UniHGKR: Unified Instruction-aware Heterogeneous Knowledge Retrievers

Existing information retrieval (IR) models often assume a homogeneous structure for knowledge sources and user queries, limiting their applicability in real-world settings where retrieval is inherently heterogeneous and diverse. In this paper, we introduce UniHGKR, a unified instruction-aware heterogeneous knowledge retriever that (1) builds a unified retrieval space for heterogeneous knowledge and (2) follows diverse user instructions to retrieve knowledge of specified types. UniHGKR consists of three principal stages: heterogeneous self-supervised pretraining, text-anchored embedding alignment, and instruction-aware retriever fine-tuning, enabling it to generalize across varied retrieval contexts. This framework is highly scalable, with a BERT-based version and a UniHGKR-7B version trained on large language models. Also, we introduce CompMix-IR, the first native heterogeneous knowledge retrieval benchmark. It includes two retrieval scenarios with various instructions, over 9,400 question-answer (QA) pairs, and a corpus of 10 million entries, covering four different types of data. Extensive experiments show that UniHGKR consistently outperforms state-of-the-art methods on CompMix-IR, achieving up to 6.36% and 54.23% relative improvements in two scenarios, respectively. Finally, by equipping our retriever for open-domain heterogeneous QA systems, we achieve a new state-of-the-art result on the popular ConvMix task, with an absolute improvement of up to 4.80 points.

A Flow-based Truncated Denoising Diffusion Model for Super-resolution Magnetic Resonance Spectroscopic Imaging

Magnetic Resonance Spectroscopic Imaging (MRSI) is a non-invasive imaging technique for studying metabolism and has become a crucial tool for understanding neurological diseases, cancers and diabetes. High spatial resolution MRSI is needed to characterize lesions, but in practice MRSI is acquired at low resolution due to time and sensitivity restrictions caused by the low metabolite concentrations. Therefore, there is an imperative need for a post-processing approach to generate high-resolution MRSI from low-resolution data that can be acquired fast and with high sensitivity. Deep learning-based super-resolution methods provided promising results for improving the spatial resolution of MRSI, but they still have limited capability to generate accurate and high-quality images. Recently, diffusion models have demonstrated superior learning capability than other generative models in various tasks, but sampling from diffusion models requires iterating through a large number of diffusion steps, which is time-consuming. This work introduces a Flow-based Truncated Denoising Diffusion Model (FTDDM) for super-resolution MRSI, which shortens the diffusion process by truncating the diffusion chain, and the truncated steps are estimated using a normalizing flow-based network. The network is conditioned on upscaling factors to enable multi-scale super-resolution. To train and evaluate the deep learning models, we developed a 1H-MRSI dataset acquired from 25 high-grade glioma patients. We demonstrate that FTDDM outperforms existing generative models while speeding up the sampling process by over 9-fold compared to the baseline diffusion model. Neuroradiologists' evaluations confirmed the clinical advantages of our method, which also supports uncertainty estimation and sharpness adjustment, extending its potential clinical applications.

Counting Ability of Large Language Models and Impact of Tokenization

Transformers, the backbone of modern large language models (LLMs), face inherent architectural limitations that impede their reasoning capabilities. Unlike recurrent networks, Transformers lack recurrent connections, confining them to constant-depth computation. This restriction places them in the complexity class TC$^0$, making them theoretically incapable of solving tasks that demand increasingly deep reasoning as input length grows. Counting, a fundamental component of many reasoning tasks, also requires reasoning depth to grow linearly to be performed inductively. While previous studies have established the upper limits of counting ability in Transformer-based expert models (i.e., models specifically trained for counting tasks), these findings do not directly extend to general-purpose LLMs due to differences in reasoning mechanisms. Recent work has highlighted how Chain of Thought (CoT) reasoning can help alleviate some of the architectural limitations of Transformers in counting tasks. However, little attention has been paid to the role of tokenization in these models. Unlike expert models that often use character-level tokenization, LLMs typically rely on byte-level (BPE) tokenizers, which fundamentally alters the way reasoning is processed. Our work investigates the impact of tokenization on the counting abilities of LLMs, uncovering substantial performance variations based on input tokenization differences. We provide both theoretical and experimental analyses, offering insights into how tokenization choices can undermine models' theoretical computability, thereby inspiring the design of new tokenization methods to enhance reasoning in LLMs.

Buckle Up: Robustifying LLMs at Every Customization Stage via Data Curation

Large language models (LLMs) are extensively adapted for downstream applications through a process known as "customization," with fine-tuning being a common method for integrating domain-specific expertise. However, recent studies have revealed a vulnerability that tuning LLMs with malicious samples can compromise their robustness and amplify harmful content, an attack known as "jailbreaking." To mitigate such attack, we propose an effective defensive framework utilizing data curation to revise commonsense texts and enhance their safety implication from the perspective of LLMs. The curated texts can mitigate jailbreaking attacks at every stage of the customization process: before customization to immunize LLMs against future jailbreak attempts, during customization to neutralize jailbreaking risks, or after customization to restore the compromised models. Since the curated data strengthens LLMs through the standard fine-tuning workflow, we do not introduce additional modules during LLM inference, thereby preserving the original customization process. Experimental results demonstrate a substantial reduction in jailbreaking effects, with up to a 100% success in generating responsible responses. Notably, our method is effective even with commonsense texts, which are often more readily available than safety-relevant data. With the every-stage defensive framework and supporting experimental performance, this work represents a significant advancement in mitigating jailbreaking risks and ensuring the secure customization of LLMs.

Imaging foundation model for universal enhancement of non-ideal measurement CT

Non-ideal measurement computed tomography (NICT), which sacrifices optimal imaging standards for new advantages in CT imaging, is expanding the clinical application scope of CT images. However, with the reduction of imaging standards, the image quality has also been reduced, extremely limiting the clinical acceptability. Although numerous studies have demonstrated the feasibility of deep learning for the NICT enhancement in specific scenarios, their high data cost and limited generalizability have become large obstacles. The recent research on the foundation model has brought new opportunities for building a universal NICT enhancement model - bridging the image quality degradation with minimal data cost. However, owing to the challenges in the collection of large pre-training datasets and the compatibility of data variation, no success has been reported. In this paper, we propose a multi-scale integrated Transformer AMPlifier (TAMP), the first imaging foundation model for universal NICT enhancement. It has been pre-trained on a large-scale physical-driven simulation dataset with 3.6 million NICT-ICT image pairs, and is able to directly generalize to the NICT enhancement tasks with various non-ideal settings and body regions. Via the adaptation with few data, it can further achieve professional performance in real-world specific scenarios. Our extensive experiments have demonstrated that the proposed TAMP has significant potential for promoting the exploration and application of NICT and serving a wider range of medical scenarios.

Cross-Modal Conditioned Reconstruction for Language-guided Medical Image Segmentation

Recent developments underscore the potential of textual information in enhancing learning models for a deeper understanding of medical visual semantics. However, language-guided medical image segmentation still faces a challenging issue. Previous works employ implicit and ambiguous architectures to embed textual information. This leads to segmentation results that are inconsistent with the semantics represented by the language, sometimes even diverging significantly. To this end, we propose a novel cross-modal conditioned Reconstruction for Language-guided Medical Image Segmentation (RecLMIS) to explicitly capture cross-modal interactions, which assumes that well-aligned medical visual features and medical notes can effectively reconstruct each other. We introduce conditioned interaction to adaptively predict patches and words of interest. Subsequently, they are utilized as conditioning factors for mutual reconstruction to align with regions described in the medical notes. Extensive experiments demonstrate the superiority of our RecLMIS, surpassing LViT by 3.74% mIoU on the publicly available MosMedData+ dataset and achieving an average increase of 1.89% mIoU for cross-domain tests on our QATA-CoV19 dataset. Simultaneously, we achieve a relative reduction of 20.2% in parameter count and a 55.5% decrease in computational load. The code will be available at https://github.com/ShashankHuang/RecLMIS.

Calibrating Multi-modal Representations: A Pursuit of Group Robustness without Annotations

Fine-tuning pre-trained vision-language models, like CLIP, has yielded success on diverse downstream tasks. However, several pain points persist for this paradigm: (i) directly tuning entire pre-trained models becomes both time-intensive and computationally costly. Additionally, these tuned models tend to become highly specialized, limiting their practicality for real-world deployment; (ii) recent studies indicate that pre-trained vision-language classifiers may overly depend on spurious features -- patterns that correlate with the target in training data, but are not related to the true labeling function; and (iii) existing studies on mitigating the reliance on spurious features, largely based on the assumption that we can identify such features, does not provide definitive assurance for real-world applications. As a piloting study, this work focuses on exploring mitigating the reliance on spurious features for CLIP without using any group annotation. To this end, we systematically study the existence of spurious correlation on CLIP and CILP+ERM. We first, following recent work on Deep Feature Reweighting (DFR), verify that last-layer retraining can greatly improve group robustness on pretrained CLIP. In view of them, we advocate a lightweight representation calibration method for fine-tuning CLIP, by first generating a calibration set using the pretrained CLIP, and then calibrating representations of samples within this set through contrastive learning, all without the need for group labels. Extensive experiments and in-depth visualizations on several benchmarks validate the effectiveness of our proposals, largely reducing reliance and significantly boosting the model generalization.

Backdoor Attack on Unpaired Medical Image-Text Foundation Models: A Pilot Study on MedCLIP

In recent years, foundation models (FMs) have solidified their role as cornerstone advancements in the deep learning domain. By extracting intricate patterns from vast datasets, these models consistently achieve state-of-the-art results across a spectrum of downstream tasks, all without necessitating extensive computational resources. Notably, MedCLIP, a vision-language contrastive learning-based medical FM, has been designed using unpaired image-text training. While the medical domain has often adopted unpaired training to amplify data, the exploration of potential security concerns linked to this approach hasn't kept pace with its practical usage. Notably, the augmentation capabilities inherent in unpaired training also indicate that minor label discrepancies can result in significant model deviations. In this study, we frame this label discrepancy as a backdoor attack problem. We further analyze its impact on medical FMs throughout the FM supply chain. Our evaluation primarily revolves around MedCLIP, emblematic of medical FM employing the unpaired strategy. We begin with an exploration of vulnerabilities in MedCLIP stemming from unpaired image-text matching, termed BadMatch. BadMatch is achieved using a modest set of wrongly labeled data. Subsequently, we disrupt MedCLIP's contrastive learning through BadDist-assisted BadMatch by introducing a Bad-Distance between the embeddings of clean and poisoned data. Additionally, combined with BadMatch and BadDist, the attacking pipeline consistently fends off backdoor assaults across diverse model designs, datasets, and triggers. Also, our findings reveal that current defense strategies are insufficient in detecting these latent threats in medical FMs' supply chains.

Heteroscedastic Uncertainty Estimation for Probabilistic Unsupervised Registration of Noisy Medical Images

This paper proposes a heteroscedastic uncertainty estimation framework for unsupervised medical image registration. Existing methods rely on objectives (e.g. mean-squared error) that assume a uniform noise level across the image, disregarding the heteroscedastic and input-dependent characteristics of noise distribution in real-world medical images. This further introduces noisy gradients due to undesired penalization on outliers, causing unnatural deformation and performance degradation. To mitigate this, we propose an adaptive weighting scheme with a relative $\gamma$-exponentiated signal-to-noise ratio (SNR) for the displacement estimator after modeling the heteroscedastic noise using a separate variance estimator to prevent the model from being driven away by spurious gradients from error residuals, leading to more accurate displacement estimation. To illustrate the versatility and effectiveness of the proposed method, we tested our framework on two representative registration architectures across three medical image datasets. Our proposed framework consistently outperforms other baselines both quantitatively and qualitatively while also providing accurate and sensible uncertainty measures. Paired t-tests show that our improvements in registration accuracy are statistically significant. The code will be publicly available at \url{https://voldemort108x.github.io/hetero_uncertainty/}.

Reti-Diff: Illumination Degradation Image Restoration with Retinex-based Latent Diffusion Model

Illumination degradation image restoration (IDIR) techniques aim to improve the visibility of degraded images and mitigate the adverse effects of deteriorated illumination. Among these algorithms, diffusion model (DM)-based methods have shown promising performance but are often burdened by heavy computational demands and pixel misalignment issues when predicting the image-level distribution. To tackle these problems, we propose to leverage DM within a compact latent space to generate concise guidance priors and introduce a novel solution called Reti-Diff for the IDIR task. Reti-Diff comprises two key components: the Retinex-based latent DM (RLDM) and the Retinex-guided transformer (RGformer). To ensure detailed reconstruction and illumination correction, RLDM is empowered to acquire Retinex knowledge and extract reflectance and illumination priors. These priors are subsequently utilized by RGformer to guide the decomposition of image features into their respective reflectance and illumination components. Following this, RGformer further enhances and consolidates the decomposed features, resulting in the production of refined images with consistent content and robustness to handle complex degradation scenarios. Extensive experiments show that Reti-Diff outperforms existing methods on three IDIR tasks, as well as downstream applications. Code will be available at \url{https://github.com/ChunmingHe/Reti-Diff}.