude of the redshift space distortion signal reaching similar precision with just one year of DESI data than with 20 years of observation from previous generation surveys. We analyse the data to directly constrain the cosmological parameters within the LambdaCDM model using perturbation theory and combine this information with the reconstructed DESI DR1 galaxy BAO. Using a Big Bang Nucleosynthesis Gaussian prior on the baryon density parameter, and a Gaussian prior on the spectral index, we constrain the matter density is Omega_m=0.296pm 0.010 and the Hubble constant H_0=(68.63 pm 0.79)[{rm km, s^{-1}Mpc^{-1}}]. Additionally, we measure the amplitude of clustering sigma_8=0.841 pm 0.034. The DESI DR1 results are in agreement with the LambdaCDM model based on general relativity with parameters consistent with those from Planck. The cosmological interpretation of these results in combination with external datasets are presented in a companion paper.

  • 198 authors
·
Nov 18, 2024

CORAG: A Cost-Constrained Retrieval Optimization System for Retrieval-Augmented Generation

Large Language Models (LLMs) have demonstrated remarkable generation capabilities but often struggle to access up-to-date information, which can lead to hallucinations. Retrieval-Augmented Generation (RAG) addresses this issue by incorporating knowledge from external databases, enabling more accurate and relevant responses. Due to the context window constraints of LLMs, it is impractical to input the entire external database context directly into the model. Instead, only the most relevant information, referred to as chunks, is selectively retrieved. However, current RAG research faces three key challenges. First, existing solutions often select each chunk independently, overlooking potential correlations among them. Second, in practice the utility of chunks is non-monotonic, meaning that adding more chunks can decrease overall utility. Traditional methods emphasize maximizing the number of included chunks, which can inadvertently compromise performance. Third, each type of user query possesses unique characteristics that require tailored handling, an aspect that current approaches do not fully consider. To overcome these challenges, we propose a cost constrained retrieval optimization system CORAG for retrieval-augmented generation. We employ a Monte Carlo Tree Search (MCTS) based policy framework to find optimal chunk combinations sequentially, allowing for a comprehensive consideration of correlations among chunks. Additionally, rather than viewing budget exhaustion as a termination condition, we integrate budget constraints into the optimization of chunk combinations, effectively addressing the non-monotonicity of chunk utility.

  • 5 authors
·
Nov 1, 2024

OneActor: Consistent Character Generation via Cluster-Conditioned Guidance

Text-to-image diffusion models benefit artists with high-quality image generation. Yet its stochastic nature prevent artists from creating consistent images of the same character. Existing methods try to tackle this challenge and generate consistent content in various ways. However, they either depend on external data or require expensive tuning of the diffusion model. For this issue, we argue that a lightweight but intricate guidance is enough to function. Aiming at this, we lead the way to formalize the objective of consistent generation, derive a clustering-based score function and propose a novel paradigm, OneActor. We design a cluster-conditioned model which incorporates posterior samples to guide the denoising trajectories towards the target cluster. To overcome the overfitting challenge shared by one-shot tuning pipelines, we devise auxiliary components to simultaneously augment the tuning and regulate the inference. This technique is later verified to significantly enhance the content diversity of generated images. Comprehensive experiments show that our method outperforms a variety of baselines with satisfactory character consistency, superior prompt conformity as well as high image quality. And our method is at least 4 times faster than tuning-based baselines. Furthermore, to our best knowledge, we first prove that the semantic space has the same interpolation property as the latent space dose. This property can serve as another promising tool for fine generation control.

  • 4 authors
·
Apr 15, 2024 2

Few-Shot Anomaly-Driven Generation for Anomaly Classification and Segmentation

Anomaly detection is a practical and challenging task due to the scarcity of anomaly samples in industrial inspection. Some existing anomaly detection methods address this issue by synthesizing anomalies with noise or external data. However, there is always a large semantic gap between synthetic and real-world anomalies, resulting in weak performance in anomaly detection. To solve the problem, we propose a few-shot Anomaly-driven Generation (AnoGen) method, which guides the diffusion model to generate realistic and diverse anomalies with only a few real anomalies, thereby benefiting training anomaly detection models. Specifically, our work is divided into three stages. In the first stage, we learn the anomaly distribution based on a few given real anomalies and inject the learned knowledge into an embedding. In the second stage, we use the embedding and given bounding boxes to guide the diffusion model to generate realistic and diverse anomalies on specific objects (or textures). In the final stage, we propose a weakly-supervised anomaly detection method to train a more powerful model with generated anomalies. Our method builds upon DRAEM and DesTSeg as the foundation model and conducts experiments on the commonly used industrial anomaly detection dataset, MVTec. The experiments demonstrate that our generated anomalies effectively improve the model performance of both anomaly classification and segmentation tasks simultaneously, \eg, DRAEM and DseTSeg achieved a 5.8\% and 1.5\% improvement in AU-PR metric on segmentation task, respectively. The code and generated anomalous data are available at https://github.com/gaobb/AnoGen.

  • 5 authors
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May 14 2

Generative augmentations for improved cardiac ultrasound segmentation using diffusion models

One of the main challenges in current research on segmentation in cardiac ultrasound is the lack of large and varied labeled datasets and the differences in annotation conventions between datasets. This makes it difficult to design robust segmentation models that generalize well to external datasets. This work utilizes diffusion models to create generative augmentations that can significantly improve diversity of the dataset and thus the generalisability of segmentation models without the need for more annotated data. The augmentations are applied in addition to regular augmentations. A visual test survey showed that experts cannot clearly distinguish between real and fully generated images. Using the proposed generative augmentations, segmentation robustness was increased when training on an internal dataset and testing on an external dataset with an improvement of over 20 millimeters in Hausdorff distance. Additionally, the limits of agreement for automatic ejection fraction estimation improved by up to 20% of absolute ejection fraction value on out of distribution cases. These improvements come exclusively from the increased variation of the training data using the generative augmentations, without modifying the underlying machine learning model. The augmentation tool is available as an open source Python library at https://github.com/GillesVanDeVyver/EchoGAINS.

  • 8 authors
·
Feb 27

Balanced Multi-Task Attention for Satellite Image Classification: A Systematic Approach to Achieving 97.23% Accuracy on EuroSAT Without Pre-Training

This work presents a systematic investigation of custom convolutional neural network architectures for satellite land use classification, achieving 97.23% test accuracy on the EuroSAT dataset without reliance on pre-trained models. Through three progressive architectural iterations (baseline: 94.30%, CBAM-enhanced: 95.98%, and balanced multi-task attention: 97.23%) we identify and address specific failure modes in satellite imagery classification. Our principal contribution is a novel balanced multi-task attention mechanism that combines Coordinate Attention for spatial feature extraction with Squeeze-Excitation blocks for spectral feature extraction, unified through a learnable fusion parameter. Experimental results demonstrate that this learnable parameter autonomously converges to alpha approximately 0.57, indicating near-equal importance of spatial and spectral modalities for satellite imagery. We employ progressive DropBlock regularization (5-20% by network depth) and class-balanced loss weighting to address overfitting and confusion pattern imbalance. The final 12-layer architecture achieves Cohen's Kappa of 0.9692 with all classes exceeding 94.46% accuracy, demonstrating confidence calibration with a 24.25% gap between correct and incorrect predictions. Our approach achieves performance within 1.34% of fine-tuned ResNet-50 (98.57%) while requiring no external data, validating the efficacy of systematic architectural design for domain-specific applications. Complete code, trained models, and evaluation scripts are publicly available.

  • 1 authors
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Oct 17 2

Pre-training for Speech Translation: CTC Meets Optimal Transport

The gap between speech and text modalities is a major challenge in speech-to-text translation (ST). Different methods have been proposed to reduce this gap, but most of them require architectural changes in ST training. In this work, we propose to mitigate this issue at the pre-training stage, requiring no change in the ST model. First, we show that the connectionist temporal classification (CTC) loss can reduce the modality gap by design. We provide a quantitative comparison with the more common cross-entropy loss, showing that pre-training with CTC consistently achieves better final ST accuracy. Nevertheless, CTC is only a partial solution and thus, in our second contribution, we propose a novel pre-training method combining CTC and optimal transport to further reduce this gap. Our method pre-trains a Siamese-like model composed of two encoders, one for acoustic inputs and the other for textual inputs, such that they produce representations that are close to each other in the Wasserstein space. Extensive experiments on the standard CoVoST-2 and MuST-C datasets show that our pre-training method applied to the vanilla encoder-decoder Transformer achieves state-of-the-art performance under the no-external-data setting, and performs on par with recent strong multi-task learning systems trained with external data. Finally, our method can also be applied on top of these multi-task systems, leading to further improvements for these models. Code and pre-trained models are available at https://github.com/formiel/fairseq.

  • 6 authors
·
Jan 27, 2023

Exploring HOD-dependent systematics for the DESI 2024 Full-Shape galaxy clustering analysis

We analyse the robustness of the DESI 2024 cosmological inference from fits to the full shape of the galaxy power spectrum to uncertainties in the Halo Occupation Distribution (HOD) model of the galaxy-halo connection and the choice of priors on nuisance parameters. We assess variations in the recovered cosmological parameters across a range of mocks populated with different HOD models and find that shifts are often greater than 20% of the expected statistical uncertainties from the DESI data. We encapsulate the effect of such shifts in terms of a systematic covariance term, C_{rm HOD}, and an additional diagonal contribution quantifying the impact of our choice of nuisance parameter priors on the ability of the effective field theory (EFT) model to correctly recover the cosmological parameters of the simulations. These two covariance contributions are designed to be added to the usual covariance term, C_{rm stat}, describing the statistical uncertainty in the power spectrum measurement, in order to fairly represent these sources of systematic uncertainty. This approach is more general and robust to choices of model free parameters or additional external datasets used in cosmological fits than the alternative approach of adding systematic uncertainties at the level of the recovered marginalised parameter posteriors. We compare the approaches within the context of a fixed LambdaCDM model and demonstrate that our method gives conservative estimates of the systematic uncertainty that nevertheless have little impact on the final posteriors obtained from DESI data.

  • 42 authors
·
Nov 18, 2024

ConViT: Improving Vision Transformers with Soft Convolutional Inductive Biases

Convolutional architectures have proven extremely successful for vision tasks. Their hard inductive biases enable sample-efficient learning, but come at the cost of a potentially lower performance ceiling. Vision Transformers (ViTs) rely on more flexible self-attention layers, and have recently outperformed CNNs for image classification. However, they require costly pre-training on large external datasets or distillation from pre-trained convolutional networks. In this paper, we ask the following question: is it possible to combine the strengths of these two architectures while avoiding their respective limitations? To this end, we introduce gated positional self-attention (GPSA), a form of positional self-attention which can be equipped with a ``soft" convolutional inductive bias. We initialise the GPSA layers to mimic the locality of convolutional layers, then give each attention head the freedom to escape locality by adjusting a gating parameter regulating the attention paid to position versus content information. The resulting convolutional-like ViT architecture, ConViT, outperforms the DeiT on ImageNet, while offering a much improved sample efficiency. We further investigate the role of locality in learning by first quantifying how it is encouraged in vanilla self-attention layers, then analysing how it is escaped in GPSA layers. We conclude by presenting various ablations to better understand the success of the ConViT. Our code and models are released publicly at https://github.com/facebookresearch/convit.

  • 6 authors
·
Mar 19, 2021

MCP-Universe: Benchmarking Large Language Models with Real-World Model Context Protocol Servers

The Model Context Protocol has emerged as a transformative standard for connecting large language models to external data sources and tools, rapidly gaining adoption across major AI providers and development platforms. However, existing benchmarks are overly simplistic and fail to capture real application challenges such as long-horizon reasoning and large, unfamiliar tool spaces. To address this critical gap, we introduce MCP-Universe, the first comprehensive benchmark specifically designed to evaluate LLMs in realistic and hard tasks through interaction with real-world MCP servers. Our benchmark encompasses 6 core domains spanning 11 different MCP servers: Location Navigation, Repository Management, Financial Analysis, 3D Design, Browser Automation, and Web Searching. To ensure rigorous evaluation, we implement execution-based evaluators, including format evaluators for agent format compliance, static evaluators for time-invariant content matching, and dynamic evaluators that automatically retrieve real-time ground truth for temporally sensitive tasks. Through extensive evaluation of leading LLMs, we find that even SOTA models such as GPT-5 (43.72%), Grok-4 (33.33%) and Claude-4.0-Sonnet (29.44%) exhibit significant performance limitations. In addition, our benchmark poses a significant long-context challenge for LLM agents, as the number of input tokens increases rapidly with the number of interaction steps. Moreover, it introduces an unknown-tools challenge, as LLM agents often lack familiarity with the precise usage of the MCP servers. Notably, enterprise-level agents like Cursor cannot achieve better performance than standard ReAct frameworks. Beyond evaluation, we open-source our extensible evaluation framework with UI support, enabling researchers and practitioners to seamlessly integrate new agents and MCP servers while fostering innovation in the rapidly evolving MCP ecosystem.

Salesforce Salesforce
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Aug 20 10

Graph2Eval: Automatic Multimodal Task Generation for Agents via Knowledge Graphs

As multimodal LLM-driven agents continue to advance in autonomy and generalization, evaluation based on static datasets can no longer adequately assess their true capabilities in dynamic environments and diverse tasks. Existing LLM-based synthetic data methods are largely designed for LLM training and evaluation, and thus cannot be directly applied to agent tasks that require tool use and interactive capabilities. While recent studies have explored automatic agent task generation with LLMs, most efforts remain limited to text or image analysis, without systematically modeling multi-step interactions in web environments. To address these challenges, we propose Graph2Eval, a knowledge graph-based framework that automatically generates both multimodal document comprehension tasks and web interaction tasks, enabling comprehensive evaluation of agents' reasoning, collaboration, and interactive capabilities. In our approach, knowledge graphs constructed from multi-source external data serve as the task space, where we translate semantic relations into structured multimodal tasks using subgraph sampling, task templates, and meta-paths. A multi-stage filtering pipeline based on node reachability, LLM scoring, and similarity analysis is applied to guarantee the quality and executability of the generated tasks. Furthermore, Graph2Eval supports end-to-end evaluation of multiple agent types (Single-Agent, Multi-Agent, Web Agent) and measures reasoning, collaboration, and interaction capabilities. We instantiate the framework with Graph2Eval-Bench, a curated dataset of 1,319 tasks spanning document comprehension and web interaction scenarios. Experiments show that Graph2Eval efficiently generates tasks that differentiate agent and model performance, revealing gaps in reasoning, collaboration, and web interaction across different settings and offering a new perspective for agent evaluation.

Dialectical Alignment: Resolving the Tension of 3H and Security Threats of LLMs

With the rise of large language models (LLMs), ensuring they embody the principles of being helpful, honest, and harmless (3H), known as Human Alignment, becomes crucial. While existing alignment methods like RLHF, DPO, etc., effectively fine-tune LLMs to match preferences in the preference dataset, they often lead LLMs to highly receptive human input and external evidence, even when this information is poisoned. This leads to a tendency for LLMs to be Adaptive Chameleons when external evidence conflicts with their parametric memory. This exacerbates the risk of LLM being attacked by external poisoned data, which poses a significant security risk to LLM system applications such as Retrieval-augmented generation (RAG). To address the challenge, we propose a novel framework: Dialectical Alignment (DA), which (1) utilizes AI feedback to identify optimal strategies for LLMs to navigate inter-context conflicts and context-memory conflicts with different external evidence in context window (i.e., different ratios of poisoned factual contexts); (2) constructs the SFT dataset as well as the preference dataset based on the AI feedback and strategies above; (3) uses the above datasets for LLM alignment to defense poisoned context attack while preserving the effectiveness of in-context knowledge editing. Our experiments show that the dialectical alignment model improves poisoned data attack defense by 20 and does not require any additional prompt engineering or prior declaration of ``you may be attacked`` to the LLMs' context window.

  • 8 authors
·
Mar 30, 2024

Surveying the Dead Minds: Historical-Psychological Text Analysis with Contextualized Construct Representation (CCR) for Classical Chinese

In this work, we develop a pipeline for historical-psychological text analysis in classical Chinese. Humans have produced texts in various languages for thousands of years; however, most of the computational literature is focused on contemporary languages and corpora. The emerging field of historical psychology relies on computational techniques to extract aspects of psychology from historical corpora using new methods developed in natural language processing (NLP). The present pipeline, called Contextualized Construct Representations (CCR), combines expert knowledge in psychometrics (i.e., psychological surveys) with text representations generated via transformer-based language models to measure psychological constructs such as traditionalism, norm strength, and collectivism in classical Chinese corpora. Considering the scarcity of available data, we propose an indirect supervised contrastive learning approach and build the first Chinese historical psychology corpus (C-HI-PSY) to fine-tune pre-trained models. We evaluate the pipeline to demonstrate its superior performance compared with other approaches. The CCR method outperforms word-embedding-based approaches across all of our tasks and exceeds prompting with GPT-4 in most tasks. Finally, we benchmark the pipeline against objective, external data to further verify its validity.

  • 4 authors
·
Mar 1, 2024

The Chronicles of RAG: The Retriever, the Chunk and the Generator

Retrieval Augmented Generation (RAG) has become one of the most popular paradigms for enabling LLMs to access external data, and also as a mechanism for grounding to mitigate against hallucinations. When implementing RAG you can face several challenges like effective integration of retrieval models, efficient representation learning, data diversity, computational efficiency optimization, evaluation, and quality of text generation. Given all these challenges, every day a new technique to improve RAG appears, making it unfeasible to experiment with all combinations for your problem. In this context, this paper presents good practices to implement, optimize, and evaluate RAG for the Brazilian Portuguese language, focusing on the establishment of a simple pipeline for inference and experiments. We explored a diverse set of methods to answer questions about the first Harry Potter book. To generate the answers we used the OpenAI's gpt-4, gpt-4-1106-preview, gpt-3.5-turbo-1106, and Google's Gemini Pro. Focusing on the quality of the retriever, our approach achieved an improvement of MRR@10 by 35.4% compared to the baseline. When optimizing the input size in the application, we observed that it is possible to further enhance it by 2.4%. Finally, we present the complete architecture of the RAG with our recommendations. As result, we moved from a baseline of 57.88% to a maximum relative score of 98.61%.

  • 8 authors
·
Jan 15, 2024

Remember, Retrieve and Generate: Understanding Infinite Visual Concepts as Your Personalized Assistant

The development of large language models (LLMs) has significantly enhanced the capabilities of multimodal LLMs (MLLMs) as general assistants. However, lack of user-specific knowledge still restricts their application in human's daily life. In this paper, we introduce the Retrieval Augmented Personalization (RAP) framework for MLLMs' personalization. Starting from a general MLLM, we turn it into a personalized assistant in three steps. (a) Remember: We design a key-value database to store user-related information, e.g., user's name, avatar and other attributes. (b) Retrieve: When the user initiates a conversation, RAP will retrieve relevant information from the database using a multimodal retriever. (c) Generate: The input query and retrieved concepts' information are fed into MLLMs to generate personalized, knowledge-augmented responses. Unlike previous methods, RAP allows real-time concept editing via updating the external database. To further improve generation quality and alignment with user-specific information, we design a pipeline for data collection and create a specialized dataset for personalized training of MLLMs. Based on the dataset, we train a series of MLLMs as personalized multimodal assistants. By pretraining on large-scale dataset, RAP-MLLMs can generalize to infinite visual concepts without additional finetuning. Our models demonstrate outstanding flexibility and generation quality across a variety of tasks, such as personalized image captioning, question answering and visual recognition. The code, data and models are available at https://github.com/Hoar012/RAP-MLLM.

  • 5 authors
·
Oct 17, 2024 2

DinoBloom: A Foundation Model for Generalizable Cell Embeddings in Hematology

In hematology, computational models offer significant potential to improve diagnostic accuracy, streamline workflows, and reduce the tedious work of analyzing single cells in peripheral blood or bone marrow smears. However, clinical adoption of computational models has been hampered by the lack of generalization due to large batch effects, small dataset sizes, and poor performance in transfer learning from natural images. To address these challenges, we introduce DinoBloom, the first foundation model for single cell images in hematology, utilizing a tailored DINOv2 pipeline. Our model is built upon an extensive collection of 13 diverse, publicly available datasets of peripheral blood and bone marrow smears, the most substantial open-source cohort in hematology so far, comprising over 380,000 white blood cell images. To assess its generalization capability, we evaluate it on an external dataset with a challenging domain shift. We show that our model outperforms existing medical and non-medical vision models in (i) linear probing and k-nearest neighbor evaluations for cell-type classification on blood and bone marrow smears and (ii) weakly supervised multiple instance learning for acute myeloid leukemia subtyping by a large margin. A family of four DinoBloom models (small, base, large, and giant) can be adapted for a wide range of downstream applications, be a strong baseline for classification problems, and facilitate the assessment of batch effects in new datasets. All models are available at github.com/marrlab/DinoBloom.

  • 8 authors
·
Apr 7, 2024

InstructRetro: Instruction Tuning post Retrieval-Augmented Pretraining

Pretraining auto-regressive large language models (LLMs) with retrieval demonstrates better perplexity and factual accuracy by leveraging external databases. However, the size of existing pretrained retrieval-augmented LLM is still limited (e.g., Retro has 7.5B parameters), which limits the effectiveness of instruction tuning and zero-shot generalization. In this work, we introduce Retro 48B, the largest LLM pretrained with retrieval before instruction tuning. Specifically, we continue to pretrain the 43B GPT model on additional 100 billion tokens using the Retro augmentation method by retrieving from 1.2 trillion tokens. The obtained foundation model, Retro 48B, largely outperforms the original 43B GPT in terms of perplexity. After instruction tuning on Retro, InstructRetro demonstrates significant improvement over the instruction tuned GPT on zero-shot question answering (QA) tasks. Specifically, the average improvement of InstructRetro is 7% over its GPT counterpart across 8 short-form QA tasks, and 10% over GPT across 4 challenging long-form QA tasks. Surprisingly, we find that one can ablate the encoder from InstructRetro architecture and directly use its decoder backbone, while achieving comparable results. We hypothesize that pretraining with retrieval makes its decoder good at incorporating context for QA. Our results highlights the promising direction to obtain a better GPT decoder for QA through continued pretraining with retrieval before instruction tuning.

  • 7 authors
·
Oct 11, 2023

DeViDe: Faceted medical knowledge for improved medical vision-language pre-training

Vision-language pre-training for chest X-rays has made significant strides, primarily by utilizing paired radiographs and radiology reports. However, existing approaches often face challenges in encoding medical knowledge effectively. While radiology reports provide insights into the current disease manifestation, medical definitions (as used by contemporary methods) tend to be overly abstract, creating a gap in knowledge. To address this, we propose DeViDe, a novel transformer-based method that leverages radiographic descriptions from the open web. These descriptions outline general visual characteristics of diseases in radiographs, and when combined with abstract definitions and radiology reports, provide a holistic snapshot of knowledge. DeViDe incorporates three key features for knowledge-augmented vision language alignment: First, a large-language model-based augmentation is employed to homogenise medical knowledge from diverse sources. Second, this knowledge is aligned with image information at various levels of granularity. Third, a novel projection layer is proposed to handle the complexity of aligning each image with multiple descriptions arising in a multi-label setting. In zero-shot settings, DeViDe performs comparably to fully supervised models on external datasets and achieves state-of-the-art results on three large-scale datasets. Additionally, fine-tuning DeViDe on four downstream tasks and six segmentation tasks showcases its superior performance across data from diverse distributions.

  • 5 authors
·
Apr 4, 2024 2

Prototype Learning to Create Refined Interpretable Digital Phenotypes from ECGs

Prototype-based neural networks offer interpretable predictions by comparing inputs to learned, representative signal patterns anchored in training data. While such models have shown promise in the classification of physiological data, it remains unclear whether their prototypes capture an underlying structure that aligns with broader clinical phenotypes. We use a prototype-based deep learning model trained for multi-label ECG classification using the PTB-XL dataset. Then without modification we performed inference on the MIMIC-IV clinical database. We assess whether individual prototypes, trained solely for classification, are associated with hospital discharge diagnoses in the form of phecodes in this external population. Individual prototypes demonstrate significantly stronger and more specific associations with clinical outcomes compared to the classifier's class predictions, NLP-extracted concepts, or broader prototype classes across all phecode categories. Prototype classes with mixed significance patterns exhibit significantly greater intra-class distances (p < 0.0001), indicating the model learned to differentiate clinically meaningful variations within diagnostic categories. The prototypes achieve strong predictive performance across diverse conditions, with AUCs ranging from 0.89 for atrial fibrillation to 0.91 for heart failure, while also showing substantial signal for non-cardiac conditions such as sepsis and renal disease. These findings suggest that prototype-based models can support interpretable digital phenotyping from physiologic time-series data, providing transferable intermediate phenotypes that capture clinically meaningful physiologic signatures beyond their original training objectives.

  • 6 authors
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Aug 2

Cardiac-CLIP: A Vision-Language Foundation Model for 3D Cardiac CT Images

Foundation models have demonstrated remarkable potential in medical domain. However, their application to complex cardiovascular diagnostics remains underexplored. In this paper, we present Cardiac-CLIP, a multi-modal foundation model designed for 3D cardiac CT images. Cardiac-CLIP is developed through a two-stage pre-training strategy. The first stage employs a 3D masked autoencoder (MAE) to perform self-supervised representation learning from large-scale unlabeled volumetric data, enabling the visual encoder to capture rich anatomical and contextual features. In the second stage, contrastive learning is introduced to align visual and textual representations, facilitating cross-modal understanding. To support the pre-training, we collect 16641 real clinical CT scans, supplemented by 114k publicly available data. Meanwhile, we standardize free-text radiology reports into unified templates and construct the pathology vectors according to diagnostic attributes, based on which the soft-label matrix is generated to supervise the contrastive learning process. On the other hand, to comprehensively evaluate the effectiveness of Cardiac-CLIP, we collect 6,722 real-clinical data from 12 independent institutions, along with the open-source data to construct the evaluation dataset. Specifically, Cardiac-CLIP is comprehensively evaluated across multiple tasks, including cardiovascular abnormality classification, information retrieval and clinical analysis. Experimental results demonstrate that Cardiac-CLIP achieves state-of-the-art performance across various downstream tasks in both internal and external data. Particularly, Cardiac-CLIP exhibits great effectiveness in supporting complex clinical tasks such as the prospective prediction of acute coronary syndrome, which is notoriously difficult in real-world scenarios.

  • 23 authors
·
Jul 29

Retrieval-Augmented Generation with Estimation of Source Reliability

Retrieval-Augmented Generation (RAG) is an effective approach to enhance the factual accuracy of large language models (LLMs) by retrieving information from external databases, which are typically composed of diverse sources, to supplement the limited internal knowledge of LLMs. However, the standard RAG often risks retrieving incorrect information, as it relies solely on relevance between a query and a document, overlooking the heterogeneous reliability of these sources. To address this issue, we propose Reliability-Aware RAG (RA-RAG), a new multi-source RAG framework that estimates the reliability of sources and leverages this information to prioritize highly reliable and relevant documents, ensuring more robust and accurate response generation. Specifically, RA-RAG first estimates source reliability by cross-checking information across multiple sources. It then retrieves documents from the top-kappa reliable and relevant sources and aggregates their information using weighted majority voting (WMV), where the selective retrieval ensures scalability while not compromising the performance. Comprehensive experiments show that RA-RAG consistently outperforms baselines in scenarios with heterogeneous source reliability while scaling efficiently as the number of sources increases. Furthermore, we demonstrate the ability of RA-RAG to estimate real-world sources' reliability, highlighting its practical applicability. Our code and data are available at \href{https://github.com/ml-postech/RA-RAG{RA-RAG}.}

  • 6 authors
·
Oct 30, 2024

Trustworthiness in Retrieval-Augmented Generation Systems: A Survey

Retrieval-Augmented Generation (RAG) has quickly grown into a pivotal paradigm in the development of Large Language Models (LLMs). While much of the current research in this field focuses on performance optimization, particularly in terms of accuracy and efficiency, the trustworthiness of RAG systems remains an area still under exploration. From a positive perspective, RAG systems are promising to enhance LLMs by providing them with useful and up-to-date knowledge from vast external databases, thereby mitigating the long-standing problem of hallucination. While from a negative perspective, RAG systems are at the risk of generating undesirable contents if the retrieved information is either inappropriate or poorly utilized. To address these concerns, we propose a unified framework that assesses the trustworthiness of RAG systems across six key dimensions: factuality, robustness, fairness, transparency, accountability, and privacy. Within this framework, we thoroughly review the existing literature on each dimension. Additionally, we create the evaluation benchmark regarding the six dimensions and conduct comprehensive evaluations for a variety of proprietary and open-source models. Finally, we identify the potential challenges for future research based on our investigation results. Through this work, we aim to lay a structured foundation for future investigations and provide practical insights for enhancing the trustworthiness of RAG systems in real-world applications.

  • 10 authors
·
Sep 16, 2024

Deep Learning Segmentation of Ascites on Abdominal CT Scans for Automatic Volume Quantification

Purpose: To evaluate the performance of an automated deep learning method in detecting ascites and subsequently quantifying its volume in patients with liver cirrhosis and ovarian cancer. Materials and Methods: This retrospective study included contrast-enhanced and non-contrast abdominal-pelvic CT scans of patients with cirrhotic ascites and patients with ovarian cancer from two institutions, National Institutes of Health (NIH) and University of Wisconsin (UofW). The model, trained on The Cancer Genome Atlas Ovarian Cancer dataset (mean age, 60 years +/- 11 [s.d.]; 143 female), was tested on two internal (NIH-LC and NIH-OV) and one external dataset (UofW-LC). Its performance was measured by the Dice coefficient, standard deviations, and 95% confidence intervals, focusing on ascites volume in the peritoneal cavity. Results: On NIH-LC (25 patients; mean age, 59 years +/- 14 [s.d.]; 14 male) and NIH-OV (166 patients; mean age, 65 years +/- 9 [s.d.]; all female), the model achieved Dice scores of 0.855 +/- 0.061 (CI: 0.831-0.878) and 0.826 +/- 0.153 (CI: 0.764-0.887), with median volume estimation errors of 19.6% (IQR: 13.2-29.0) and 5.3% (IQR: 2.4-9.7) respectively. On UofW-LC (124 patients; mean age, 46 years +/- 12 [s.d.]; 73 female), the model had a Dice score of 0.830 +/- 0.107 (CI: 0.798-0.863) and median volume estimation error of 9.7% (IQR: 4.5-15.1). The model showed strong agreement with expert assessments, with r^2 values of 0.79, 0.98, and 0.97 across the test sets. Conclusion: The proposed deep learning method performed well in segmenting and quantifying the volume of ascites in concordance with expert radiologist assessments.

  • 7 authors
·
Jun 22, 2024

SynthBA: Reliable Brain Age Estimation Across Multiple MRI Sequences and Resolutions

Brain age is a critical measure that reflects the biological ageing process of the brain. The gap between brain age and chronological age, referred to as brain PAD (Predicted Age Difference), has been utilized to investigate neurodegenerative conditions. Brain age can be predicted using MRIs and machine learning techniques. However, existing methods are often sensitive to acquisition-related variabilities, such as differences in acquisition protocols, scanners, MRI sequences, and resolutions, significantly limiting their application in highly heterogeneous clinical settings. In this study, we introduce Synthetic Brain Age (SynthBA), a robust deep-learning model designed for predicting brain age. SynthBA utilizes an advanced domain randomization technique, ensuring effective operation across a wide array of acquisition-related variabilities. To assess the effectiveness and robustness of SynthBA, we evaluate its predictive capabilities on internal and external datasets, encompassing various MRI sequences and resolutions, and compare it with state-of-the-art techniques. Additionally, we calculate the brain PAD in a large cohort of subjects with Alzheimer's Disease (AD), demonstrating a significant correlation with AD-related measures of cognitive dysfunction. SynthBA holds the potential to facilitate the broader adoption of brain age prediction in clinical settings, where re-training or fine-tuning is often unfeasible. The SynthBA source code and pre-trained models are publicly available at https://github.com/LemuelPuglisi/SynthBA.

  • 6 authors
·
Jun 1, 2024

A Novel Predictive-Coding-Inspired Variational RNN Model for Online Prediction and Recognition

This study introduces PV-RNN, a novel variational RNN inspired by the predictive-coding ideas. The model learns to extract the probabilistic structures hidden in fluctuating temporal patterns by dynamically changing the stochasticity of its latent states. Its architecture attempts to address two major concerns of variational Bayes RNNs: how can latent variables learn meaningful representations and how can the inference model transfer future observations to the latent variables. PV-RNN does both by introducing adaptive vectors mirroring the training data, whose values can then be adapted differently during evaluation. Moreover, prediction errors during backpropagation, rather than external inputs during the forward computation, are used to convey information to the network about the external data. For testing, we introduce error regression for predicting unseen sequences as inspired by predictive coding that leverages those mechanisms. The model introduces a weighting parameter, the meta-prior, to balance the optimization pressure placed on two terms of a lower bound on the marginal likelihood of the sequential data. We test the model on two datasets with probabilistic structures and show that with high values of the meta-prior the network develops deterministic chaos through which the data's randomness is imitated. For low values, the model behaves as a random process. The network performs best on intermediate values, and is able to capture the latent probabilistic structure with good generalization. Analyzing the meta-prior's impact on the network allows to precisely study the theoretical value and practical benefits of incorporating stochastic dynamics in our model. We demonstrate better prediction performance on a robot imitation task with our model using error regression compared to a standard variational Bayes model lacking such a procedure.

  • 2 authors
·
Nov 4, 2018

ProxyDet: Synthesizing Proxy Novel Classes via Classwise Mixup for Open-Vocabulary Object Detection

Open-vocabulary object detection (OVOD) aims to recognize novel objects whose categories are not included in the training set. In order to classify these unseen classes during training, many OVOD frameworks leverage the zero-shot capability of largely pretrained vision and language models, such as CLIP. To further improve generalization on the unseen novel classes, several approaches proposed to additionally train with pseudo region labeling on the external data sources that contain a substantial number of novel category labels beyond the existing training data. Albeit its simplicity, these pseudo-labeling methods still exhibit limited improvement with regard to the truly unseen novel classes that were not pseudo-labeled. In this paper, we present a novel, yet simple technique that helps generalization on the overall distribution of novel classes. Inspired by our observation that numerous novel classes reside within the convex hull constructed by the base (seen) classes in the CLIP embedding space, we propose to synthesize proxy-novel classes approximating novel classes via linear mixup between a pair of base classes. By training our detector with these synthetic proxy-novel classes, we effectively explore the embedding space of novel classes. The experimental results on various OVOD benchmarks such as LVIS and COCO demonstrate superior performance on novel classes compared to the other state-of-the-art methods. Code is available at https://github.com/clovaai/ProxyDet.

  • 5 authors
·
Dec 12, 2023

GPSFormer: A Global Perception and Local Structure Fitting-based Transformer for Point Cloud Understanding

Despite the significant advancements in pre-training methods for point cloud understanding, directly capturing intricate shape information from irregular point clouds without reliance on external data remains a formidable challenge. To address this problem, we propose GPSFormer, an innovative Global Perception and Local Structure Fitting-based Transformer, which learns detailed shape information from point clouds with remarkable precision. The core of GPSFormer is the Global Perception Module (GPM) and the Local Structure Fitting Convolution (LSFConv). Specifically, GPM utilizes Adaptive Deformable Graph Convolution (ADGConv) to identify short-range dependencies among similar features in the feature space and employs Multi-Head Attention (MHA) to learn long-range dependencies across all positions within the feature space, ultimately enabling flexible learning of contextual representations. Inspired by Taylor series, we design LSFConv, which learns both low-order fundamental and high-order refinement information from explicitly encoded local geometric structures. Integrating the GPM and LSFConv as fundamental components, we construct GPSFormer, a cutting-edge Transformer that effectively captures global and local structures of point clouds. Extensive experiments validate GPSFormer's effectiveness in three point cloud tasks: shape classification, part segmentation, and few-shot learning. The code of GPSFormer is available at https://github.com/changshuowang/GPSFormer.

  • 8 authors
·
Jul 18, 2024

SELF-GUIDE: Better Task-Specific Instruction Following via Self-Synthetic Finetuning

Large language models (LLMs) hold the promise of solving diverse tasks when provided with appropriate natural language prompts. However, prompting often leads models to make predictions with lower accuracy compared to finetuning a model with ample training data. On the other hand, while finetuning LLMs on task-specific data generally improves their performance, abundant annotated datasets are not available for all tasks. Previous work has explored generating task-specific data from state-of-the-art LLMs and using this data to finetune smaller models, but this approach requires access to a language model other than the one being trained, which introduces cost, scalability challenges, and legal hurdles associated with continuously relying on more powerful LLMs. In response to these, we propose SELF-GUIDE, a multi-stage mechanism in which we synthesize task-specific input-output pairs from the student LLM, then use these input-output pairs to finetune the student LLM itself. In our empirical evaluation of the Natural Instructions V2 benchmark, we find that SELF-GUIDE improves the performance of LLM by a substantial margin. Specifically, we report an absolute improvement of approximately 15% for classification tasks and 18% for generation tasks in the benchmark's metrics. This sheds light on the promise of self-synthesized data guiding LLMs towards becoming task-specific experts without any external learning signals.

  • 5 authors
·
Jul 16, 2024

BEATs: Audio Pre-Training with Acoustic Tokenizers

The massive growth of self-supervised learning (SSL) has been witnessed in language, vision, speech, and audio domains over the past few years. While discrete label prediction is widely adopted for other modalities, the state-of-the-art audio SSL models still employ reconstruction loss for pre-training. Compared with reconstruction loss, semantic-rich discrete label prediction encourages the SSL model to abstract the high-level audio semantics and discard the redundant details as in human perception. However, a semantic-rich acoustic tokenizer for general audio pre-training is usually not straightforward to obtain, due to the continuous property of audio and unavailable phoneme sequences like speech. To tackle this challenge, we propose BEATs, an iterative audio pre-training framework to learn Bidirectional Encoder representation from Audio Transformers, where an acoustic tokenizer and an audio SSL model are optimized by iterations. In the first iteration, we use random projection as the acoustic tokenizer to train an audio SSL model in a mask and label prediction manner. Then, we train an acoustic tokenizer for the next iteration by distilling the semantic knowledge from the pre-trained or fine-tuned audio SSL model. The iteration is repeated with the hope of mutual promotion of the acoustic tokenizer and audio SSL model. The experimental results demonstrate our acoustic tokenizers can generate discrete labels with rich audio semantics and our audio SSL models achieve state-of-the-art results across various audio classification benchmarks, even outperforming previous models that use more training data and model parameters significantly. Specifically, we set a new state-of-the-art mAP 50.6% on AudioSet-2M for audio-only models without using any external data, and 98.1% accuracy on ESC-50. The code and pre-trained models are available at https://aka.ms/beats.

  • 7 authors
·
Dec 18, 2022

MetaFormer Baselines for Vision

MetaFormer, the abstracted architecture of Transformer, has been found to play a significant role in achieving competitive performance. In this paper, we further explore the capacity of MetaFormer, again, without focusing on token mixer design: we introduce several baseline models under MetaFormer using the most basic or common mixers, and summarize our observations as follows: (1) MetaFormer ensures solid lower bound of performance. By merely adopting identity mapping as the token mixer, the MetaFormer model, termed IdentityFormer, achieves >80% accuracy on ImageNet-1K. (2) MetaFormer works well with arbitrary token mixers. When specifying the token mixer as even a random matrix to mix tokens, the resulting model RandFormer yields an accuracy of >81%, outperforming IdentityFormer. Rest assured of MetaFormer's results when new token mixers are adopted. (3) MetaFormer effortlessly offers state-of-the-art results. With just conventional token mixers dated back five years ago, the models instantiated from MetaFormer already beat state of the art. (a) ConvFormer outperforms ConvNeXt. Taking the common depthwise separable convolutions as the token mixer, the model termed ConvFormer, which can be regarded as pure CNNs, outperforms the strong CNN model ConvNeXt. (b) CAFormer sets new record on ImageNet-1K. By simply applying depthwise separable convolutions as token mixer in the bottom stages and vanilla self-attention in the top stages, the resulting model CAFormer sets a new record on ImageNet-1K: it achieves an accuracy of 85.5% at 224x224 resolution, under normal supervised training without external data or distillation. In our expedition to probe MetaFormer, we also find that a new activation, StarReLU, reduces 71% FLOPs of activation compared with GELU yet achieves better performance. We expect StarReLU to find great potential in MetaFormer-like models alongside other neural networks.

  • 8 authors
·
Oct 24, 2022

An Analysis of Approaches Taken in the ACM RecSys Challenge 2018 for Automatic Music Playlist Continuation

The ACM Recommender Systems Challenge 2018 focused on the task of automatic music playlist continuation, which is a form of the more general task of sequential recommendation. Given a playlist of arbitrary length with some additional meta-data, the task was to recommend up to 500 tracks that fit the target characteristics of the original playlist. For the RecSys Challenge, Spotify released a dataset of one million user-generated playlists. Participants could compete in two tracks, i.e., main and creative tracks. Participants in the main track were only allowed to use the provided training set, however, in the creative track, the use of external public sources was permitted. In total, 113 teams submitted 1,228 runs to the main track; 33 teams submitted 239 runs to the creative track. The highest performing team in the main track achieved an R-precision of 0.2241, an NDCG of 0.3946, and an average number of recommended songs clicks of 1.784. In the creative track, an R-precision of 0.2233, an NDCG of 0.3939, and a click rate of 1.785 was obtained by the best team. This article provides an overview of the challenge, including motivation, task definition, dataset description, and evaluation. We further report and analyze the results obtained by the top performing teams in each track and explore the approaches taken by the winners. We finally summarize our key findings, discuss generalizability of approaches and results to domains other than music, and list the open avenues and possible future directions in the area of automatic playlist continuation.

  • 4 authors
·
Oct 2, 2018