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Miscellaneous Aspects of Machine Learning · Unsupervised and Semi-supervised Learning

Yan Sun, Stanley Kok

Learning effective graph similarities is crucial for tasks like clustering, yet selecting the optimal kernel to evaluate such similarities in unsupervised settings remains a major challenge. Despite the development of various graph kernels, determining the most appropriate one for a specific task is particularly difficult in the absence of labeled data. Existing methods often struggle to handle the complex structure of graph data and rely on heuristic approaches that fail to adequately capture the global relationships between graphs. To overcome these limitations, we propose Unsupervised Multiple Kernel Learning for Graphs (UMKL-G), a model that combines multiple graph kernels without requiring labels or predefined local neighbors. Our approach preserves the topology of the data by maintaining ordinal relationships among graphs through a probability simplex, allowing for a unified and adaptive kernel learning process. We provide theoretical guarantees on the stability, robustness, and generalization of our method. Empirical results demonstrate that UMKL-G outperforms individual kernels and other state-of-the-art methods, offering a robust solution for unsupervised graph analysis.

Optimization · Learning for Optimization

Hao Yuan, wenli ouyang, Changwen Zhang, Yong Sun, Liming Gong, Junchi Yan

Learning to solve large-scale Mixed Integer Program (MIP) problems is an emerging research topic, and policy learning-based Large Neighborhood Search (LNS) has been a popular paradigm. However, the explored space of LNS policy is often limited even in the training phase, making the learned policy sometimes wrongly fix some potentially important variables early in the search, leading to local optimum in some cases. Moreover, many methods only assume binary variables to deal with. We present a practical approach, termed Binarized-Tightening Branch-and-Search for Large Neighborhood Search (BTBS-LNS). It comprises three key techniques: 1) the ``Binarized Tightening" technique for integer variables to handle their wide range by binary encoding and bound tightening; 2) an attention-based tripartite graph to capture global correlations among variables and constraints for an MIP instance; 3) an extra branching network as a global view, to identify and optimize wrongly-fixed backdoor variables at each search step. Experiments show its superior performance over the open-source solver SCIP and LNS baselines. Moreover, it performs competitively with, and sometimes better than the commercial solver Gurobi (v9.5.0), especially on the MIPLIB2017 benchmark chosen by Hans Mittelmann, where our method can deliver 10\% better primal gaps compared with Gurobi in a 300s cut-off time.

Deep Learning · Graph Neural Networks

Celia Rubio-Madrigal, Adarsh Jamadandi, Rebekka Burkholz

Maximizing the spectral gap through graph rewiring has been proposed to enhance the performance of message-passing graph neural networks (GNNs) by addressing over-squashing. However, as we show, minimizing the spectral gap can also improve generalization. To explain this, we analyze how rewiring can benefit GNNs within the context of stochastic block models. Since spectral gap optimization primarily influences community strength, it improves performance when the community structure aligns with node labels. Building on this insight, we propose three distinct rewiring strategies that explicitly target community structure, node labels, and their alignment: (a) community structure-based rewiring (ComMa), a more computationally efficient alternative to spectral gap optimization that achieves similar goals; (b) feature similarity-based rewiring (FeaSt), which focuses on maximizing global homophily; and (c) a hybrid approach (ComFy), which enhances local feature similarity while preserving community structure to optimize label-community alignment. Extensive experiments confirm the effectiveness of these strategies and support our theoretical insights.

Deep Learning · Generative Models and Autoencoders

Minh-Quan Le, Gaurav Mittal, Tianjian Meng, A S M Iftekhar, Vishwas Suryanarayanan, Barun Patra, Dimitris Samaras, Mei Chen

While diffusion models are powerful in generating high-quality, diverse synthetic data for object-centric tasks, existing methods struggle with scene-aware tasks such as Visual Question Answering (VQA) and Human-Object Interaction (HOI) Reasoning, where it is critical to preserve scene attributes in generated images consistent with a multimodal context, i.e. a reference image with accompanying text guidance query. To address this, we introduce **Hummingbird**, the first diffusion-based image generator which, given a multimodal context, generates highly diverse images w.r.t. the reference image while ensuring high fidelity by accurately preserving scene attributes, such as object interactions and spatial relationships from the text guidance. Hummingbird employs a novel Multimodal Context Evaluator that simultaneously optimizes our formulated Global Semantic and Fine-grained Consistency Rewards to ensure generated images preserve the scene attributes of reference images in relation to the text guidance while maintaining diversity. As the first model to address the task of maintaining both diversity and fidelity given a multimodal context, we introduce a new benchmark formulation incorporating MME Perception and Bongard HOI datasets. Benchmark experiments show Hummingbird outperforms all existing methods by achieving superior fidelity while maintaining diversity, validating Hummingbird's potential as a robust multimodal context-aligned image generator in complex visual tasks. Project page: https://roar-ai.github.io/hummingbird

Optimization · Global Optimization

Thomas Robert, Mher Safaryan, Ionut-Vlad Modoranu, Dan Alistarh

We introduce LDAdam, a memory-efficient optimizer for training large models, that performs adaptive optimization steps within lower dimensional subspaces, while consistently exploring the full parameter space during training. This strategy keeps the optimizer's memory footprint to a fraction of the model size. LDAdam relies on a new projection-aware update rule for the optimizer states that allows for transitioning between subspaces, i.e., estimation of the statistics of the projected gradients. To mitigate the errors due to low-rank projection, LDAdam integrates a new generalized error feedback mechanism, which explicitly accounts for both gradient and optimizer state compression. We prove the convergence of LDAdam under standard assumptions, and provide empirical evidence that LDAdam allows for efficient fine-tuning and pre-training of language models.

Applications · Chemistry and Drug Discovery

Vincent Mallet, Yangyang Miao, Souhaib Attaiki, Bruno Correia, Maks Ovsjanikov

While there has been significant progress in evaluating and comparing different representations for learning on protein data, the role of surface-based learning approaches remains not well-understood. In particular, there is a lack of direct and fair benchmark comparison between the best available surface-based learning methods against alternative representations such as graphs. Moreover, the few existing surface-based approaches either use surface information in isolation or, at best, perform global pooling between surface and graph-based architectures. In this work, we fill this gap by first adapting a state-of-the-art surface encoder for protein learning tasks. We then perform a direct and fair comparison of the resulting method against alternative approaches within the Atom3D benchmark, highlighting the limitations of pure surface-based learning. Finally, we propose an integrated approach, which allows learned feature sharing between graphs and surface representations on the level of nodes and vertices \textit{across all layers}. We demonstrate that the resulting architecture achieves state-of-the-art results on all tasks in the Atom3D benchmark, while adhering to the strict benchmark protocol, as well as more broadly on binding site identification and binding pocket classification. Furthermore, we use coarsened surfaces and optimize our approach for efficiency, making our tool competitive in training and inference time with existing techniques.Code can be found online: https://github.com/Vincentx15/atomsurf

Applications · Computer Vision

Tuan Ngo, Peiye Zhuang, Evangelos Kalogerakis, Chuang Gan, Sergey Tulyakov, Hsin-Ying Lee, Chaoyang Wang

Tracking dense 3D motion from monocular videos remains challenging, particularly when aiming for pixel-level precision over long sequences. We introduce DELTA, a novel method that efficiently tracks every pixel in 3D space, enabling accurate motion estimation across entire videos. Our approach leverages a joint global-local attention mechanism for reduced-resolution tracking, followed by a transformer-based upsampler to achieve high-resolution predictions. Unlike existing methods, which are limited by computational inefficiency or sparse tracking, DELTA delivers dense 3D tracking at scale, running over 8x faster than previous methods while achieving state-of-the-art accuracy. Furthermore, we explore the impact of depth representation on tracking performance and identify log-depth as the optimal choice. Extensive experiments demonstrate the superiority of DELTA on multiple benchmarks, achieving new state-of-the-art results in both 2D and 3D dense tracking tasks. Our method provides a robust solution for applications requiring fine-grained, long-term motion tracking in 3D space.

Theory · Learning Theory

Andreas C. Schneider, Valentin Neuhaus, David Ehrlich, Abdullah Makkeh, Alexander S Ecker, Viola Priesemann, Michael Wibral

In modern deep neural networks, the learning dynamics of individual neurons are often obscure, as the networks are trained via global optimization. Conversely, biological systems build on self-organized, local learning, achieving robustness and efficiency with limited global information. Here, we show how self-organization between individual artificial neurons can be achieved by designing abstract bio-inspired local learning goals. These goals are parameterized using a recent extension of information theory, Partial Information Decomposition (PID), which decomposes the information that a set of information sources holds about an outcome into unique, redundant and synergistic contributions. Our framework enables neurons to locally shape the integration of information from various input classes, i.e., feedforward, feedback, and lateral, by selecting which of the three inputs should contribute uniquely, redundantly or synergistically to the output. This selection is expressed as a weighted sum of PID terms, which, for a given problem, can be directly derived from intuitive reasoning or via numerical optimization, offering a window into understanding task-relevant local information processing. Achieving neuron-level interpretability while enabling strong performance using local learning, our work advances a principled information-theoretic foundation for local learning strategies.

Theory · Learning Theory

Andreas C. Schneider, Valentin Neuhaus, David Ehrlich, Abdullah Makkeh, Alexander S Ecker, Viola Priesemann, Michael Wibral

In modern deep neural networks, the learning dynamics of individual neurons are often obscure, as the networks are trained via global optimization. Conversely, biological systems build on self-organized, local learning, achieving robustness and efficiency with limited global information. Here, we show how self-organization between individual artificial neurons can be achieved by designing abstract bio-inspired local learning goals. These goals are parameterized using a recent extension of information theory, Partial Information Decomposition (PID), which decomposes the information that a set of information sources holds about an outcome into unique, redundant and synergistic contributions. Our framework enables neurons to locally shape the integration of information from various input classes, i.e., feedforward, feedback, and lateral, by selecting which of the three inputs should contribute uniquely, redundantly or synergistically to the output. This selection is expressed as a weighted sum of PID terms, which, for a given problem, can be directly derived from intuitive reasoning or via numerical optimization, offering a window into understanding task-relevant local information processing. Achieving neuron-level interpretability while enabling strong performance using local learning, our work advances a principled information-theoretic foundation for local learning strategies.

Optimization · Global Optimization

Quan Xiao, Tianyi Chen

Bilevel optimization has witnessed a resurgence of interest, driven by its critical role in trustworthy and efficient AI applications. Recent focus has been on finding efficient methods with provable convergence guarantees. However, while many prior works have established convergence to stationary points or local minima, obtaining the global optimum of bilevel optimization remains an important yet open problem. The difficulty lies in the fact that unlike many prior non-convex single-level problems, bilevel problems often do not admit a ``benign" landscape, and may indeed have multiple spurious local solutions. Nevertheless, attaining the global optimality is indispensable for ensuring reliability, safety, and cost-effectiveness, particularly in high-stakes engineering applications that rely on bilevel optimization. In this paper, we first explore the challenges of establishing a global convergence theory for bilevel optimization, and present two sufficient conditions for global convergence. We provide {\em algorithm-dependent} proofs to rigorously substantiate these sufficient conditions on two specific bilevel learning scenarios: representation learning and data hypercleaning (a.k.a. reweighting). Experiments corroborate the theoretical findings, demonstrating convergence to global minimum in both cases.

Theory · Optimization

Liangliang Shi, Yufeng Li, Kaipeng Zeng, Yihui Tu, Junchi Yan

The Sinkhorn algorithm, based on Entropic Regularized Optimal Transport (OT), has garnered significant attention due to its computational efficiency enabled by GPU-friendly matrix-vector multiplications. However, vanilla OT primarily deals with computations between the source and target nodes in a bipartite graph, limiting its practical application in real-world transportation scenarios.In this paper, we introduce the concept of Optimal Flow Transport (OFT) as an extension, where we consider a more general graph setting and the marginal constraints in vanilla OT are replaced by flow balance constraints. To obtain solutions, we incorporate entropic regularization into the OFT and introduce virtual flows for individual nodes to tackle the issue of potentially numerous isolated nodes lacking flow passages. Our proposition, the OFT-Sinkhorn algorithm, utilizes GPU-friendly matrix iterations to maintain flow balance constraints and minimize the objective function, and theoretical results for global convergence is also proposed in this paper.Furthermore, we enhance OFT by introducing capacity constraints on nodes and edges, transforming the OFT problem into a minimum-cost flow problem. We then present the Capacity-Constrained EOFT-Sinkhorn algorithm and compare it with the traditional Minimum cost flow (MCF) algorithm, showing that our algorithm is quite efficient for calculation. In particular, our EOFT-Sinkhorn is evaluated on high-precision and integer-precision MCF problems with different scales from one hundred to five thousand size, exhibiting significant time efficiency and the ability to approximate optimal solutions.

Social Aspects · Accountability, Transparency and Interpretability

Vinitra Swamy, Syrielle Montariol, Julian Blackwell, Jibril Frej, Martin Jaggi, Tanja Käser

In human-centric settings like education or healthcare, model accuracy and model explainability are key factors for user adoption. Towards these two goals, intrinsically interpretable deep learning models have gained popularity, focusing on accurate predictions alongside faithful explanations. However, there exists a gap in the human-centeredness of these approaches, which often produce nuanced and complex explanations that are not easily actionable for downstream users. We present InterpretCC (interpretable conditional computation), a family of intrinsically interpretable neural networks at a unique point in the design space that optimizes for ease of human understanding and explanation faithfulness, while maintaining comparable performance to state-of-the-art models. InterpretCC achieves this through adaptive sparse activation of features before prediction, allowing the model to use a different, minimal set of features for each instance. We extend this idea into an interpretable, global mixture-of-experts (MoE) model that allows users to specify topics of interest, discretely separates the feature space for each data point into topical subnetworks, and adaptively and sparsely activates these topical subnetworks for prediction. We apply InterpretCC for text, time series and tabular data across several real-world datasets, demonstrating comparable performance with non-interpretable baselines and outperforming intrinsically interpretable baselines. Through a user study involving 56 teachers, InterpretCC explanations are found to have higher actionability and usefulness over other intrinsically interpretable approaches.

Optimization · Zero-order and Black-box Optimization

Taiwo Adebiyi, Bach Do, Ruda Zhang

Bayesian optimization devolves the global optimization of a costly objective function to the global optimization of a sequence of acquisition functions. This inner-loop optimization can be catastrophically difficult if it involves posterior sample paths, especially in higher dimensions. We introduce an efficient global optimization strategy for posterior samples based on global rootfinding. It provides gradient-based optimizers with two sets of judiciously selected starting points, designed to combine exploration and exploitation. The number of starting points can be kept small without sacrificing optimization quality. Remarkably, even with just one point from each set, the global optimum is discovered most of the time. The algorithm scales practically linearly to high dimensions, breaking the curse of dimensionality. For Gaussian process Thompson sampling (GP-TS), we demonstrate remarkable improvement in both inner- and outer-loop optimization, surprisingly outperforming alternatives like EI and GP-UCB in most cases. Our approach also improves the performance of other posterior sample-based acquisition functions, such as variants of entropy search. Furthermore, we propose a sample-average formulation of GP-TS, which has a parameter to explicitly control exploitation and can be computed at the cost of one posterior sample.

Deep Learning · Theory

Sungyoon Kim, Aaron Mishkin, Mert Pilanci

We discuss several aspects of the loss landscape of regularized neural networks: the structure of stationary points, connectivity of optimal solutions, path with non-increasing loss to arbitrary global optimum, and the nonuniqueness of optimal solutions, by casting the problem into an equivalent convex problem and considering its dual. Starting from two-layer neural networks with scalar output, we first characterize the solution set of the convex problem using its dual and further characterize all stationary points. With the characterization, we show that the topology of the global optima goes through a phase transition as the width of the network changes, and construct counterexamples where the problem may have a continuum of optimal solutions. Finally, we show that the solution set characterization and connectivity results can be extended to different architectures, including two layer vector-valued neural networks and parallel three-layer neural networks.

Deep Learning · Theory

Sungyoon Kim, Aaron Mishkin, Mert Pilanci

We discuss several aspects of the loss landscape of regularized neural networks: the structure of stationary points, connectivity of optimal solutions, path with non-increasing loss to arbitrary global optimum, and the nonuniqueness of optimal solutions, by casting the problem into an equivalent convex problem and considering its dual. Starting from two-layer neural networks with scalar output, we first characterize the solution set of the convex problem using its dual and further characterize all stationary points. With the characterization, we show that the topology of the global optima goes through a phase transition as the width of the network changes, and construct counterexamples where the problem may have a continuum of optimal solutions. Finally, we show that the solution set characterization and connectivity results can be extended to different architectures, including two layer vector-valued neural networks and parallel three-layer neural networks.

Reinforcement Learning · Deep RL

Qifan Liang, Yixiang Shan, Haipeng Liu, Zhengbang Zhu, Ting Long, Weinan Zhang, Yuan Tian

An important challenge in multi-agent reinforcement learning is partial observability, where agents cannot access the global state of the environment during execution and can only receive observations within their field of view. To address this issue, previous works typically use the dimensional-wise state, which is obtained by applying MLP or dimensional-based attention on the global state, for decision-making during training and relying on a reconstructed dimensional-wise state during execution. However, dimensional-wise states tend to divert agent attention to specific features, neglecting potential dependencies between agents, making it difficult to make optimal decisions. Moreover, the inconsistency between the states used in training and execution further increases additional errors. To resolve these issues, we propose a method called Reconstruction-Guided Policy (RGP) to reconstruct the agent-wise state, which represents the information of inter-agent relationships, as input for decision-making during both training and execution. This not only preserves the potential dependencies between agents but also ensures consistency between the states used in training and execution. We conducted extensive experiments on both discrete and continuous action environments to evaluate RGP, and the results demonstrates its superior effectiveness. Our code is public in https://anonymous.4open.science/r/RGP-9F79

Applications · Physics

Philipp Scholl, Katharina Bieker, Hillary Hauger, Gitta Kutyniok

The problem of symbolic regression (SR) arises in many different applications, such as identifying physical laws or deriving mathematical equations describing the behavior of financial markets from given data. Various methods exist to address the problem of SR, often based on genetic programming. However, these methods are usually complicated and involve various hyperparameters. In this paper, we present our new approach ParFam that utilizes parametric families of suitable symbolic functions to translate the discrete symbolic regression problem into a continuous one, resulting in a more straightforward setup compared to current state-of-the-art methods. In combination with a global optimizer, this approach results in a highly effective method to tackle the problem of SR. We theoretically analyze the expressivity of ParFam and demonstrate its performance with extensive numerical experiments based on the common SR benchmark suit SRBench, showing that we achieve state-of-the-art results. Moreover, we present an extension incorporating a pre-trained transformer network (DL-ParFam) to guide ParFam, accelerating the optimization process by up to two magnitudes. Our code and results can be found at https://anonymous.4open.science/r/parfam-D402.

Deep Learning · Generative Models and Autoencoders

Junwei Zhou, Xueting Li, Lu Qi, Ming-Hsuan Yang

We present Layout-Your-3D, a framework that allows controllable and compositional 3D generation from text prompts. Existing text-to-3D methods often struggle to generate assets with plausible object interactions or require tedious optimization processes. To address these challenges, our approach leverages 2D layouts as a blueprint to facilitate precise and plausible control over 3D generation. Starting with a 2D layout provided by a user or generated from a text description, we first create a coarse 3D scene using a carefully designed initialization process based on efficient reconstruction models. To enforce coherent global 3D layouts and enhance the quality of instance appearances, we propose a collision-aware layout optimization process followed by instance-wise refinement. Experimental results demonstrate that Layout-Your-3D yields more reasonable and visually appealing compositional 3D assets while significantly reducing the time required for each prompt. Additionally, Layout-Your-3D can be easily applicable to downstream tasks, such as 3D editing and object insertion.

Applications · Computer Vision

Junyi Zhang, Charles Herrmann, Junhwa Hur, Varun Jampani, trevor darrell, Forrester Cole, Deqing Sun, Ming-Hsuan Yang

Estimating geometry from dynamic scenes, where objects move and deform over time, remains a core challenge in computer vision. Current approaches often rely on multi-stage pipelines or global optimizations that decompose the problem into subtasks, like depth and flow, leading to complex systems prone to errors. In this paper, we present Motion DUSt3R (MonST3R), a novel geometry-first approachthat directly estimates per-timestep geometry from dynamic scenes. Our key insight is that by simply estimating a pointmap for each timestep, we can effectively adapt DUSt3R’s representation, previously only used for static scenes, to dynamic scenes. However, this approach presents a significant challenge: the scarcity of suitable training data, namely dynamic, posed videos with depth labels. Despite this, we show that by posing the problem as a fine-tuning task, identifying several suitable datasets, and strategically training the model on this limited data, we can surprisingly enable the model to handle dynamics, even without an explicit motion representation. Based on this, we introduce new optimizations for several downstream video-specific tasks and demonstrate strong performance on video depth and camera pose estimation, outperforming prior work in terms of robustness and efficiency. Moreover, MonST3R shows promising results for primarily feed-forward 4D reconstruction. Interactive 4D results, source code, and trained models are available at: https://monst3r-project.github.io/.

Optimization · Global Optimization

Yuze Ge, Rujun Jiang

The spectral risk has wide applications in machine learning, especially in real-world decision-making, where people are concerned with more than just average model performance. By assigning different weights to the losses of different sample points, rather than the same weights as in the empirical risk, it allows the model's performance to lie between the average performance and the worst-case performance. In this paper, we propose SOREL, the first stochastic gradient-based algorithm with convergence guarantees for spectral risks minimization. Previous approaches often rely on smoothing the spectral risk by adding a strongly concave function, thereby lacking convergence guarantees for the original spectral risk. We theoretically prove that our algorithm achieves a near-optimal rate of $\widetilde{O}(1/\sqrt{\epsilon})$ to obtain an $\epsilon$-optimal solution in terms $\epsilon$. Experiments on real datasets show that our algorithm outperforms existing ones in most cases, both in terms of runtime and sample complexity.