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General Machine Learning · Scalable Algorithms

Nate Veldt, Thomas Stanley, Benjamin Priest, Trevor Steil, Keita Iwabuchi, T.S. Jayram, Geoffrey Sanders

Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a framework for metric MSTs that first (1) finds a forest of trees using practical heuristics, and then (2) finds a small weight set of edges to connect disjoint components in the forest into a spanning tree. We prove that optimally solving step (2) still takes $\Omega(n^2)$ time, but we provide a subquadratic 2.62-approximation algorithm. In the spirit of learning-augmented algorithms, we then show that if the heuristic forest found in step (1) overlaps with an optimal MST, we can approximate the original MST problem in subquadratic time, where the approximation factor depends on a measure of overlap. In practice, we find nearly optimal spanning trees for a wide range of metrics, while being orders of magnitude faster than exact algorithms.

Probabilistic Methods

Charita Dellaporta, Patrick O'Hara, Theodoros Damoulas

Decision making under uncertainty is challenging as the data-generating process (DGP) is often unknown. Bayesian inference proceeds by estimating the DGP through posterior beliefs on the model’s parameters. However, minimising the expected risk under these beliefs can lead to suboptimal decisions due to model uncertainty or limited, noisy observations. To address this, we introduce Distributionally Robust Optimisation with Bayesian Ambiguity Sets (DRO-BAS) which hedges against model uncertainty by optimising the worst-case risk over a posterior-informed ambiguity set. We provide two such sets, based on the posterior expectation (DRO-BAS(PE)) or the posterior predictive (DRO-BAS(PP)) and prove that both admit, under conditions, strong dual formulations leading to efficient single-stage stochastic programs which are solved with a sample average approximation. For DRO-BAS(PE), this covers all conjugate exponential family members while for DRO-BAS(PP) this is shown under conditions on the predictive's moment generating function. Our DRO-BAS formulations outperform existing Bayesian DRO on the Newsvendor problem and achieve faster solve times with comparable robustness on the Portfolio problem.

Applications · Everything Else

Dihan Zheng, Bo Huang

Fluorescence microscopy is ubiquitously used in cell biology research to characterize the cellular role of a protein. To help elucidate the relationship between the amino acid sequence of a protein and its cellular function, we introduce CELL-Diff, a unified diffusion model facilitating bidirectional transformations between protein sequences and their corresponding microscopy images. Utilizing reference cell morphology images and a protein sequence, CELL-Diff efficiently generates corresponding protein images. Conversely, given a protein image, the model outputs protein sequences. CELL-Diff integrates continuous and diffusion models within a unified framework and is implemented using a transformer-based network. We train CELL-Diff on the Human Protein Atlas (HPA) dataset and fine-tune it on the OpenCell dataset. Experimental results demonstrate that CELL-Diff outperforms existing methods in generating high-fidelity protein images, making it a practical tool for investigating subcellular protein localization and interactions.

Deep Learning · Large Language Models

Fangxu Yu, Lai Jiang, Haoqiang Kang, Shibo Hao, Lianhui Qin

The ability to generate diverse solutions to a given problem is a hallmark of human creativity. This divergent reasoning is also crucial for machines, enhancing their robustness and enabling them to assist humans in many applications such as scientific discovery. However, existing approaches to multi-step reasoning with large language models (LLMs) have mostly focused only on reasoning accuracy, without further discovering more diverse valid solutions. For example, supervised fine-tuning improves reasoning quality but requires vast labeled data, while reward-maximizing reinforcement learning finds top-reward solutions while neglecting the solution diversity. To fill this gap, we propose Flow of Reasoning (FoR), an efficient diversity-seeking LLM finetuning method aimed at improving reasoning quality and diversity with minimal data. FoR formulates multi-step LLM reasoning as a Markovian flow on a DAG-structured reasoning graph. This formulation allows us to incorporate and adapt principled GFlowNet approaches, for finetuning LLMs to sample divergent paths with probabilities proportional to the (unnormalized) reward of target problems. Extensive experiments show that, with limited training examples (e.g., 15 examples), FoR enables the discovery of diverse, creative, high-quality solutions, greatly outperforming a wide range of existing inference and training methods across six challenging reasoning tasks, including BlocksWorld (embodied reasoning), Game24 (math puzzle solving), Rubik's Cube (spatial reasoning), 1D-ARC (abstraction reasoning), GSM8k (math reasoning), and ProntoQA (logical reasoning). Code is available at https://github.com/Yu-Fangxu/FoR.

Probabilistic Methods · Monte Carlo and Sampling Methods

Huanjian Zhou, Masashi Sugiyama

Sampling from high-dimensional probability distributions is fundamental in machine learning and statistics. As datasets grow larger, computational efficiency becomes increasingly important, particularly in reducing *adaptive complexity*, namely the number of sequential rounds required for sampling algorithms. While recent works have introduced several parallelizable techniques, they often exhibit suboptimal convergence rates and remain significantly weaker than the latest lower bounds for log-concave sampling.To address this, we propose a novel parallel sampling method that improves adaptive complexity dependence on dimension $d$ reducing it from $\widetilde{\mathcal{O}}(\log^2 d)$ to $\widetilde{\mathcal{O}}(\log d)$. Our approach builds on parallel simulation techniques from scientific computing.

Social Aspects · Fairness

Haruka Kiyohara, Fan Yao, Sarah Dean

In two-sided platforms (e.g., video streaming or e-commerce), viewers and providers engage in interactive dynamics: viewers benefit from increases in provider populations, while providers benefit from increases in viewer population. Despite the importance of such “population effects” on long-term platform health, recommendation policies do not generally take the participation dynamics into account. This paper thus studies the dynamics and recommender policy design on two-sided platforms under the population effects for the first time. Our control- and game-theoretic findings warn against the use of the standard “myopic-greedy” policy and shed light on the importance of provider-side considerations (i.e., effectively distributing exposure among provider groups) to improve social welfare via population growth. We also present a simple algorithm to optimize long-term social welfare by taking the population effects into account, and demonstrate its effectiveness in synthetic and real-data experiments. Our experiment code is available at https://github.com/sdean-group/dynamics-two-sided-market.

Applications · Chemistry, Physics, and Earth Sciences

Ye DU, Chen Yang, Nanxi Yu, Wanyu LIN, Qian Zhao, Shujun Wang

*De novo* peptide sequencing is a fundamental computational technique for ascertaining amino acid sequences of peptides directly from tandem mass spectrometry data, eliminating the need for reference databases. Cutting-edge models encode the observed mass spectra into latent representations from which peptides are predicted auto-regressively. However, the issue of missing fragmentation, attributable to factors such as suboptimal fragmentation efficiency and instrumental constraints, presents a formidable challenge in practical applications. To tackle this obstacle, we propose a novel computational paradigm called $\underline{\textbf{L}}$atent $\underline{\textbf{I}}$mputation before $\underline{\textbf{P}}$rediction (LIPNovo). LIPNovo is devised to compensate for missing fragmentation information within observed spectra before executing the final peptide prediction. Rather than generating raw missing data, LIPNovo performs imputation in the latent space, guided by the theoretical peak profile of the target peptide sequence. The imputation process is conceptualized as a set-prediction problem, utilizing a set of learnable peak queries to reason about the relationships among observed peaks and directly generate the latent representations of theoretical peaks through optimal bipartite matching. In this way, LIPNovo manages to supplement missing information during inference and thus boosts performance. Despite its simplicity, experiments on three benchmark datasets demonstrate that LIPNovo outperforms state-of-the-art methods by large margins. Code is available at https://github.com/usr922/LIPNovo.

Theory · Reinforcement Learning and Planning

Joongkyu Lee, Min-hwan Oh

In this paper, we consider combinatorial reinforcement learning with preference feedback, where a learning agent sequentially offers an action—an assortment of multiple items—to a user, whose preference feedback follows a multinomial logistic (MNL) model. This framework allows us to model real-world scenarios, particularly those involving long-term user engagement, such as in recommender systems and online advertising. However, this framework faces two main challenges: (1) the unknown value of each item, unlike traditional MNL bandits that only address single-step preference feedback, and (2) the difficulty of ensuring optimism while maintaining tractable assortment selection in the combinatorial action space with unknown values. In this paper, we assume a contextual MNL preference model, where the mean utilities are linear, and the value of each item is approximated by a general function. We propose an algorithm, MNL-VQL, that addresses these challenges, making it both computationally and statistically efficient. As a special case, for linear MDPs (with the MNL preference feedback), we establish the first regret lower bound in this framework and show that MNL-VQL achieves near-optimal regret. To the best of our knowledge, this is the first work to provide statistical guarantees in combinatorial RL with preference feedback.

Deep Learning · Algorithms

Ganchao Wei, Li Ma

Flow matching (FM) is a family of training algorithms for fitting continuous normalizing flows (CNFs). Conditional flow matching (CFM) exploits the fact that the marginal vector field of a CNF can be learned by fitting least-squares regression to the conditional vector field specified given one or both ends of the flow path. In this paper, we extend the CFM algorithm by defining conditional probability paths along "streams'', instances of latent stochastic paths that connect data pairs of source and target, which are modeled with Gaussian process (GP) distributions. The unique distributional properties of GPs help preserve the ``simulation-free'' nature of CFM training. We show that this generalization of the CFM can effectively reduce the variance in the estimated marginal vector field at a moderate computational cost, thereby improving the quality of the generated samples under common metrics. Additionally, adopting the GP on the streams allows for flexibly linking multiple correlated training data points (e.g., time series). We empirically validate our claim through both simulations and applications to image and neural time series data.

Deep Learning · Everything Else

Akira Ito, Masanori Yamada, Atsutoshi Kumagai

Ainsworth et al. empirically demonstrated that linear mode connectivity (LMC) can be achieved between two independently trained neural networks (NNs) by applying an appropriate parameter permutation. LMC is satisfied if a linear path with non-increasing test loss exists between the models, suggesting that NNs trained with stochastic gradient descent (SGD) converge to a single approximately convex low-loss basin under permutation symmetries. However, Ainsworth et al. verified LMC for two models and provided only limited discussion on its extension to multiple models. In this paper, we conduct a more detailed empirical analysis. First, we show that existing permutation search methods designed for two models can fail to transfer multiple models into the same convex low-loss basin. Next, we propose a permutation search method using a straight-through estimator for multiple models (STE-MM). We then experimentally demonstrate that even when multiple models are given, the test loss of the merged model remains nearly the same as the losses of the original models when using STE-MM, and the loss barriers between all permuted model pairs are also small. Additionally, from the perspective of the trace of the Hessian matrix, we show that the loss sharpness around the merged model decreases as the number of models increases with STE-MM, indicating that LMC for multiple models is more likely to hold. The source code implementing our method is available at https://github.com/e5-a/STE-MM.

Optimization

Guner Dilsad ER, Sebastian Trimpe, Michael Muehlebach

We consider a distributed learning problem, where agents minimize a global objective function by exchanging information over a network. Our approach has two distinct features: (i) It substantially reduces communication by triggering communication only when necessary, and (ii) it is agnostic to the data-distribution among the different agents. We can therefore guarantee convergence even if the local data-distributions of the agents are arbitrarily distinct. We analyze the convergence rate of the algorithm both in convex and nonconvex settings and derive accelerated convergence rates in a convex setting. We also characterize the effect of communication failures and demonstrate that our algorithm is robust to communication failures. The article concludes by presenting numerical results from distributed learning tasks on the MNIST and CIFAR-10 datasets. The experiments underline communication savings of 35\% or more due to the event-based communication strategy, show resilience towards heterogeneous data-distributions, and highlight that our approach outperforms common baselines such as FedAvg, FedProx, SCAFFOLD and FedADMM.

Applications · Language, Speech and Dialog

Huadai Liu, Tianyi Luo, Kaicheng Luo, Qikai Jiang, Peiwen Sun, Jialei Wang, Rongjie Huang, Qian Chen, Wen Wang, Xiangtai Li 等

Traditional video-to-audio generation techniques primarily focus on perspective video and non-spatial audio, often missing the spatial cues necessary for accurately representing sound sources in 3D environments. To address this limitation, we introduce a novel task, \textbf{360V2SA}, to generate spatial audio from 360-degree videos, specifically producing First-order Ambisonics (FOA) audio - a standard format for representing 3D spatial audio that captures sound directionality and enables realistic 3D audio reproduction. We first create \textbf{Sphere360}, a novel dataset tailored for this task that is curated from real-world data. We also design an efficient semi-automated pipeline for collecting and cleaning paired video-audio data. To generate spatial audio from 360-degree video, we propose a novel framework \textbf{OmniAudio}, which leverages self-supervised pre-training using both spatial audio data (in FOA format) and large-scale non-spatial data. Furthermore, OmniAudio features a dual-branch framework that utilizes both panoramic and perspective video inputs to capture comprehensive local and global information from 360-degree videos. Experimental results demonstrate that OmniAudio achieves state-of-the-art performance across both objective and subjective metrics on Sphere360. Code and datasets are available at~\href{https://github.com/liuhuadai/OmniAudio}{\texttt{github.com/liuhuadai/OmniAudio}}. The project website is available at \href{https://OmniAudio-360V2SA.github.io}{\texttt{OmniAudio-360V2SA.github.io}}.

Deep Learning · Large Language Models

Yuri Gardinazzi, Karthik Viswanathan, Giada Panerai, Alessio Ansuini, Alberto Cazzaniga, Matteo Biagetti

Understanding the decision-making processes of large language models is critical given their widespread applications. To achieve this, we aim to connect a formal mathematical framework—zigzag persistence from topological data analysis —with practical and easily applicable algorithms. Zigzag persistence is particularly effective for characterizing data as it dynamically transforms across model layers. Within this framework, we introduce topological descriptors that measure how topological features, $p$-dimensional holes, persist and evolve throughout the layers. Unlike methods that assess each layer individually and then aggregate the results, our approach directly tracks the full evolutionary path of these features. This offers a statistical perspective on how prompts are rearranged and their relative positions changed in the representation space, providing insights into the system’s operation as an integrated whole. To demonstrate the expressivity and applicability of our framework, we highlight how sensitive these descriptors are to different models and a variety of datasets. As a showcase application to a downstream task, we use zigzag persistence to establish a criterion for layer pruning, achieving results comparable to state-of-the-art methods while preserving the system-level perspective.

Theory · Learning Theory

Yijun Dong, Yicheng Li, Yunai Li, Jason Lee, Qi Lei

Weak-to-strong (W2S) generalization is a type of finetuning (FT) where a strong (large) student model is trained on pseudo-labels generated by a weak teacher. Surprisingly, W2S FT often outperforms the weak teacher. We seek to understand this phenomenon through the observation that FT often occurs in intrinsically low-dimensional spaces. Leveraging the low intrinsic dimensionality of FT, we analyze W2S in the ridgeless regression setting from a variance reduction perspective. For a strong student-weak teacher pair with sufficiently expressive low-dimensional feature subspaces $\mathcal{V}_s, \mathcal{V}_w$, we provide an exact characterization of the variance that dominates the generalization error of W2S. This unveils a virtue of discrepancy between the strong and weak models in W2S: the variance of the weak teacher is inherited by the strong student in $\mathcal{V}_s \cap \mathcal{V}_w$, while reduced by a factor of $\mathrm{dim}(\mathcal{V}_s)/N$ in the subspace of discrepancy $\mathcal{V}_w \setminus \mathcal{V}_s$ with $N$ pseudo-labels for W2S. Our analysis further casts light on the sample complexities and the scaling of performance gap recovery in W2S. The analysis is supported by experiments on synthetic regression problems, as well as real vision and NLP tasks.

Theory · Game Theory

Eric Frankel, Kshitij Kulkarni, Dmitriy Drusvyatskiy, Sewoong Oh, Lillian Ratliff

Decision-makers often adaptively influence downstream competitive agents' behavior to minimize their cost, yet in doing so face critical challenges: $(i)$ decision-makers might not *a priori* know the agents' objectives; $(ii)$ agents might *learn* their responses, introducing stochasticity and non-stationarity into the decision-making process; and $(iii)$ there may be additional non-strategic environmental stochasticity. Characterizing convergence of this complex system is contingent on how the decision-maker controls for the tradeoff between the induced drift and additional noise from the learning agent behavior and environmental stochasticity. To understand how the learning agents' behavior is influenced by the decision-maker’s actions, we first consider a decision-maker that deploys an arbitrary sequence of actions which induces a sequence of games and corresponding equilibria. We characterize how the drift and noise in the agents' stochastic algorithms decouples from their optimization error. Leveraging this decoupling and accompanying finite-time efficiency estimates, we design decision-maker algorithms that control the induced drift relative to the agent noise. This enables efficient finite-time tracking of game theoretic equilibrium concepts that adhere to the incentives of the players' collective learning processes.

Deep Learning · Generative Models and Autoencoders

Fan Shi, Bin Li, Xiangyang Xue

Abstract visual reasoning (AVR) enables humans to quickly discover and generalize abstract rules to new scenarios. Designing intelligent systems with human-like AVR abilities has been a long-standing topic in the artificial intelligence community. Deep AVR solvers have recently achieved remarkable success in various AVR tasks. However, they usually use task-specific designs or parameters in different tasks. In such a paradigm, solving new tasks often means retraining the model, and sometimes retuning the model architectures, which increases the cost of solving AVR problems. In contrast to task-specific approaches, this paper proposes a novel Unified Conditional Generative Solver (UCGS), aiming to address multiple AVR tasks in a unified framework. First, we prove that some well-known AVR tasks can be reformulated as the problem of estimating the predictability of target images in problem panels. Then, we illustrate that, under the proposed framework, training one conditional generative model can solve various AVR tasks. The experiments show that with a single round of multi-task training, UCGS demonstrates abstract reasoning ability across various AVR tasks. Especially, UCGS exhibits the ability of zero-shot reasoning, enabling it to perform abstract reasoning on problems from unseen AVR tasks in the testing phase.

Reinforcement Learning · Everything Else

Shuo Han, German Espinosa, Junda Huang, Daniel A. Dombeck, Malcolm MacIver, Bradly Stadie

Recent advances in reinforcement learning (RL) have demonstrated impressive capabilities in complex decision-making tasks. This progress raises a natural question: how do these artificial systems compare to biological agents, which have been shaped by millions of years of evolution? To help answer this question, we undertake a comparative study of biological mice and RL agents in a predator-avoidance maze environment. Through this analysis, we identify a striking disparity: RL agents consistently demonstrate a lack of self-preservation instinct, readily risking ``death'' for marginal efficiency gains. These risk-taking strategies are in contrast to biological agents, which exhibit sophisticated risk-assessment and avoidance behaviors. Towards bridging this gap between the biological and artificial, we propose two novel mechanisms that encourage more naturalistic risk-avoidance behaviors in RL agents. Our approach leads to the emergence of naturalistic behaviors, including strategic environment assessment, cautious path planning, and predator avoidance patterns that closely mirror those observed in biological systems.

Deep Learning · Sequential Models, Time series

Peiyuan Liu, Beiliang Wu, Yifan Hu, Naiqi Li, Tao Dai, Jigang Bao, Shutao Xia

Non-stationarity poses significant challenges for multivariate time series forecasting due to the inherent short-term fluctuations and long-term trends that can lead to spurious regressions or obscure essential long-term relationships. Most existing methods either eliminate or retain non-stationarity without adequately addressing its distinct impacts on short-term and long-term modeling. Eliminating non-stationarity is essential for avoiding spurious regressions and capturing local dependencies in short-term modeling, while preserving it is crucial for revealing long-term cointegration across variates. In this paper, we propose TimeBridge, a novel framework designed to bridge the gap between non-stationarity and dependency modeling in long-term time series forecasting. By segmenting input series into smaller patches, TimeBridge applies Integrated Attention to mitigate short-term non-stationarity and capture stable dependencies within each variate, while Cointegrated Attention preserves non-stationarity to model long-term cointegration across variates. Extensive experiments show that TimeBridge consistently achieves state-of-the-art performance in both short-term and long-term forecasting. Additionally, TimeBridge demonstrates exceptional performance in financial forecasting on the CSI 500 and S&P 500 indices, further validating its robustness and effectiveness. Code is available at https://github.com/Hank0626/TimeBridge.

Deep Learning · Graph Neural Networks

James Rowbottom, Georg Maierhofer, Teo Deveney, Eike Müller, Alberto Paganini, Katharina Schratz, Pietro Lió, Carola-Bibiane Schönlieb, Chris Budd

We present a novel, and effective, approach to achieve optimal mesh relocation in finite element methods (FEMs). The cost and accuracy of FEMs is critically dependent on the choice of mesh points. Mesh relocation (r-adaptivity) seeks to optimise the mesh geometry to obtain the best solution accuracy at given computational budget. Classical r-adaptivity relies on the solution of a separate nonlinear ``meshing'' PDE to determine mesh point locations. This incurs significant cost at remeshing, and relies on estimates that relate interpolation- and FEM-error. Recent machine learning approaches have focused on the construction of fast surrogates for such classical methods. Instead, our new approach trains a graph neural network (GNN) to determine mesh point locations by directly minimising the FE solution error from the PDE system Firedrake to achieve higher solution accuracy. Our GNN architecture closely aligns the mesh solution space to that of classical meshing methodologies, thus replacing classical estimates for optimality with a learnable strategy. This allows for rapid and robust training and results in an extremely efficient and effective GNN approach to online r-adaptivity. Our method outperforms both classical, and prior ML, approaches to r-adaptive meshing. In particular, it achieves lower FE solution error, whilst retaining the significant speed-up over classical methods observed in prior ML work.

Deep Learning · Generative Models and Autoencoders

Linqi (Alex) Zhou, Stefano Ermon, Jiaming Song

Diffusion models and Flow Matching generate high-quality samples but are slow at inference, and distilling them into few-step models often leads to instability and extensive tuning. To resolve these trade-offs, we propose Moment Matching Self-Distillation (MMSD), a new class of generative models for one- or few-step sampling with a single-stage training procedure. Unlike distillation, MMSD does not require pre-training initialization and optimization of two networks; and unlike Consistency Models, MMSD guarantees distribution-level convergence and remains stable under various hyperparameters and standard model architectures. MMSD surpasses diffusion models on ImageNet-256x256 with 2.13 FID using only 8 inference steps and achieves state-of-the-art 2-step FID of 2.05 on CIFAR-10 for a model trained from scratch.