Large Language Models for Bioinformatics

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

Visual Style Prompt Learning Using Diffusion Models for Blind Face Restoration

Blind face restoration aims to recover high-quality facial images from various unidentified sources of degradation, posing significant challenges due to the minimal information retrievable from the degraded images. Prior knowledge-based methods, leveraging geometric priors and facial features, have led to advancements in face restoration but often fall short of capturing fine details. To address this, we introduce a visual style prompt learning framework that utilizes diffusion probabilistic models to explicitly generate visual prompts within the latent space of pre-trained generative models. These prompts are designed to guide the restoration process. To fully utilize the visual prompts and enhance the extraction of informative and rich patterns, we introduce a style-modulated aggregation transformation layer. Extensive experiments and applications demonstrate the superiority of our method in achieving high-quality blind face restoration. The source code is available at \href{https://github.com/LonglongaaaGo/VSPBFR}{https://github.com/LonglongaaaGo/VSPBFR}.

Implementing Trust in Non-Small Cell Lung Cancer Diagnosis with a Conformalized Uncertainty-Aware AI Framework in Whole-Slide Images

Ensuring trustworthiness is fundamental to the development of artificial intelligence (AI) that is considered societally responsible, particularly in cancer diagnostics, where a misdiagnosis can have dire consequences. Current digital pathology AI models lack systematic solutions to address trustworthiness concerns arising from model limitations and data discrepancies between model deployment and development environments. To address this issue, we developed TRUECAM, a framework designed to ensure both data and model trustworthiness in non-small cell lung cancer subtyping with whole-slide images. TRUECAM integrates 1) a spectral-normalized neural Gaussian process for identifying out-of-scope inputs and 2) an ambiguity-guided elimination of tiles to filter out highly ambiguous regions, addressing data trustworthiness, as well as 3) conformal prediction to ensure controlled error rates. We systematically evaluated the framework across multiple large-scale cancer datasets, leveraging both task-specific and foundation models, illustrate that an AI model wrapped with TRUECAM significantly outperforms models that lack such guidance, in terms of classification accuracy, robustness, interpretability, and data efficiency, while also achieving improvements in fairness. These findings highlight TRUECAM as a versatile wrapper framework for digital pathology AI models with diverse architectural designs, promoting their responsible and effective applications in real-world settings.

OpenAI o1 System Card

The o1 model series is trained with large-scale reinforcement learning to reason using chain of thought. These advanced reasoning capabilities provide new avenues for improving the safety and robustness of our models. In particular, our models can reason about our safety policies in context when responding to potentially unsafe prompts, through deliberative alignment. This leads to state-of-the-art performance on certain benchmarks for risks such as generating illicit advice, choosing stereotyped responses, and succumbing to known jailbreaks. Training models to incorporate a chain of thought before answering has the potential to unlock substantial benefits, while also increasing potential risks that stem from heightened intelligence. Our results underscore the need for building robust alignment methods, extensively stress-testing their efficacy, and maintaining meticulous risk management protocols. This report outlines the safety work carried out for the OpenAI o1 and OpenAI o1-mini models, including safety evaluations, external red teaming, and Preparedness Framework evaluations.

SemDP: Semantic-level Differential Privacy Protection for Face Datasets

While large-scale face datasets have advanced deep learning-based face analysis, they also raise privacy concerns due to the sensitive personal information they contain. Recent schemes have implemented differential privacy to protect face datasets. However, these schemes generally treat each image as a separate database, which does not fully meet the core requirements of differential privacy. In this paper, we propose a semantic-level differential privacy protection scheme that applies to the entire face dataset. Unlike pixel-level differential privacy approaches, our scheme guarantees that semantic privacy in faces is not compromised. The key idea is to convert unstructured data into structured data to enable the application of differential privacy. Specifically, we first extract semantic information from the face dataset to build an attribute database, then apply differential perturbations to obscure this attribute data, and finally use an image synthesis model to generate a protected face dataset. Extensive experimental results show that our scheme can maintain visual naturalness and balance the privacy-utility trade-off compared to the mainstream schemes.

Red Pill and Blue Pill: Controllable Website Fingerprinting Defense via Dynamic Backdoor Learning

Website fingerprint (WF) attacks, which covertly monitor user communications to identify the web pages they visit, pose a serious threat to user privacy. Existing WF defenses attempt to reduce the attacker's accuracy by disrupting unique traffic patterns; however, they often suffer from the trade-off between overhead and effectiveness, resulting in less usefulness in practice. To overcome this limitation, we introduce Controllable Website Fingerprint Defense (CWFD), a novel defense perspective based on backdoor learning. CWFD exploits backdoor vulnerabilities in neural networks to directly control the attacker's model by designing trigger patterns based on network traffic. Specifically, CWFD injects only incoming packets on the server side into the target web page's traffic, keeping overhead low while effectively poisoning the attacker's model during training. During inference, the defender can influence the attacker's model through a 'red pill, blue pill' choice: traces with the trigger (red pill) lead to misclassification as the target web page, while normal traces (blue pill) are classified correctly, achieving directed control over the defense outcome. We use the Fast Levenshtein-like distance as the optimization objective to compute trigger patterns that can be effectively associated with our target page. Experiments show that CWFD significantly reduces RF's accuracy from 99% to 6% with 74% data overhead. In comparison, FRONT reduces accuracy to only 97% at similar overhead, while Palette achieves 32% accuracy with 48% more overhead. We further validate the practicality of our method in a real Tor network environment.

Mel-Refine: A Plug-and-Play Approach to Refine Mel-Spectrogram in Audio Generation

Text-to-audio (TTA) model is capable of generating diverse audio from textual prompts. However, most mainstream TTA models, which predominantly rely on Mel-spectrograms, still face challenges in producing audio with rich content. The intricate details and texture required in Mel-spectrograms for such audio often surpass the models' capacity, leading to outputs that are blurred or lack coherence. In this paper, we begin by investigating the critical role of U-Net in Mel-spectrogram generation. Our analysis shows that in U-Net structure, high-frequency components in skip-connections and the backbone influence texture and detail, while low-frequency components in the backbone are critical for the diffusion denoising process. We further propose ``Mel-Refine'', a plug-and-play approach that enhances Mel-spectrogram texture and detail by adjusting different component weights during inference. Our method requires no additional training or fine-tuning and is fully compatible with any diffusion-based TTA architecture. Experimental results show that our approach boosts performance metrics of the latest TTA model Tango2 by 25\%, demonstrating its effectiveness.

Dynamic Disentangled Fusion Network for RGBT Tracking

RGBT tracking usually suffers from various challenging factors of low resolution, similar appearance, extreme illumination, thermal crossover and occlusion, to name a few. Existing works often study complex fusion models to handle challenging scenarios, but can not well adapt to various challenges, which might limit tracking performance. To handle this problem, we propose a novel Dynamic Disentangled Fusion Network called DDFNet, which disentangles the fusion process into several dynamic fusion models via the challenge attributes to adapt to various challenging scenarios, for robust RGBT tracking. In particular, we design six attribute-based fusion models to integrate RGB and thermal features under the six challenging scenarios respectively.Since each fusion model is to deal with the corresponding challenges, such disentangled fusion scheme could increase the fusion capacity without the dependence on large-scale training data. Considering that every challenging scenario also has different levels of difficulty, we propose to optimize the combination of multiple fusion units to form each attribute-based fusion model in a dynamic manner, which could well adapt to the difficulty of the corresponding challenging scenario. To address the issue that which fusion models should be activated in the tracking process, we design an adaptive aggregation fusion module to integrate all features from attribute-based fusion models in an adaptive manner with a three-stage training algorithm. In addition, we design an enhancement fusion module to further strengthen the aggregated feature and modality-specific features. Experimental results on benchmark datasets demonstrate the effectiveness of our DDFNet against other state-of-the-art methods.

ScribbleVS: Scribble-Supervised Medical Image Segmentation via Dynamic Competitive Pseudo Label Selection

In clinical medicine, precise image segmentation can provide substantial support to clinicians. However, achieving such precision often requires a large amount of finely annotated data, which can be costly. Scribble annotation presents a more efficient alternative, boosting labeling efficiency. However, utilizing such minimal supervision for medical image segmentation training, especially with scribble annotations, poses significant challenges. To address these challenges, we introduce ScribbleVS, a novel framework that leverages scribble annotations. We introduce a Regional Pseudo Labels Diffusion Module to expand the scope of supervision and reduce the impact of noise present in pseudo labels. Additionally, we propose a Dynamic Competitive Selection module for enhanced refinement in selecting pseudo labels. Experiments conducted on the ACDC and MSCMRseg datasets have demonstrated promising results, achieving performance levels that even exceed those of fully supervised methodologies. The codes of this study are available at https://github.com/ortonwang/ScribbleVS.

Pattern Integration and Enhancement Vision Transformer for Self-Supervised Learning in Remote Sensing

Recent self-supervised learning (SSL) methods have demonstrated impressive results in learning visual representations from unlabeled remote sensing images. However, most remote sensing images predominantly consist of scenographic scenes containing multiple ground objects without explicit foreground targets, which limits the performance of existing SSL methods that focus on foreground targets. This raises the question: Is there a method that can automatically aggregate similar objects within scenographic remote sensing images, thereby enabling models to differentiate knowledge embedded in various geospatial patterns for improved feature representation? In this work, we present the Pattern Integration and Enhancement Vision Transformer (PIEViT), a novel self-supervised learning framework designed specifically for remote sensing imagery. PIEViT utilizes a teacher-student architecture to address both image-level and patch-level tasks. It employs the Geospatial Pattern Cohesion (GPC) module to explore the natural clustering of patches, enhancing the differentiation of individual features. The Feature Integration Projection (FIP) module further refines masked token reconstruction using geospatially clustered patches. We validated PIEViT across multiple downstream tasks, including object detection, semantic segmentation, and change detection. Experiments demonstrated that PIEViT enhances the representation of internal patch features, providing significant improvements over existing self-supervised baselines. It achieves excellent results in object detection, land cover classification, and change detection, underscoring its robustness, generalization, and transferability for remote sensing image interpretation tasks.