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 Deep Learning


Enhancing Fractional Gradient Descent with Learned Optimizers

arXiv.org Machine Learning

Fractional Gradient Descent (FGD) offers a novel and promising way to accelerate optimization by incorporating fractional calculus into machine learning. Although FGD has shown encouraging initial results across various optimization tasks, it faces significant challenges with convergence behavior and hyperparameter selection. Moreover, the impact of its hyperparameters is not fully understood, and scheduling them is particularly difficult in non-convex settings such as neural network training. To address these issues, we propose a novel approach called Learning to Optimize Caputo Fractional Gradient Descent (L2O-CFGD), which meta-learns how to dynamically tune the hyperparameters of Caputo FGD (CFGD). Our method's meta-learned schedule outperforms CFGD with static hyperparameters found through an extensive search and, in some tasks, achieves performance comparable to a fully black-box meta-learned optimizer. L2O-CFGD can thus serve as a powerful tool for researchers to identify high-performing hyperparameters and gain insights on how to leverage the history-dependence of the fractional differential in optimization.


Protein generation with embedding learning for motif diversification

arXiv.org Machine Learning

A fundamental challenge in protein design is the trade-off between generating structural diversity while preserving motif biological function. Current state-of-the-art methods, such as partial diffusion in RFdiffusion, often fail to resolve this trade-off: small perturbations yield motifs nearly identical to the native structure, whereas larger perturbations violate the geometric constraints necessary for biological function. We introduce Protein Generation with Embedding Learning (PGEL), a general framework that learns high-dimensional embeddings encoding sequence and structural features of a target motif in the representation space of a diffusion model's frozen denoiser, and then enhances motif diversity by introducing controlled perturbations in the embedding space. PGEL is thus able to loosen geometric constraints while satisfying typical design metrics, leading to more diverse yet viable structures. We demonstrate PGEL on three representative cases: a monomer, a protein-protein interface, and a cancer-related transcription factor complex. In all cases, PGEL achieves greater structural diversity, better designability, and improved self-consistency, as compared to partial diffusion. Our results establish PGEL as a general strategy for embedding-driven protein generation allowing for systematic, viable diversification of functional motifs.


A Frequentist Statistical Introduction to Variational Inference, Autoencoders, and Diffusion Models

arXiv.org Machine Learning

While Variational Inference (VI) is central to modern generative models like Variational Autoencoders (VAEs) and Denoising Diffusion Models (DDMs), its pedagogical treatment is split across disciplines. In statistics, VI is typically framed as a Bayesian method for posterior approximation. In machine learning, however, VAEs and DDMs are developed from a Frequentist viewpoint, where VI is used to approximate a maximum likelihood estimator. This creates a barrier for statisticians, as the principles behind VAEs and DDMs are hard to contextualize without a corresponding Frequentist introduction to VI. This paper provides that introduction: we explain the theory for VI, VAEs, and DDMs from a purely Frequentist perspective, starting with the classical Expectation-Maximization (EM) algorithm. We show how VI arises as a scalable solution for intractable E-steps and how VAEs and DDMs are natural, deep-learning-based extensions of this framework, thereby bridging the gap between classical statistical inference and modern generative AI.


Interval Prediction of Annual Average Daily Traffic on Local Roads via Quantile Random Forest with High-Dimensional Spatial Data

arXiv.org Machine Learning

Accurate annual average daily traffic (AADT) data are vital for transport planning and infrastructure management. However, automatic traffic detectors across national road networks often provide incomplete coverage, leading to underrepresentation of minor roads. While recent machine learning advances have improved AADT estimation at unmeasured locations, most models produce only point predictions and overlook estimation uncertainty. This study addresses that gap by introducing an interval prediction approach that explicitly quantifies predictive uncertainty. We integrate a Quantile Random Forest model with Principal Component Analysis to generate AADT prediction intervals, providing plausible traffic ranges bounded by estimated minima and maxima. Using data from over 2,000 minor roads in England and Wales, and evaluated with specialized interval metrics, the proposed method achieves an interval coverage probability of 88.22%, a normalized average width of 0.23, and a Winkler Score of 7,468.47. By combining machine learning with spatial and high-dimensional analysis, this framework enhances both the accuracy and interpretability of AADT estimation, supporting more robust and informed transport planning.


Uncertainty Estimation by Flexible Evidential Deep Learning

arXiv.org Machine Learning

Uncertainty quantification (UQ) is crucial for deploying machine learning models in high-stakes applications, where overconfident predictions can lead to serious consequences. An effective UQ method must balance computational efficiency with the ability to generalize across diverse scenarios. Evidential deep learning (EDL) achieves efficiency by modeling uncertainty through the prediction of a Dirichlet distribution over class probabilities. However, the restrictive assumption of Dirichlet-distributed class probabilities limits EDL's robustness, particularly in complex or unforeseen situations. To address this, we propose \textit{flexible evidential deep learning} ($\mathcal{F}$-EDL), which extends EDL by predicting a flexible Dirichlet distribution -- a generalization of the Dirichlet distribution -- over class probabilities. This approach provides a more expressive and adaptive representation of uncertainty, significantly enhancing UQ generalization and reliability under challenging scenarios. We theoretically establish several advantages of $\mathcal{F}$-EDL and empirically demonstrate its state-of-the-art UQ performance across diverse evaluation settings, including classical, long-tailed, and noisy in-distribution scenarios.


Generalization Below the Edge of Stability: The Role of Data Geometry

arXiv.org Machine Learning

Understanding generalization in overparameterized neural networks hinges on the interplay between the data geometry, neural architecture, and training dynamics. In this paper, we theoretically explore how data geometry controls this implicit bias. This paper presents theoretical results for overparameterized two-layer ReLU networks trained below the edge of stability. First, for data distributions supported on a mixture of low-dimensional balls, we derive generalization bounds that provably adapt to the intrinsic dimension. Second, for a family of isotropic distributions that vary in how strongly probability mass concentrates toward the unit sphere, we derive a spectrum of bounds showing that rates deteriorate as the mass concentrates toward the sphere. These results instantiate a unifying principle: When the data is harder to "shatter" with respect to the activation thresholds of the ReLU neurons, gradient descent tends to learn representations that capture shared patterns and thus finds solutions that generalize well. On the other hand, for data that is easily shattered (e.g., data supported on the sphere) gradient descent favors memorization. Our theoretical results consolidate disparate empirical findings that have appeared in the literature.


VERA-V: Variational Inference Framework for Jailbreaking Vision-Language Models

arXiv.org Machine Learning

Vision-Language Models (VLMs) extend large language models with visual reasoning, but their multimodal design also introduces new, underexplored vulnerabilities. Existing multimodal red-teaming methods largely rely on brittle templates, focus on single-attack settings, and expose only a narrow subset of vulnerabilities. To address these limitations, we introduce VERA-V, a variational inference framework that recasts multimodal jailbreak discovery as learning a joint posterior distribution over paired text-image prompts. This probabilistic view enables the generation of stealthy, coupled adversarial inputs that bypass model guardrails. We train a lightweight attacker to approximate the posterior, allowing efficient sampling of diverse jailbreaks and providing distributional insights into vulnerabilities. VERA-V further integrates three complementary strategies: (i) typography-based text prompts that embed harmful cues, (ii) diffusion-based image synthesis that introduces adversarial signals, and (iii) structured distractors to fragment VLM attention. Experiments on HarmBench and HADES benchmarks show that VERA-V consistently outperforms state-of-the-art baselines on both open-source and frontier VLMs, achieving up to 53.75% higher attack success rate (ASR) over the best baseline on GPT-4o.


Memorizing Long-tail Data Can Help Generalization Through Composition

arXiv.org Machine Learning

The relationship between memorization and generalization has always been an intriguing topic in deep learning. It has long been known that neural networks used for supervised learning can memorize noisy or even random labels (Zhang et al., 2017), and recent large language models can still memorize long text despite not being overparametrized (Carlini et al., 2019, 2022). Conventional wisdom from statistical learning theory suggests that memorization might be detrimental to generalization performance, yet neural networks often generalize well with memorization, sometimes even better compared to networks that do not memorize. Trying to understand this relationship from a theoretical perspective has led to the idea of implicit regularization and benign overfitting (Belkin et al., 2019; Bartlett et al., 2020; Belkin et al., 2020; Hastie et al., 2022; Gunasekar et al., 2017), where the training process and architecture choices of neural networks prefer certain solutions that have good generalization despite memorizing the training data. Another interesting line of work (Feldman, 2020; Feldman and Zhang, 2020) demonstrated that memorization can actively help generalization by capturing long-tail behaviors in the training data.


OpenAI launches AI browser Atlas in latest challenge to Google

The Japan Times

OpenAI has unveiled ChatGPT Atlas, a long-anticipated artificial intelligence-powered web browser built around its popular chatbot, in a direct challenge to Google Chrome's dominance. OpenAI on Tuesday unveiled ChatGPT Atlas, a long-anticipated artificial intelligence-powered web browser built around its popular chatbot, in a direct challenge to Google Chrome's dominance. The launch marks OpenAI's latest move to capitalize on 800 million weekly active ChatGPT users, as it expands into more aspects of users' online lives by collecting data about consumers' browser behavior. It could accelerate a broader shift toward AI-driven search, as users increasingly turn to conversational tools that synthesize information instead of relying on traditional keyword-based results from Google -- intensifying competition between OpenAI and Google. Shares of Alphabet, which owns the Chrome browser, were down 1.8% in afternoon trading.


A I-designed compounds can kill drug-resistant bacteria

MIT Technology Review

An MIT team used artificial intelligence to design novel antibiotics, two of which showed promise against MRSA and gonorrhea. With help from artificial intelligence, MIT researchers have designed novel antibiotics that can combat two hard-to-treat bacteria: multi-drug-resistant and (MRSA). The team used two approaches. First, they directed generative AI to design molecules based on a chemical fragment their model had predicted would show antimicrobial activity, and second, they let the algorithms generate molecules without constraints. They designed more than 36 million possible compounds this way and computationally screened them for antimicrobial properties. The top candidates they discovered are structurally distinct from any existing antibiotics, and they appear to work by novel mechanisms that disrupt bacterial cell membranes.