Deep Learning
CWFBind: Geometry-Awareness for Fast and Accurate Protein-Ligand Docking
Jia, Liyan, Ren, Chuan-Xian, Yan, Hong
Accurately predicting the binding conformation of small-molecule ligands to protein targets is a critical step in rational drug design. Although recent deep learning-based docking surpasses traditional methods in speed and accuracy, many approaches rely on graph representations and language model-inspired encoders while neglecting critical geometric information, resulting in inaccurate pocket localization and unrealistic binding conformations. In this study, we introduce CWFBind, a weighted, fast, and accurate docking method based on local curvature features. Specifically, we integrate local curvature descriptors during the feature extraction phase to enrich the geometric representation of both proteins and ligands, complementing existing chemical, sequence, and structural features. Furthermore, we embed degree-aware weighting mechanisms into the message passing process, enhancing the model's ability to capture spatial structural distinctions and interaction strengths. To address the class imbalance challenge in pocket prediction, CWFBind employs a ligand-aware dynamic radius strategy alongside an enhanced loss function, facilitating more precise identification of binding regions and key residues. Comprehensive experimental evaluations demonstrate that CWFBind achieves competitive performance across multiple docking benchmarks, offering a balanced trade-off between accuracy and efficiency.
From Ranking to Selection: A Simple but Efficient Dynamic Passage Selector for Retrieval Augmented Generation
Meng, Siyuan, Liu, Junming, Chen, Yirong, Mao, Song, Cai, Pinlong, Yan, Guohang, Shi, Botian, Wang, Ding
Retrieval-augmented generation (RAG) systems are often bottlenecked by their reranking modules, which typically score passages independently and select a fixed Top-K size. This approach struggles with complex multi-hop queries that require synthesizing evidence across multiple documents, creating a trade-off where small K values omit crucial information and large K values introduce noise. To address this, we introduce the Dynamic Passage Selector (DPS), a novel reranking framework that treats passage selection as a supervised learning problem. Unlike traditional point-wise or list-wise methods, DPS is fine-tuned to capture inter-passage dependencies and dynamically select the most relevant set of passages for generation. As a seamless plug-and-play module, DPS requires no modifications to the standard RAG pipeline. Comprehensive evaluations on five benchmarks show that DPS consistently outperforms state-of-the-art rerankers and fine-tuning methods. Notably, on the challenging MuSiQue dataset, DPS improves the F1-score by 30.06% and 15.4% over strong baselines like Qwen3-reranker and RankingGPT, respectively. Our results demonstrate that by enabling adaptive evidence selection, DPS substantially enhances reasoning capabilities in complex RAG scenarios.
Learning Facts at Scale with Active Reading
Lin, Jessy, Berges, Vincent-Pierre, Chen, Xilun, Yih, Wen-Tau, Ghosh, Gargi, Oฤuz, Barlas
LLMs are known to store vast amounts of knowledge in their parametric memory. However, learning and recalling facts from this memory is known to be unreliable, depending largely on the prevalence of particular facts in the training data and other factors which are poorly understood. Practitioners are lacking tools which will allow them to ensure that the models learn a given body of knowledge reliably and consistently. To this end, we propose Active Reading: a framework where we train models to study a given set of material with self-generated learning strategies. First, we demonstrate models trained with Active Reading on expert domains absorb significantly more knowledge than vanilla finetuning and other data augmentations. We train expert 8B models that achieve 66% on a Wikipedia-grounded subset of SimpleQA (+313% relative over vanilla finetuning) and 26% on FinanceBench (+160% relative over vanilla finetuning) by applying Active Reading to the source documents for each benchmark. Finally, we show that Active Reading can be utilized at pre-training scale to build more factual models. As a demonstration of this, we release Meta WikiExpert-8B, a Wikipedia-expert model trained on 1 trillion generated tokens, which outcompetes models with hundreds of billions of parameters on factual QA.
NeuronTune: Fine-Grained Neuron Modulation for Balanced Safety-Utility Alignment in LLMs
Pan, Birong, Xu, Mayi, Pi, Qiankun, Chen, Jianhao, Zhu, Yuanyuan, Zhong, Ming, Qian, Tieyun
Ensuring robust safety alignment while preserving utility is critical for the reliable deployment of Large Language Models (LLMs). However, current techniques fundamentally suffer from intertwined deficiencies: insufficient robustness against malicious attacks, frequent refusal of benign queries, degradation in generated text quality and general task performance--the former two reflecting deficits in robust safety and the latter constituting utility impairment . We trace these limitations to the coarse-grained layer-wise interventions in existing methods. To resolve this, we propose NeuronT une, a fine-grained framework that dynamically modulates sparse neurons to achieve simultaneous safety-utility optimization. Our approach first identifies safety-critical and utility-preserving neurons across all layers via attribution, then employs meta-learning to adaptively amplify safety-neuron activations and suppress utility-neuron activations. Crucially, NeuronTune enables tunable adjustment of intervention scope via neuron-count thresholds, supporting flexible adaptation to security-critical or utility-priority scenarios. Extensive experimental results demonstrate that our method significantly outperforms existing state-of-the-art technologies, achieving superior model safety while maintaining excellent utility.
EGGS-PTP: An Expander-Graph Guided Structured Post-training Pruning Method for Large Language Models
Bazarbachi, Omar, Sun, Zijun, Shen, Yanning
As Large Language Models (LLMs) become more widely adopted and scale up in size, the computational and memory challenges involved in deploying these massive foundation models have grown increasingly severe. This underscores the urgent need to develop more efficient model variants. Faced with this challenge, the present work introduces EGGS-PTP: an Expander-Graph Guided Structured Post-training Pruning method. The proposed approach leverages graph theory to guide the design of N:M structured pruning, effectively reducing model size and computational demands. By incorporating concepts from expander graphs, EGGS-PTP ensures information flow within the pruned network, preserving essential model functionality. Extensive numerical experiments demonstrate that EGGS-PTP not only achieves significant acceleration and memory savings due to structured sparsity but also outperforms existing structured pruning techniques in terms of accuracy across various LLMs.
User-centric Subjective Leaderboard by Customizable Reward Modeling
Jia, Qi, Song, Xiujie, Zhang, Zicheng, Guo, Yijin, Zhang, Kaiwei, Chen, Zijian, Zhai, Guangtao
Existing benchmarks for large language models (LLMs) predominantely focus on assessing their capabilities through verifiable tasks. Such objective and static benchmarks offer limited utility for practical LLM selection, making it difficult for users to find suitable models for their individual needs. To bridge this gap, we present the first User-Centric Subjective Leaderboard (USL), which provides a preference-driven, dynamic ranking of LLMs across diverse real-world scenarios. Our work is built upon a thorough investigation of real human preference data, involving more than 10K subjective queries. Our investigation reveals significant diversity and contradictions in human preferences, which limit the effectiveness of state-of-the-art reward models. To address this, we introduce Customizable Reward Models (CRMs). With only 4B parameters, our CRM surpasses the performance of leading models such as GPT-4.1 and Gemini-2.5-pro, showing exceptional generalization capabilities across new topics and criteria. The USL, powered by CRMs, exhibits strong negative correlations to contradictory preferences.
Gen-AFFECT: Generation of Avatar Fine-grained Facial Expressions with Consistent identiTy
Yu, Hao, Mallick, Rupayan, Betke, Margrit, Bargal, Sarah Adel
Different forms of customized 2D avatars are widely used in gaming applications, virtual communication, education, and content creation. However, existing approaches often fail to capture fine-grained facial expressions and struggle to preserve identity across different expressions. We propose GEN-AFFECT, a novel framework for personalized avatar generation that generates expressive and identity-consistent avatars with a diverse set of facial expressions. Our framework proposes conditioning a multimodal diffusion transformer on an extracted identity-expression representation. This enables identity preservation and representation of a wide range of facial expressions. GEN-AFFECT additionally employs consistent attention at inference for information sharing across the set of generated expressions, enabling the generation process to maintain identity consistency over the array of generated fine-grained expressions. GEN-AFFECT demonstrates superior performance compared to previous state-of-the-art methods on the basis of the accuracy of the generated expressions, the preservation of the identity and the consistency of the target identity across an array of fine-grained facial expressions.
HyperKD: Distilling Cross-Spectral Knowledge in Masked Autoencoders via Inverse Domain Shift with Spatial-Aware Masking and Specialized Loss
Matin, Abdul, Faruk, Tanjim Bin, Pallickara, Shrideep, Pallickara, Sangmi Lee
The proliferation of foundation models, pretrained on large-scale unlabeled datasets, has emerged as an effective approach in creating adaptable and reusable architectures that can be leveraged for various downstream tasks using satellite observations. However, their direct application to hyperspectral remote sensing remains challenging due to inherent spectral disparities and the scarcity of available observations. In this work, we present HyperKD, a novel knowledge distillation framework that enables transferring learned representations from a teacher model into a student model for effective development of a foundation model on hyperspectral images. Unlike typical knowledge distillation frameworks, which use a complex teacher to guide a simpler student, HyperKD enables an inverse form of knowledge transfer across different types of spectral data, guided by a simpler teacher model. Building upon a Masked Autoencoder, HyperKD distills knowledge from the Prithvi foundational model into a student tailored for EnMAP hyperspectral imagery. HyperKD addresses the inverse domain adaptation problem with spectral gaps by introducing a feature-based strategy that includes spectral range-based channel alignment, spatial feature-guided masking, and an enhanced loss function tailored for hyperspectral images. HyperKD bridges the substantial spectral domain gap, enabling the effective use of pretrained foundation models for geospatial applications. Extensive experiments show that HyperKD significantly improves representation learning in MAEs, leading to enhanced reconstruction fidelity and more robust performance on downstream tasks such as land cover classification, crop type identification, and soil organic carbon prediction, underpinning the potential of knowledge distillation frameworks in remote sensing analytics with hyperspectral imagery.
From Charts to Fair Narratives: Uncovering and Mitigating Geo-Economic Biases in Chart-to-Text
Mahbub, Ridwan, Islam, Mohammed Saidul, Nayeem, Mir Tafseer, Laskar, Md Tahmid Rahman, Rahman, Mizanur, Joty, Shafiq, Hoque, Enamul
Charts are very common for exploring data and communicating insights, but extracting key takeaways from charts and articulating them in natural language can be challenging. The chart-to-text task aims to automate this process by generating textual summaries of charts. While with the rapid advancement of large Vision-Language Models (VLMs), we have witnessed great progress in this domain, little to no attention has been given to potential biases in their outputs. This paper investigates how VLMs can amplify geo-economic biases when generating chart summaries, potentially causing societal harm. Specifically, we conduct a large-scale evaluation of geo-economic biases in VLM-generated chart summaries across 6,000 chart-country pairs from six widely used proprietary and open-source models to understand how a country's economic status influences the sentiment of generated summaries. Our analysis reveals that existing VLMs tend to produce more positive descriptions for high-income countries compared to middle- or low-income countries, even when country attribution is the only variable changed. We also find that models such as GPT-4o-mini, Gemini-1.5-Flash, and Phi-3.5 exhibit varying degrees of bias. We further explore inference-time prompt-based debiasing techniques using positive distractors but find them only partially effective, underscoring the complexity of the issue and the need for more robust debiasing strategies. Our code and dataset are publicly available here.
Leveraging Zipformer Model for Effective Language Identification in Code-Switched Child-Directed Speech
Shankar, Lavanya, Perera, Leibny Paola Garcia
This paper addresses this challenge by using Zipformer to handle the nuances of speech which contains two imbalanced languages - Mandarin and English - in an utterance. This work demonstrates that the internal layers of the Zipformer effectively encode the language characteristics, which can be leveraged in language identification. We present the selection methodology of the inner layers to extract the em-beddings and make a comparison with different back-ends. Our analysis shows that Zipformer is robust across these backends. Our approach effectively handles imbalanced data, achieving a Balanced Accuracy (BAC) of 81.89%, a 15.47% improvement over the language identification baseline.