Investigating Data Pruning for Pretraining Biological Foundation Models at Scale

Biological foundation models (BioFMs), pretrained on large-scale biological sequences, have recently shown strong potential in providing meaningful representations for diverse downstream bioinformatics tasks. However, such models often rely on millions to billions of training sequences and billions of parameters, resulting in prohibitive computational costs and significant barriers to reproducibility and accessibility, particularly for academic labs. To address these challenges, we investigate the feasibility of data pruning for BioFM pretraining and propose a post-hoc influence-guided data pruning framework tailored to biological domains. Our approach introduces a subset-based self-influence formulation that enables efficient estimation of sample importance at low computational cost, and builds upon it two simple yet effective selection strategies, namely Top-k Influence (Top I) and Coverage-Centric Influence (CCI). We empirically validate our method on two representative BioFMs, RNA-FM and ESM-C. For RNA, our framework consistently outperforms random selection baselines under an extreme pruning rate of over 99 percent, demonstrating its effectiveness. Furthermore, we show the generalizability of our framework on protein-related tasks using ESM-C. In particular, our coreset even outperforms random subsets that are ten times larger in both RNA and protein settings, revealing substantial redundancy in biological sequence datasets. These findings underscore the potential of influence-guided data pruning to substantially reduce the computational cost of BioFM pretraining, paving the way for more efficient, accessible, and sustainable biological AI research.

Advanced Black-Box Tuning of Large Language Models with Limited API Calls

Black-box tuning is an emerging paradigm for adapting large language models (LLMs) to better achieve desired behaviors, particularly when direct access to model parameters is unavailable. Current strategies, however, often present a dilemma of suboptimal extremes: either separately train a small proxy model and then use it to shift the predictions of the foundation model, offering notable efficiency but often yielding limited improvement; or making API calls in each tuning iteration to the foundation model, which entails prohibitive computational costs. Therefore, we propose a novel advanced black-box tuning method for LLMs with limited API calls. Our core strategy involves training a Gaussian Process (GP) surrogate model with "LogitMap Pairs" derived from querying the foundation model on a minimal but highly informative training subset. This surrogate can approximate the outputs of the foundation model to guide the training of the proxy model, thereby effectively reducing the need for direct queries to the foundation model. Extensive experiments verify that our approach elevates pre-trained language model accuracy from 55.92% to 86.85%, reducing the frequency of API queries to merely 1.38%. This significantly outperforms offline approaches that operate entirely without API access. Notably, our method also achieves comparable or superior accuracy to query-intensive approaches, while significantly reducing API costs. This offers a robust and high-efficiency paradigm for language model adaptation.

Explore and Establish Synergistic Effects Between Weight Pruning and Coreset Selection in Neural Network Training

Modern deep neural networks rely heavily on massive model weights and training samples, incurring substantial computational costs. Weight pruning and coreset selection are two emerging paradigms proposed to improve computational efficiency. In this paper, we first explore the interplay between redundant weights and training samples through a transparent analysis: redundant samples, particularly noisy ones, cause model weights to become unnecessarily overtuned to fit them, complicating the identification of irrelevant weights during pruning; conversely, irrelevant weights tend to overfit noisy data, undermining coreset selection effectiveness. To further investigate and harness this interplay in deep learning, we develop a Simultaneous Weight and Sample Tailoring mechanism (SWaST) that alternately performs weight pruning and coreset selection to establish a synergistic effect in training. During this investigation, we observe that when simultaneously removing a large number of weights and samples, a phenomenon we term critical double-loss can occur, where important weights and their supportive samples are mistakenly eliminated at the same time, leading to model instability and nearly irreversible degradation that cannot be recovered in subsequent training. Unlike classic machine learning models, this issue can arise in deep learning due to the lack of theoretical guarantees on the correctness of weight pruning and coreset selection, which explains why these paradigms are often developed independently. We mitigate this by integrating a state preservation mechanism into SWaST, enabling stable joint optimization. Extensive experiments reveal a strong synergy between pruning and coreset selection across varying prune rates and coreset sizes, delivering accuracy boosts of up to 17.83% alongside 10% to 90% FLOPs reductions.

Towards Robust Influence Functions with Flat Validation Minima

The Influence Function (IF) is a widely used technique for assessing the impact of individual training samples on model predictions. However, existing IF methods often fail to provide reliable influence estimates in deep neural networks, particularly when applied to noisy training data. This issue does not stem from inaccuracies in parameter change estimation, which has been the primary focus of prior research, but rather from deficiencies in loss change estimation, specifically due to the sharpness of validation risk. In this work, we establish a theoretical connection between influence estimation error, validation set risk, and its sharpness, underscoring the importance of flat validation minima for accurate influence estimation. Furthermore, we introduce a novel estimation form of Influence Function specifically designed for flat validation minima. Experimental results across various tasks validate the superiority of our approach.

Large Language Model Compression with Global Rank and Sparsity Optimization

Low-rank and sparse composite approximation is a natural idea to compress Large Language Models (LLMs). However, such an idea faces two primary challenges that adversely affect the performance of existing methods. The first challenge relates to the interaction and cooperation between low-rank and sparse matrices, while the second involves determining weight allocation across different layers, as redundancy varies considerably among them. To address these challenges, we propose a novel two-stage LLM compression method with the capability of global rank and sparsity optimization. It is noteworthy that the overall optimization space is vast, making comprehensive optimization computationally prohibitive. Therefore, to reduce the optimization space, our first stage utilizes robust principal component analysis to decompose the weight matrices of LLMs into low-rank and sparse components, which span the low dimensional and sparse spaces containing the resultant low-rank and sparse matrices, respectively. In the second stage, we propose a probabilistic global optimization technique to jointly identify the low-rank and sparse structures within the above two spaces. The appealing feature of our approach is its ability to automatically detect the redundancy across different layers and to manage the interaction between the sparse and low-rank components. Extensive experimental results indicate that our method significantly surpasses state-of-the-art techniques for sparsification and composite approximation.

Efficient Fine-Tuning of Quantized Models via Adaptive Rank and Bitwidth

QLoRA effectively combines low-bit quantization and LoRA to achieve memory-friendly fine-tuning for large language models (LLM). Recently, methods based on SVD for continuous update iterations to initialize LoRA matrices to accommodate quantization errors have generally failed to consistently improve performance. Dynamic mixed precision is a natural idea for continuously improving the fine-tuning performance of quantized models, but previous methods often optimize low-rank subspaces or quantization components separately, without considering their synergy. To address this, we propose \textbf{QR-Adaptor}, a unified, gradient-free strategy that uses partial calibration data to jointly search the quantization components and the rank of low-rank spaces for each layer, thereby continuously improving model performance. QR-Adaptor does not minimize quantization error but treats precision and rank allocation as a discrete optimization problem guided by actual downstream performance and memory usage. Compared to state-of-the-art (SOTA) quantized LoRA fine-tuning methods, our approach achieves a 4.89\% accuracy improvement on GSM8K, and in some cases even outperforms the 16-bit fine-tuned model while maintaining the memory footprint of the 4-bit setting.

Optimized Gradient Clipping for Noisy Label Learning

Previous research has shown that constraining the gradient of loss function with respect to model-predicted probabilities can enhance the model robustness against noisy labels. These methods typically specify a fixed optimal threshold for gradient clipping through validation data to obtain the desired robustness against noise. However, this common practice overlooks the dynamic distribution of gradients from both clean and noisy-labeled samples at different stages of training, significantly limiting the model capability to adapt to the variable nature of gradients throughout the training process. To address this issue, we propose a simple yet effective approach called Optimized Gradient Clipping (OGC), which dynamically adjusts the clipping threshold based on the ratio of noise gradients to clean gradients after clipping, estimated by modeling the distributions of clean and noisy samples. This approach allows us to modify the clipping threshold at each training step, effectively controlling the influence of noise gradients. Additionally, we provide statistical analysis to certify the noise-tolerance ability of OGC. Our extensive experiments across various types of label noise, including symmetric, asymmetric, instance-dependent, and real-world noise, demonstrate the effectiveness of our approach. The code and a technical appendix for better digital viewing are included as supplementary materials and scheduled to be open-sourced upon publication.

Revisiting Energy-Based Model for Out-of-Distribution Detection

Out-of-distribution (OOD) detection is an essential approach to robustifying deep learning models, enabling them to identify inputs that fall outside of their trained distribution. Existing OOD detection methods usually depend on crafted data, such as specific outlier datasets or elaborate data augmentations. While this is reasonable, the frequent mismatch between crafted data and OOD data limits model robustness and generalizability. In response to this issue, we introduce Outlier Exposure by Simple Transformations (OEST), a framework that enhances OOD detection by leveraging "peripheral-distribution" (PD) data. Specifically, PD data are samples generated through simple data transformations, thus providing an efficient alternative to manually curated outliers. We adopt energy-based models (EBMs) to study PD data. We recognize the "energy barrier" in OOD detection, which characterizes the energy difference between in-distribution (ID) and OOD samples and eases detection. PD data are introduced to establish the energy barrier during training. Furthermore, this energy barrier concept motivates a theoretically grounded energy-barrier loss to replace the classical energy-bounded loss, leading to an improved paradigm, OEST*, which achieves a more effective and theoretically sound separation between ID and OOD samples. We perform empirical validation of our proposal, and extensive experiments across various benchmarks demonstrate that OEST* achieves better or similar accuracy compared with state-of-the-art methods.

Active Negative Loss: A Robust Framework for Learning with Noisy Labels

Deep supervised learning has achieved remarkable success across a wide range of tasks, yet it remains susceptible to overfitting when confronted with noisy labels. To address this issue, noise-robust loss functions offer an effective solution for enhancing learning in the presence of label noise. In this work, we systematically investigate the limitation of the recently proposed Active Passive Loss (APL), which employs Mean Absolute Error (MAE) as its passive loss function. Despite the robustness brought by MAE, one of its key drawbacks is that it pays equal attention to clean and noisy samples; this feature slows down convergence and potentially makes training difficult, particularly in large-scale datasets. To overcome these challenges, we introduce a novel loss function class, termed Normalized Negative Loss Functions (NNLFs), which serve as passive loss functions within the APL framework. NNLFs effectively address the limitations of MAE by concentrating more on memorized clean samples. By replacing MAE in APL with our proposed NNLFs, we enhance APL and present a new framework called Active Negative Loss (ANL). Moreover, in non-symmetric noise scenarios, we propose an entropy-based regularization technique to mitigate the vulnerability to the label imbalance. Extensive experiments demonstrate that the new loss functions adopted by our ANL framework can achieve better or comparable performance to state-of-the-art methods across various label noise types and in image segmentation tasks. The source code is available at: https://github.com/Virusdoll/Active-Negative-Loss.

MagicFace: Training-free Universal-Style Human Image Customized Synthesis

Existing human image personalized generation methods often require tedious training: either fine-tuning with a few images or retraining on large-scale datasets. In such cases, these methods are prone to overfitting and encounter difficulties when personalizing individuals of diverse styles. Moreover, these training-based approaches also struggle with multi-concept human image customizing. To this end, we propose MagicFace, the first method for universal-style human image personalized synthesis that enables single/multi-concept customization for humans of any style in a training-free manner. MagicFace introduces a coarse-to-fine generation pipeline, involving two sequential stages: semantic scene construction and concept feature injection. This is achieved by our Reference-aware Self-Attention (RSA) and Region-grouped Blend Attention (RBA) mechanisms. Specifically, in the first stage, RSA enables the latent image to query features from reference concepts simultaneously, extracting the coarse-grained overall semantic understanding to facilitate the initial semantic layout establishment. In the second stage, we employ an attention-based semantic segmentation method to pinpoint the generated regions of all concepts in the latent image at each step. Following this, RBA divides the pixels of the latent image into semantic groups, with each group querying fine-grained features from its reference concept, which ensures precise attribute alignment and feature injection. Throughout the two-stage process, a weight mask strategy is employed to ensure the model focuses more on the reference concepts. Extensive experiments demonstrate our superiority in both human-centric subject-to-image synthesis and multi-concept human image customization. Our approach also can be applied to texture transformation, further enhancing its versatility and applicability.