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Applications · Health / Medicine

Etowah Adams, Liam Bai, Minji Lee, Yiyang Yu, Mohammed AlQuraishi

Protein language models (pLMs) are powerful predictors of protein structure and function, learning through unsupervised training on millions of protein sequences. pLMs are thought to capture common motifs in protein sequences, but the specifics of pLM features are not well understood. Identifying these features would not only shed light on how pLMs work, but potentially uncover novel protein biology––studying the model to study the biology. Motivated by this, we train sparse autoencoders (SAEs) on the residual stream of a pLM, ESM-2. By characterizing SAE features, we determine that pLMs use a combination of generic features and family-specific features to represent a protein. In addition, we demonstrate how known sequence determinants of properties such as thermostability and subcellular localization can be identified by linear probing of SAE features. For predictive features without known functional associations, we hypothesize their role in unknown mechanisms and provide visualization tools to aid their interpretation. Our study gives a better understanding of the limitations of pLMs, and demonstrates how SAE features can be used to help generate hypotheses for biological mechanisms. We release our code, model weights, and feature visualizer.

Deep Learning · Algorithms

Dongyeop Lee, Kwanhee Lee, Jinseok Chung, Namhoon Lee

Sparsifying neural networks often suffers from seemingly inevitable performance degradation, and it remains challenging to restore the original performance despite much recent progress.Motivated by recent studies in robust optimization, we aim to tackle this problem by finding subnetworks that are both sparse and flat at the same time.Specifically, we formulate pruning as a sparsity-constrained optimization problem where flatness is encouraged as an objective.We solve it explicitly via an augmented Lagrange dual approach and extend it further by proposing a generalized projection operation, resulting in novel pruning methods called SAFE and its extension, SAFE$^+$.Extensive evaluations on standard image classification and language modeling tasks reveal that SAFE consistently yields sparse networks with improved generalization performance, which compares competitively to well-established baselines.In addition, SAFE demonstrates resilience to noisy data, making it well-suited for real-world conditions.

Probabilistic Methods · Monte Carlo and Sampling Methods

Jie Hu, Yi-Ting Ma, Do-Young Eun

We propose a *history-driven target (HDT)* framework in Markov Chain Monte Carlo (MCMC) to improve any random walk algorithm on discrete state spaces, such as general undirected graphs, for efficient sampling from target distribution $\\boldsymbol{\\mu}$. With broad applications in network science and distributed optimization, recent innovations like the self-repellent random walk (SRRW) achieve near-zero variance by prioritizing under-sampled states through transition kernel modifications based on past visit frequencies. However, SRRW's reliance on explicit computation of transition probabilities for all neighbors at each step introduces substantial computational overhead, while its strict dependence on time-reversible Markov chains excludes advanced non-reversible MCMC methods. To overcome these limitations, instead of direct modification of transition kernel, HDT introduces a history-dependent target distribution $\\boldsymbol{\\pi}[\\mathbf{x}]$ to replace the original target $\\boldsymbol{\\mu}$ in any graph sampler, where $\\mathbf{x}$ represents the empirical measure of past visits. This design preserves lightweight implementation by requiring only local information between the current and proposed states and achieves compatibility with both reversible and non-reversible MCMC samplers, while retaining unbiased samples with target distribution $\\boldsymbol{\\mu}$ and near-zero variance performance. Extensive experiments in graph sampling demonstrate consistent performance gains, and a memory-efficient Least Recently Used (LRU) cache ensures scalability to large general graphs.

Deep Learning · Other Representation Learning

Shizhan Gong, Yankai Jiang, DOU QI, Farzan Farnia

Vision-language models, such as CLIP, have achieved significant success in aligning visual and textual representations, becoming essential components of many multi-modal large language models (MLLMs) like LLaVA and OpenFlamingo. However, numerous studies have identified CLIP's limited fine-grained perception as a critical drawback, leading to substantial failures in downstream MLLMs. In contrast, vision-centric foundation models like DINOv2 demonstrate remarkable capabilities in capturing fine details from images. In this work, we propose a novel kernel-based method to align CLIP's visual representation with that of DINOv2, ensuring that the resulting embeddings maintain compatibility with text embeddings while enhancing perceptual capabilities. Our alignment objective is designed for efficient stochastic optimization. Following this image-only alignment fine-tuning, the visual encoder retains compatibility with the frozen text encoder and exhibits significant improvements in zero-shot object recognition, fine-grained spatial reasoning, and localization. By integrating the aligned visual encoder, downstream MLLMs also demonstrate enhanced performance. The code and models are available at https://github.com/peterant330/KUEA.

Deep Learning · Large Language Models

Gaotang Li, Yuzhong Chen, Hanghang Tong

Language Models (LMs) often encounter knowledge conflicts when parametric memory contradicts contextual knowledge. Previous works attribute this conflict to the interplay between "memory heads" and "context heads", attention heads assumed to promote either memory or context exclusively. In this study, we go beyond this fundamental assumption by uncovering a critical phenomenon we term the *superposition of contextual information and parametric memory*, where highly influential attention heads simultaneously contribute to both memory and context. Building upon this insight, we propose Just Run Twice (JuICE), a test-time attention intervention method that steers LMs toward either parametric beliefs or contextual knowledge without requiring fine-tuning. JuICE identifies a set of reliable attention heads and leverages a dual-run approach to mitigate the superposition effects. Extensive experiments across 11 datasets and 6 model architectures demonstrate that JuICE sets the new state-of-the-art performance and robust generalization, achieving significant and consistent improvement across different domains under various conflict types. Finally, we theoretically analyze knowledge conflict and the superposition of contextual information and parametric memory in attention heads, which further elucidates the effectiveness of JuICE in these settings. Our code is available at https://github.com/GaotangLi/JUICE.

Deep Learning · Generative Models and Autoencoders

Yuang Zhang, Jiaxi Gu, Li-Wen Wang, Han Wang, JunqiCheng, Yuefeng Zhu, FangYuan Zou

In recent years, while generative AI has advanced significantly in image generation, video generation continues to face challenges in controllability, length, and detail quality, which hinder its application. We present MimicMotion, a framework for generating high-quality human videos of arbitrary length using motion guidance. Our approach has several highlights. Firstly, we introduce confidence-aware pose guidance that ensures high frame quality and temporal smoothness. Secondly, we introduce regional loss amplification based on pose confidence, which reduces image distortion in key regions. Lastly, we propose a progressive latent fusion strategy to generate long and smooth videos. Experiments demonstrate the effectiveness of our approach in producing high-quality human motion videos. Videos and comparisons are available at [https://tencent.github.io/MimicMotion](https://tencent.github.io/MimicMotion).

Theory · Learning Theory

Amir R. Asadi

Machine learning, the predominant approach in the field of artificial intelligence, enables computers to learn from data and experience. In the supervised learning framework, accurate and efficient learning of dependencies between data instances and their corresponding labels requires auxiliary information about the data distribution and the target function. This central concept aligns with the notion of regularization in statistical learning theory. Real-world datasets are often characterized by multiscale data instance distributions and well-behaved, smooth target functions. Scale-invariant probability distributions, such as power-law distributions, provide notable examples of multiscale data instance distributions in various contexts. This paper introduces a hierarchical learning model that leverages such a multiscale data structure with a multiscale entropy-based training procedure and explores its statistical and computational advantages. The hierarchical learning model is inspired by the logical progression in human learning from easy to complex tasks and features interpretable levels. In this model, the logarithm of any data instance’s norm can be construed as the data instance's complexity, and the allocation of computational resources is tailored to this complexity, resulting in benefits such as increased inference speed. Furthermore, our multiscale analysis of the statistical risk yields stronger guarantees compared to conventional uniform convergence bounds.

General Machine Learning · Evaluation

Chengpiao Huang, Yuhang Wu, Kaizheng Wang

We investigate the use of large language models (LLMs) to simulate human responses to survey questions, and perform uncertainty quantification to gain reliable insights. Our approach converts imperfect, LLM-simulated responses into confidence sets for population parameters of human responses, addressing the distribution shift between the simulated and real populations. A key innovation lies in determining the optimal number of simulated responses: too many produce overly narrow confidence sets with poor coverage, while too few yield excessively loose estimates. To resolve this, our method adaptively selects the simulation sample size, ensuring valid average-case coverage guarantees. It is broadly applicable to any LLM, irrespective of its fidelity, and any procedure for constructing confidence sets. Additionally, the selected sample size quantifies the degree of misalignment between the LLM and the target human population. We illustrate our method on real datasets and LLMs.

Position · Risk_safety_policy

Haoming Jing, Yorie Nakahira

Many systems contain latent variables that make their dynamics partially unidentifiable or cause distribution shifts in the observed statistics between offline and online data. However, existing control techniques often assume access to complete dynamics or perfect simulators with fully observable states, which are necessary to verify whether the system remains within a safe set (forward invariance) or safe actions are consistently feasible at all times. To address this limitation, we propose a technique for designing probabilistic safety certificates for systems with latent variables. A key technical enabler is the formulation of invariance conditions in probability space, which can be constructed using observed statistics in the presence of distribution shifts due to latent variables. We use this invariance condition to construct a safety certificate that can be implemented efficiently in real-time control. The proposed safety certificate can continuously find feasible actions that control long-term risk to stay within tolerance. Stochastic safe control and (causal) reinforcement learning have been studied in isolation until now. To the best of our knowledge, the proposed work is the first to use causal reinforcement learning to quantify long-term risk for the design of safety certificates. This integration enables safety certificates to efficiently ensure long-term safety in the presence of latent variables. The effectiveness of the proposed safety certificate is demonstrated in numerical simulations.

Deep Learning · Sequential Models, Time series

Wenjie Wu, Dexuan Huo, Hong Chen

Spiking Neural Networks (SNNs) have demonstrated remarkable potential across many domains, including computer vision and natural language processing, owing to their energy efficiency and biological plausibility. However, their application in long-term prediction tasks remains underexplored, which is primarily due to two critical challenges: (1) current SNN encoding methods are unable to effectively encode long temporal information, leading to increased computational complexity and energy consumption; (2) though Transformer-based models have achieved state-of-the-art accuracy in temporal prediction tasks, the absence of proper positional encoding for spiking self-attention restricts Spiking Transformer from effectively utilizing positional information, resulting in performance degradation. To address these challenges, we introduce an attention-free framework, **Spik**ing **F**ourier Network (**SpikF**), that encodes input sequences in patches and employs an innovative frequency domain selection mechanism to effectively utilize the sequential properties of time-series data. Extensive evaluations on eight well-established long-term prediction datasets demonstrate that SpikF achieves an averaged $1.9\\%$ reduction in Mean Absolute Error (MAE) compared to state-of-the-art models, while lowering total energy consumption by $3.16\times$. Our code is available at https://github.com/WWJ-creator/SpikF.

Deep Learning · Generative Models and Autoencoders

Ignacio Peis, Batuhan Koyuncu, Isabel Valera, Jes Frellsen

We introduce a novel generative framework for functions by integrating Implicit Neural Representations (INRs) and Transformer-based hypernetworks into latent variable models. Unlike prior approaches that rely on MLP-based hypernetworks with scalability limitations, our method employs a Transformer-based decoder to generate INR parameters from latent variables, addressing both representation capacity and computational efficiency. Our framework extends latent diffusion models (LDMs) to INR generation by replacing standard decoders with a Transformer-based hypernetwork, which can be trained either from scratch or via hyper-transforming—a strategy that fine-tunes only the decoder while freezing the pre-trained latent space. This enables efficient adaptation of existing generative models to INR-based representations without requiring full retraining. We validate our approach across multiple modalities, demonstrating improved scalability, expressiveness, and generalization over existing INR-based generative models. Our findings establish a unified and flexible framework for learning structured function representations.

Deep Learning · Generative Models and Autoencoders

Zhengqi Gao, Kaiwen Zha, Tianyuan Zhang, Zihui Xue, Duane Boning

Guidance techniques are simple yet effective for improving conditional generation in diffusion models. Albeit their empirical success, the practical implementation of guidance diverges significantly from its theoretical motivation. In this paper, we reconcile this discrepancy by replacing the scaled marginal distribution target, which we prove theoretically invalid, with a valid scaled joint distribution objective. Additionally, we show that the established guidance implementations are approximations to the intractable optimal solution under no future foresight constraint. Building on these theoretical insights, we propose rectified gradient guidance (REG), a versatile enhancement designed to boost the performance of existing guidance methods. Experiments on 1D and 2D demonstrate that REG provides a better approximation to the optimal solution than prior guidance techniques, validating the proposed theoretical framework. Extensive experiments on class-conditional ImageNet and text-to-image generation tasks show that incorporating REG consistently improves FID and Inception/CLIP scores across various settings compared to its absence.

General Machine Learning · Online Learning, Active Learning and Bandits

Osman Berke Guney, Ketan Saichandran, Karim Elzokm, Ziming Zhang, Vijaya Kolachalama

In many practical applications, including medicine, acquiring all relevant data for machine learning models is often infeasible due to constraints on time, cost, and resources. This makes it important to selectively acquire only the most informative features, yet traditional static feature selection methods fall short in scenarios where feature importance varies across instances. Here, we propose an active feature acquisition (AFA) framework, which dynamically selects features based on their importance to each individual case. Our method leverages local explanation techniques to generate instance-specific feature importance rankings. We then reframe the AFA problem as a feature prediction task, introducing a policy network grounded in a decision transformer architecture. This policy network is trained to select the next most informative feature by learning from the feature importance rankings. As a result, features are acquired sequentially, ordered by their predictive significance, leading to more efficient feature selection and acquisition. Extensive experiments on multiple datasets demonstrate that our approach outperforms current state-of-the-art AFA methods in both predictive accuracy and feature acquisition efficiency. These findings highlight the promise of an explainability-driven AFA strategy in scenarios where the cost of feature acquisition is a key concern.

Probabilistic Methods · Monte Carlo and Sampling Methods

Narayan Srinivasan, Matthew Sutton, Christopher Drovandi, Leah South

We propose a novel method for measuring the discrepancy between a set of samples and a desired posterior distribution for Bayesian inference. Classical methods for assessing sample quality like the effective sample size are not appropriate for scalable Bayesian sampling algorithms, such as stochastic gradient Langevin dynamics, that are asymptotically biased. Instead, the gold standard is to use the kernel Stein Discrepancy (KSD), which is itself not scalable given its quadratic cost in the number of samples. The KSD and its faster extensions also typically suffer from the curse-of-dimensionality and can require extensive tuning. To address these limitations, we develop the polynomial Stein discrepancy (PSD) and an associated goodness-of-fit test. While the new test is not fully convergence-determining, we prove that it detects differences in the first $r$ moments for Gaussian targets. We empirically show that the test has higher power than its competitors in several examples, and at a lower computational cost. Finally, we demonstrate that the PSD can assist practitioners to select hyper-parameters of Bayesian sampling algorithms more efficiently than competitors.

Reyhane Askari Hemmat, Mohammad Pezeshki, Elvis Dohmatob, Florian Bordes, Pietro Astolfi, Melissa Hall, Jakob Verbeek, Michal Drozdzal, Adriana Romero-Soriano

Inspired by the principle of deliberate practice in human learning, we propose Deliberate Practice for Synthetic Data Generation (DP), a novel framework that improves sample efficiency through dynamic synthetic data generation. Prior work has shown that scaling synthetic data is inherently challenging, as naively adding new data leads to diminishing returns. To address this, pruning has been identified as a key mechanism for improving scaling, enabling models to focus on the most informative synthetic samples. Rather than generating a large dataset and pruning it afterward, DP efficiently approximates the direct generation of informative samples. We theoretically show how training on challenging, informative examples improves scaling laws and empirically validate that DP achieves better scaling performance with significantly fewer training samples and iterations. On ImageNet-100, DP generates 3.4x fewer samples and requires six times fewer iterations, while on ImageNet-1k, it generates 8x fewer samples with a 30% reduction in iterations, all while achieving superior performance compared to prior work.

Probabilistic Methods · Monte Carlo and Sampling Methods

Jie Hu, Yi-Ting Ma, Do-Young Eun

We propose a *history-driven target (HDT)* framework in Markov Chain Monte Carlo (MCMC) to improve any random walk algorithm on discrete state spaces, such as general undirected graphs, for efficient sampling from target distribution $\\boldsymbol{\\mu}$. With broad applications in network science and distributed optimization, recent innovations like the self-repellent random walk (SRRW) achieve near-zero variance by prioritizing under-sampled states through transition kernel modifications based on past visit frequencies. However, SRRW's reliance on explicit computation of transition probabilities for all neighbors at each step introduces substantial computational overhead, while its strict dependence on time-reversible Markov chains excludes advanced non-reversible MCMC methods. To overcome these limitations, instead of direct modification of transition kernel, HDT introduces a history-dependent target distribution $\\boldsymbol{\\pi}[\\mathbf{x}]$ to replace the original target $\\boldsymbol{\\mu}$ in any graph sampler, where $\\mathbf{x}$ represents the empirical measure of past visits. This design preserves lightweight implementation by requiring only local information between the current and proposed states and achieves compatibility with both reversible and non-reversible MCMC samplers, while retaining unbiased samples with target distribution $\\boldsymbol{\\mu}$ and near-zero variance performance. Extensive experiments in graph sampling demonstrate consistent performance gains, and a memory-efficient Least Recently Used (LRU) cache ensures scalability to large general graphs.

Deep Learning · Large Language Models

Tom A. Lamb, Adam Davies, Alasdair J Paren, Phil Torr, Francesco Pinto

Despite the success of Instruction Tuning (IT) in training large language models (LLMs), such models often leverage spurious or biased features learnt from their training data and can become misaligned, leading to undesired behaviours. While existing techniques can steer model behaviour at inference-time, they are often post-hoc and do not embed steering as an intrinsic model feature. In this work, we introduce Focus Instruction Tuning (FIT), which trains LLMs to condition their responses by focusing on specific features whilst ignoring others, leading to different behaviours based on what features are specified. Across diverse benchmarks, we demonstrate that FIT: (i) successfully steers behaviour at inference time; (ii) increases robustness by amplifying core task signals and down-weighting spurious cues; (iii) mitigates social bias by suppressing demographic attributes; and (iv) generalises under distribution shifts and to previously unseen focus features. FIT therefore offers a lightweight, intrinsic mechanism for building more robust, fair, and easily controllable LLMs.

Unai Fischer Abaigar, Christoph Kern, Juan Perdomo

Machine learning is increasingly used in government programs to identify and support the most vulnerable individuals, prioritizing assistance for those at greatest risk over optimizing aggregate outcomes. This paper examines the welfare impacts of prediction in equity-driven contexts, and how they compare to other policy levers, such as expanding bureaucratic capacity. Through mathematical models and a real-world case study on long-term unemployment amongst German residents, we develop a comprehensive understanding of the relative effectiveness of prediction in surfacing the worst-off. Our findings provide clear analytical frameworks and practical, data-driven tools that empower policymakers to make principled decisions when designing these systems.

Santhosh Karnik, Anna Veselovska, Mark Iwen, Felix Krahmer

We provide a rigorous analysis of implicit regularization in an overparametrized tensor factorization problem beyond the lazy training regime. For matrix factorization problems, this phenomenon has been studied in a number of works. A particular challenge has been to design universal initialization strategies which provably lead to implicit regularization in gradient-descent methods. At the same time, it has been argued by Cohen et. al. 2016 that more general classes of neural networks can be captured by considering tensor factorizations. However, in the tensor case, implicit regularization has only been rigorously established for gradient flow or in the lazy training regime. In this paper, we prove the first tensor result of its kind for gradient descent rather than gradient flow. We focus on the tubal tensor product and the associated notion of low tubal rank, encouraged by the relevance of this model for image data. We establish that gradient descent in an overparametrized tensor factorization model with a small random initialization exhibits an implicit bias towards solutions of low tubal rank. Our theoretical findings are illustrated in an extensive set of numerical simulations show-casing the dynamics predicted by our theory as well as the crucial role of using a small random initialization.

Shuangfei Zhai, Ruixiang Zhang, Preetum Nakkiran, David Berthelot, Jiatao Gu, Huangjie Zheng, Tianrong Chen, Miguel Angel Bautista Martin, Navdeep Jaitly, Joshua M Susskind

Normalizing Flows (NFs) are likelihood-based models for continuous inputs. They have demonstrated promising results on both density estimation and generative modeling tasks, but have received relatively little attention in recent years. In this work, we demonstrate that NFs are more powerful than previously believed. We present TarFlow: a simple and scalable architecture that enables highly performant NF models. TarFlow can be thought of as a Transformer-based variant of Masked Autoregressive Flows (MAFs): it consists of a stack of autoregressive Transformer blocks on image patches, alternating the autoregression direction between layers. TarFlow is straightforward to train end-to-end, and capable of directly modeling and generating pixels. We also propose three key techniques to improve sample quality: Gaussian noise augmentation during training, a post training denoising procedure, and an effective guidance method for both class-conditional and unconditional settings. Putting these together, TarFlow sets new state-of-the-art results on likelihood estimation for images, beating the previous best methods by a large margin, and generates samples with quality and diversity comparable to diffusion models, for the first time with a stand-alone NF model. We make our code available at https://github.com/apple/ml-tarflow.