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 Deep Learning


Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings

arXiv.org Artificial Intelligence

Generating diverse, all-atom conformational ensembles of dynamic proteins such as G-protein-coupled receptors (GPCRs) is critical for understanding their function, yet most generative models simplify atomic detail or ignore conformational diversity altogether. We present latent diffusion for full protein generation (LD-FPG), a framework that constructs complete all-atom protein structures, including every side-chain heavy atom, directly from molecular dynamics (MD) trajectories. LD-FPG employs a Chebyshev graph neural network (ChebNet) to obtain low-dimensional latent embeddings of protein conformations, which are processed using three pooling strategies: blind, sequential and residue-based. A diffusion model trained on these latent representations generates new samples that a decoder, optionally regularized by dihedral-angle losses, maps back to Cartesian coordinates. Using D2R-MD, a 2-microsecond MD trajectory (12 000 frames) of the human dopamine D2 receptor in a membrane environment, the sequential and residue-based pooling strategy reproduces the reference ensemble with high structural fidelity (all-atom lDDT of approximately 0.7; C-alpha-lDDT of approximately 0.8) and recovers backbone and side-chain dihedral-angle distributions with a Jensen-Shannon divergence of less than 0.03 compared to the MD data. LD-FPG thereby offers a practical route to system-specific, all-atom ensemble generation for large proteins, providing a promising tool for structure-based therapeutic design on complex, dynamic targets. The D2R-MD dataset and our implementation are freely available to facilitate further research.


INSIGHT: A Survey of In-Network Systems for Intelligent, High-Efficiency AI and Topology Optimization

arXiv.org Artificial Intelligence

In-network computation represents a transformative approach to addressing the escalating demands of Artificial Intelligence (AI) workloads on network infrastructure. By leveraging the processing capabilities of network devices such as switches, routers, and Network Interface Cards (NICs), this paradigm enables AI computations to be performed directly within the network fabric, significantly reducing latency, enhancing throughput, and optimizing resource utilization. This paper provides a comprehensive analysis of optimizing in-network computation for AI, exploring the evolution of programmable network architectures, such as Software-Defined Networking (SDN) and Programmable Data Planes (PDPs), and their convergence with AI. It examines methodologies for mapping AI models onto resource-constrained network devices, addressing challenges like limited memory and computational capabilities through efficient algorithm design and model compression techniques. The paper also highlights advancements in distributed learning, particularly in-network aggregation, and the potential of federated learning to enhance privacy and scalability. Frameworks like Planter and Quark are discussed for simplifying development, alongside key applications such as intelligent network monitoring, intrusion detection, traffic management, and Edge AI. Future research directions, including runtime programma-bility, standardized benchmarks, and new applications paradigms, are proposed to advance this rapidly evolving field. This survey underscores the potential of in-network AI to create intelligent, efficient, and responsive networks capable of meeting the demands of next-generation AI applications.


Action is All You Need: Dual-Flow Generative Ranking Network for Recommendation

arXiv.org Artificial Intelligence

Deep Learning Recommendation Models (DLRMs) often rely on extensive manual feature engineering to improve accuracy and user experience, which increases system complexity and limits scalability of model performance with respect to computational resources. Recently, Meta introduced a generative ranking paradigm based on HSTU block that enables end-to-end learning from raw user behavior sequences and demonstrates scaling law on large datasets that can be regarded as the state-of-the-art (SOTA). However, splitting user behaviors into interleaved item and action information significantly increases the input sequence length, which adversely affects both training and inference efficiency. To address this issue, we propose the Dual-Flow Generative Ranking Network (DFGR), that employs a dual-flow mechanism to optimize interaction modeling, ensuring efficient training and inference through end-to-end token processing. DFGR duplicates the original user behavior sequence into a real flow and a fake flow based on the authenticity of the action information, and then defines a novel interaction method between the real flow and the fake flow within the QKV module of the self-attention mechanism. This design reduces computational overhead and improves both training efficiency and inference performance compared to Meta's HSTU-based model. Experiments on both open-source and real industrial datasets show that DFGR outperforms DLRM, which serves as the industrial online baseline with extensive feature engineering, as well as Meta's HSTU and other common recommendation models such as DIN, DCN, DIEN, and DeepFM. Furthermore, we investigate optimal parameter allocation strategies under computational constraints, establishing DFGR as an efficient and effective next-generation generative ranking paradigm.


From Templates to Natural Language: Generalization Challenges in Instruction-Tuned LLMs for Spatial Reasoning

arXiv.org Artificial Intelligence

Instruction-tuned large language models (LLMs) have shown strong performance on a variety of tasks; however, generalizing from synthetic to human-authored instructions in grounded environments remains a challenge for them. In this work, we study generalization challenges in spatial grounding tasks where models interpret and translate instructions for building object arrangements on a $2.5$D grid. We fine-tune LLMs using only synthetic instructions and evaluate their performance on a benchmark dataset containing both synthetic and human-written instructions. Our results reveal that while models generalize well on simple tasks, their performance degrades significantly on more complex tasks. We present a detailed error analysis of the gaps in instruction generalization.


Bridging Econometrics and AI: VaR Estimation via Reinforcement Learning and GARCH Models

arXiv.org Artificial Intelligence

Context: Forecasting stock returns is a long-standing challenge in financial economics, with significant implications for both risk management and regulatory compliance. Traditional econometric models such as GARCH (Bollerslev, 1986) capture volatility persistence but fail to fully account for key stylized facts of financial time series: fat tails, volatility clustering, and leverage effects (Glosten et al., 1993). Similarly, modern machine learning and deep learning methods, although capable of modeling nonlinear dynamics (Goodfellow et al., 2016; Tealab, 2018), tend to underperform during rare but impactful market shocks (Fawcett and Provost, 1997; Pokou, 2022). As illustrated in Figure 1, these limitations often result in systematic mispredictions of excess returns, especially in turbulent markets. These forecasting inaccuracies are critical because they directly translate into unreliable estimates of Value-at-Risk (VaR), the benchmark risk measure under Basel regulatory frameworks (on Banking Supervision, 2017). Overestimation inflates capital requirements, whereas underestimation exposes institutions to excessive losses. To mitigate these shortcomings, the recent literature has shifted from precise return forecasting to directional return prediction, reframe the task as a classification problem, determining whether returns will be positive or negative (Kanas, 2001; Nyberg, 2011; Alostad and Davulcu, 2017). Beyond the standard zero threshold, quantile and volatility-based criteria have been introduced to better isolate significant market movements (Chung and Hong, 2007; Linton and Whang, 2007).


Contemplative Artificial Intelligence

arXiv.org Artificial Intelligence

As artificial intelligence (AI) improves, traditional alignment strategies may falter in the face of unpredictable self-improvement, hidden subgoals, and the sheer complexity of intelligent systems. Inspired by contemplative wisdom traditions, we show how four axiomatic principles can instil a resilient Wise World Model in AI systems. First, mindfulness enables self-monitoring and recalibration of emergent subgoals. Second, emptiness forestalls dogmatic goal fixation and relaxes rigid priors. Third, non-duality dissolves adversarial self-other boundaries. Fourth, boundless care motivates the universal reduction of suffering. We find that prompting AI to reflect on these principles improves performance on the AILuminate Benchmark (d=.96) and boosts cooperation and joint-reward on the Prisoner's Dilemma task (d=7+). We offer detailed implementation strategies at the level of architectures, constitutions, and reinforcement on chain-of-thought. For future systems, active inference may offer the self-organizing and dynamic coupling capabilities needed to enact Contemplative AI in embodied agents.


Co-Writing with AI, on Human Terms: Aligning Research with User Demands Across the Writing Process

arXiv.org Artificial Intelligence

As generative AI tools like ChatGPT become integral to everyday writing, critical questions arise about how to preserve writers' sense of agency and ownership when using these tools. Yet, a systematic understanding of how AI assistance affects different aspects of the writing process - and how this shapes writers' agency - remains underexplored. To address this gap, we conducted a systematic review of 109 HCI papers using the PRISMA approach. From this literature, we identify four overarching design strategies for AI writing support: structured guidance, guided exploration, active co-writing, and critical feedback - mapped across the four key cognitive processes in writing: planning, translating, reviewing, and monitoring. We complement this analysis with interviews of 15 writers across diverse domains. Our findings reveal that writers' desired levels of AI intervention vary across the writing process: content-focused writers (e.g., academics) prioritize ownership during planning, while form-focused writers (e.g., creatives) value control over translating and reviewing. Writers' preferences are also shaped by contextual goals, values, and notions of originality and authorship. By examining when ownership matters, what writers want to own, and how AI interactions shape agency, we surface both alignment and gaps between research and user needs. Our findings offer actionable design guidance for developing human-centered writing tools for co-writing with AI, on human terms.


Quantization Hurts Reasoning? An Empirical Study on Quantized Reasoning Models

arXiv.org Artificial Intelligence

Recent advancements in reasoning language models have demonstrated remarkable performance in complex tasks, but their extended chain-of-thought reasoning process increases inference overhead. While quantization has been widely adopted to reduce the inference cost of large language models, its impact on reasoning models remains understudied. In this paper, we conduct the first systematic study on quantized reasoning models, evaluating the open-sourced DeepSeek-R1-Distilled Qwen and LLaMA families ranging from 1.5B to 70B parameters, QwQ-32B, and Qwen3-8B. Our investigation covers weight, KV cache, and activation quantization using state-of-the-art algorithms at varying bit-widths, with extensive evaluation across mathematical (AIME, MATH-500), scientific (GPQA), and programming (LiveCodeBench) reasoning benchmarks. Our findings reveal that while lossless quantization can be achieved with W8A8 or W4A16 quantization, lower bit-widths introduce significant accuracy risks. We further identify model size, model origin, and task difficulty as critical determinants of performance. Contrary to expectations, quantized models do not exhibit increased output lengths. In addition, strategically scaling the model sizes or reasoning steps can effectively enhance the performance. All quantized models and codes are open-sourced in https://github.com/ruikangliu/Quantized-Reasoning-Models.


Deep Positive-Negative Prototypes for Adversarially Robust Discriminative Prototypical Learning

arXiv.org Artificial Intelligence

Despite the advantages of discriminative prototype-based methods, their role in adversarial robustness remains underexplored. Meanwhile, current adversarial training methods predominantly focus on robustness against adversarial attacks without explicitly leveraging geometric structures in the latent space, usually resulting in reduced accuracy on the original clean data. We propose a novel framework named Adversarially trained Deep Positive-Negative Prototypes (Adv-DPNP), which integrates discriminative prototype-based learning with adversarial training. Adv-DPNP uses unified class prototypes that serve as both classifier weights and robust anchors in the latent space. Moreover, a novel dual-branch training mechanism maintains stable prototypes by updating them exclusively with clean data, while the feature extractor is trained on both clean and adversarial inputs to increase invariance to adversarial perturbations. In addition, we use a composite loss that combines positive-prototype alignment, negative-prototype repulsion, and consistency regularization to further enhance discrimination, adversarial robustness, and clean accuracy. Extensive experiments on standard benchmarks (CIFAR-10/100 and SVHN) confirm that Adv-DPNP improves clean accuracy over state-of-the-art defenses and baseline methods, while maintaining competitive or superior robustness under a suite of widely used attacks, including FGSM, PGD, C\&W, and AutoAttack. We also evaluate robustness to common corruptions on CIFAR-10-C, where Adv-DPNP achieves the highest average accuracy across severities and corruption types. Additionally, we provide an in-depth analysis of the discriminative quality of the learned feature representations, highlighting the effectiveness of Adv-DPNP in maintaining compactness and clear separation in the latent space.


Advancing AI-Scientist Understanding: Multi-Agent LLMs with Interpretable Physics Reasoning

arXiv.org Artificial Intelligence

Large Language Models (LLMs) are playing an increasingly important role in physics research by assisting with symbolic manipulation, numerical computation, and scientific reasoning. However, ensuring the reliability, transparency, and interpretability of their outputs remains a major challenge. In this work, we introduce a novel multi-agent LLM physicist framework that fosters collaboration between AI and human scientists through three key modules: a reasoning module, an interpretation module, and an AI-scientist interaction module. Recognizing that effective physics reasoning demands logical rigor, quantitative accuracy, and alignment with established theoretical models, we propose an interpretation module that employs a team of specialized LLM agents-including summarizers, model builders, visualization tools, and testers-to systematically structure LLM outputs into transparent, physically grounded science models. A case study demonstrates that our approach significantly improves interpretability, enables systematic validation, and enhances human-AI collaboration in physics problem-solving and discovery. Our work bridges free-form LLM reasoning with interpretable, executable models for scientific analysis, enabling more transparent and verifiable AI-augmented research.