Transformer-based Single-Cell Language Model: A Survey

The transformers have achieved significant accomplishments in the natural language processing as its outstanding parallel processing capabilities and highly flexible attention mechanism. In addition, increasing studies based on transformers have been proposed to model single-cell data. In this review, we attempt to systematically summarize the single-cell language models and applications based on transformers. First, we provide a detailed introduction about the structure and principles of transformers. Then, we review the single-cell language models and large language models for single-cell data analysis. Moreover, we explore the datasets and applications of single-cell language models in downstream tasks such as batch correction, cell clustering, cell type annotation, gene regulatory network inference and perturbation response. Further, we discuss the challenges of single-cell language models and provide promising research directions. We hope this review will serve as an up-to-date reference for researchers interested in the direction of single-cell language models.

Watch Every Step! LLM Agent Learning via Iterative Step-Level Process Refinement

Large language model agents have exhibited exceptional performance across a range of complex interactive tasks. Recent approaches have utilized tuning with expert trajectories to enhance agent performance, yet they primarily concentrate on outcome rewards, which may lead to errors or suboptimal actions due to the absence of process supervision signals. In this paper, we introduce the Iterative step-level Process Refinement (IPR) framework, which provides detailed step-by-step guidance to enhance agent training. Specifically, we adopt the Monte Carlo method to estimate step-level rewards. During each iteration, the agent explores along the expert trajectory and generates new actions. These actions are then evaluated against the corresponding step of expert trajectory using step-level rewards. Such comparison helps identify discrepancies, yielding contrastive action pairs that serve as training data for the agent. Our experiments on three complex agent tasks demonstrate that our framework outperforms a variety of strong baselines. Moreover, our analytical findings highlight the effectiveness of IPR in augmenting action efficiency and its applicability to diverse models.

Sharing Matters: Analysing Neurons Across Languages and Tasks in LLMs

Multilingual large language models (LLMs) have greatly increased the ceiling of performance on non-English tasks. However the mechanisms behind multilingualism in these LLMs are poorly understood. Of particular interest is the degree to which internal representations are shared between languages. Recent work on neuron analysis of LLMs has focused on the monolingual case, and the limited work on the multilingual case has not considered the interaction between tasks and linguistic representations. In our work, we investigate how neuron activation is shared across languages by categorizing neurons into four distinct groups according to their responses across different languages for a particular input: all-shared, partial-shared, specific, and non-activated. This categorization is combined with a study of neuron attribution, i.e. the importance of a neuron w.r.t an output. Our analysis reveals the following insights: (i) the linguistic sharing patterns are strongly affected by the type of task, but neuron behaviour changes across different inputs even for the same task; (ii) all-shared neurons play a key role in generating correct responses; (iii) boosting multilingual alignment by increasing all-shared neurons can enhance accuracy on multilingual tasks. The code is available at https://github.com/weixuan-wang123/multilingual-neurons.

A Survey on Hallucination in Large Vision-Language Models

Recent development of Large Vision-Language Models (LVLMs) has attracted growing attention within the AI landscape for its practical implementation potential. However, ``hallucination'', or more specifically, the misalignment between factual visual content and corresponding textual generation, poses a significant challenge of utilizing LVLMs. In this comprehensive survey, we dissect LVLM-related hallucinations in an attempt to establish an overview and facilitate future mitigation. Our scrutiny starts with a clarification of the concept of hallucinations in LVLMs, presenting a variety of hallucination symptoms and highlighting the unique challenges inherent in LVLM hallucinations. Subsequently, we outline the benchmarks and methodologies tailored specifically for evaluating hallucinations unique to LVLMs. Additionally, we delve into an investigation of the root causes of these hallucinations, encompassing insights from the training data and model components. We also critically review existing methods for mitigating hallucinations. The open questions and future directions pertaining to hallucinations within LVLMs are discussed to conclude this survey.

Towards General Purpose Vision Foundation Models for Medical Image Analysis: An Experimental Study of DINOv2 on Radiology Benchmarks

The integration of deep learning systems into the medical domain has been hindered by the resource-intensive process of data annotation and the inability of these systems to generalize to different data distributions. Foundation models, which are models pre-trained on large datasets, have emerged as a solution to reduce reliance on annotated data and enhance model generalizability and robustness. DINOv2, an open-source foundation model pre-trained with self-supervised learning on 142 million curated natural images, excels in extracting general-purpose visual representations, exhibiting promising capabilities across various vision tasks. Nevertheless, a critical question remains unanswered regarding DINOv2's adaptability to radiological imaging, and the clarity on whether its features are sufficiently general to benefit radiology image analysis is yet to be established. Therefore, this study comprehensively evaluates DINOv2 for radiology, conducting over 100 experiments across diverse modalities (X-ray, CT, and MRI). Tasks include disease classification and organ segmentation on both 2D and 3D images, evaluated under different settings like kNN, few-shot learning, linear-probing, end-to-end fine-tuning, and parameter-efficient fine-tuning, to measure the effectiveness and generalizability of the DINOv2 feature embeddings. Comparative analyses with established medical image analysis models, U-Net and TransUnet for segmentation, and CNN and ViT models pre-trained via supervised, weakly supervised, and self-supervised learning for classification, reveal DINOv2's superior performance in segmentation tasks and competitive results in disease classification. The findings contribute insights to potential avenues for optimizing pre-training strategies for medical imaging and enhancing the broader understanding of DINOv2's role in bridging the gap between natural and radiological image analysis.

Align before Adapt: Leveraging Entity-to-Region Alignments for Generalizable Video Action Recognition

Large-scale visual-language pre-trained models have achieved significant success in various video tasks. However, most existing methods follow an "adapt then align" paradigm, which adapts pre-trained image encoders to model video-level representations and utilizes one-hot or text embedding of the action labels for supervision. This paradigm overlooks the challenge of mapping from static images to complicated activity concepts. In this paper, we propose a novel "Align before Adapt" (ALT) paradigm. Prior to adapting to video representation learning, we exploit the entity-to-region alignments for each frame. The alignments are fulfilled by matching the region-aware image embeddings to an offline-constructed text corpus. With the aligned entities, we feed their text embeddings to a transformer-based video adapter as the queries, which can help extract the semantics of the most important entities from a video to a vector. This paradigm reuses the visual-language alignment of VLP during adaptation and tries to explain an action by the underlying entities. This helps understand actions by bridging the gap with complex activity semantics, particularly when facing unfamiliar or unseen categories. ALT achieves competitive performance and superior generalizability while requiring significantly low computational costs. In fully supervised scenarios, it achieves 88.1% top-1 accuracy on Kinetics-400 with only 4947 GFLOPs. In 2-shot experiments, ALT outperforms the previous state-of-the-art by 7.1% and 9.2% on HMDB-51 and UCF-101, respectively.

MedSyn: Text-guided Anatomy-aware Synthesis of High-Fidelity 3D CT Images

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

Assessing the Reliability of Large Language Model Knowledge

Large language models (LLMs) have been treated as knowledge bases due to their strong performance in knowledge probing tasks. LLMs are typically evaluated using accuracy, yet this metric does not capture the vulnerability of LLMs to hallucination-inducing factors like prompt and context variability. How do we evaluate the capabilities of LLMs to consistently produce factually correct answers? In this paper, we propose MOdel kNowledge relIabiliTy scORe (MONITOR), a novel metric designed to directly measure LLMs' factual reliability. MONITOR computes the distance between the probability distributions of a valid output and its counterparts produced by the same LLM probing the same fact using different styles of prompts and contexts.Experiments on a comprehensive range of 12 LLMs demonstrate the effectiveness of MONITOR in evaluating the factual reliability of LLMs while maintaining a low computational overhead. In addition, we release the FKTC (Factual Knowledge Test Corpus) test set, containing 210,158 prompts in total to foster research along this line (https://github.com/Vicky-Wil/MONITOR).

Metadata-Conditioned Generative Models to Synthesize Anatomically-Plausible 3D Brain MRIs

Generative AI models hold great potential in creating synthetic brain MRIs that advance neuroimaging studies by, for example, enriching data diversity. However, the mainstay of AI research only focuses on optimizing the visual quality (such as signal-to-noise ratio) of the synthetic MRIs while lacking insights into their relevance to neuroscience. To gain these insights with respect to T1-weighted MRIs, we first propose a new generative model, BrainSynth, to synthesize metadata-conditioned (e.g., age- and sex-specific) MRIs that achieve state-of-the-art visual quality. We then extend our evaluation with a novel procedure to quantify anatomical plausibility, i.e., how well the synthetic MRIs capture macrostructural properties of brain regions, and how accurately they encode the effects of age and sex. Results indicate that more than half of the brain regions in our synthetic MRIs are anatomically accurate, i.e., with a small effect size between real and synthetic MRIs. Moreover, the anatomical plausibility varies across cortical regions according to their geometric complexity. As is, our synthetic MRIs can significantly improve the training of a Convolutional Neural Network to identify accelerated aging effects in an independent study. These results highlight the opportunities of using generative AI to aid neuroimaging research and point to areas for further improvement.

LSOR: Longitudinally-Consistent Self-Organized Representation Learning

Interpretability is a key issue when applying deep learning models to longitudinal brain MRIs. One way to address this issue is by visualizing the high-dimensional latent spaces generated by deep learning via self-organizing maps (SOM). SOM separates the latent space into clusters and then maps the cluster centers to a discrete (typically 2D) grid preserving the high-dimensional relationship between clusters. However, learning SOM in a high-dimensional latent space tends to be unstable, especially in a self-supervision setting. Furthermore, the learned SOM grid does not necessarily capture clinically interesting information, such as brain age. To resolve these issues, we propose the first self-supervised SOM approach that derives a high-dimensional, interpretable representation stratified by brain age solely based on longitudinal brain MRIs (i.e., without demographic or cognitive information). Called Longitudinally-consistent Self-Organized Representation learning (LSOR), the method is stable during training as it relies on soft clustering (vs. the hard cluster assignments used by existing SOM). Furthermore, our approach generates a latent space stratified according to brain age by aligning trajectories inferred from longitudinal MRIs to the reference vector associated with the corresponding SOM cluster. When applied to longitudinal MRIs of the Alzheimer's Disease Neuroimaging Initiative (ADNI, N=632), LSOR generates an interpretable latent space and achieves comparable or higher accuracy than the state-of-the-art representations with respect to the downstream tasks of classification (static vs. progressive mild cognitive impairment) and regression (determining ADAS-Cog score of all subjects). The code is available at https://github.com/ouyangjiahong/longitudinal-som-single-modality.