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Deep Learning · Generative Models and Autoencoders

Sophia Hager, Aleem Khan, Andrew Wang, Nicholas Andrews

Most successful applications of deep learning involve similar training and test conditions. However, tasks such as biological sequence design involve searching for sequences that improve desirable properties beyond previously known values, which requires novel hypotheses that \emph{extrapolate} beyond training data. In these settings, extrapolation may be achieved by using random search methods such as Markov chain Monte Carlo (MCMC), which, given an initial state, sample local transformations to approximate a target density that rewards states with the desired properties. However, even with a well-designed proposal, MCMC may struggle to explore large structured state spaces efficiently. Rather than relying on stochastic search, it would be desirable to have a model that greedily optimizes the properties of interest, successfully extrapolating in as few steps as possible. We propose to learn such a model from the Markov chains resulting from MCMC search. Specifically, our approach uses selected states from Markov chains as a source of training data for an autoregressive model, which is then able to efficiently generate novel sequences that extrapolate along the sequence-level properties of interest. The proposed approach is validated on three problems: protein sequence design, text sentiment control, and text anonymization. We find that the autoregressive model can extrapolate as well or better than MCMC, but with the additional benefits of scalability and significantly higher sample efficiency.

Deep Learning · Generative Models and Autoencoders

Hila Chefer, Uriel Singer, Amit Zohar, Yuval Kirstain, Adam Polyak, Yaniv Taigman, Lior Wolf, Shelly Sheynin

Despite tremendous recent progress, generative video models still struggle to capture real-world motion, dynamics, and physics. We show that this limitation arises from the conventional pixel reconstruction objective, which biases models toward appearance fidelity at the expense of motion coherence.To address this, we introduce **VideoJAM**, a novel framework that instills an effective motion prior to video generators, by encouraging the model to learn *a joint appearance-motion representation*. VideoJAM is composed of two complementary units. During training, we extend the objective to predict both the generated pixels and their corresponding motion from a single learned representation. During inference, we introduce **Inner-Guidance**, a mechanism that steers the generation toward coherent motion by leveraging the model's own evolving motion prediction as a dynamic guidance signal.Notably, our framework can be applied to any video model with minimal adaptations, requiring no modifications to the training data or scaling of the model.VideoJAM achieves state-of-the-art performance in motion coherence, surpassing highly competitive proprietary models while also enhancing the perceived visual quality of the generations.These findings emphasize that appearance and motion can be complementary and, when effectively integrated, enhance both the visual quality and the coherence of video generation.

Theory · Learning Theory

Linda Lu, Ayush Sekhari, Karthik Sridharan

Machine unlearning addresses the problem of updating a machine learning model/system trained on a dataset $S$ so that the influence of a set of deletion requests $U \subseteq S$ on the unlearned model is minimized. The gold standard definition of unlearning demands that the updated model, after deletion, be nearly identical to the model obtained by retraining. This definition is designed for a worst-case attacker (one who can recover not only the unlearned model but also the remaining data samples, i.e., $S \setminus U$). Such a stringent definition has made developing efficient unlearning algorithms challenging. However, such strong attackers are also unrealistic. In this work, we propose a new definition, *system-aware unlearning*, which aims to provide unlearning guarantees against an attacker that can at best only gain access to the data stored in the system for learning/unlearning requests and not all of $S\setminus U$. With this new definition, we use the simple intuition that if a system can store less to make its learning/unlearning updates, it can be more secure and update more efficiently against a system-aware attacker. Towards that end, we present an exact system-aware unlearning algorithm for linear classification using a selective sampling-based approach, and we generalize the method for classification with general function classes. We theoretically analyze the tradeoffs between deletion capacity, accuracy, memory, and computation time.

General Machine Learning · Representation Learning

Kei Sen Fong, Mehul Motani

In this work, we propose a novel approach that combines the strengths of FEAT and TabNet through knowledge distillation (KD), which we term FEAT-KD. FEAT is an intrinsically interpretable machine learning (ML) algorithm that constructs a weighted linear combination of concisely-represented features discovered via genetic programming optimization, which can often be inefficient. FEAT-KD leverages TabNet's deep-learning-based optimization and feature selection mechanisms instead. FEAT-KD finds a weighted linear combination of concisely-represented, symbolic features that are derived from piece-wise distillation of a trained TabNet model. We analyze FEAT-KD on regression tasks from two perspectives: (i) compared to TabNet, FEAT-KD significantly reduces model complexity while retaining competitive predictive performance, effectively converting a black-box deep learning model into a more interpretable white-box representation, (ii) compared to FEAT, our method consistently outperforms in prediction accuracy, produces more compact models, and reduces the complexity of learned symbolic expressions. In addition, we demonstrate that FEAT-KD easily supports multi-target regression, in which the shared features contribute to the interpretability of the system. Our results suggest that FEAT-KD is a promising direction for interpretable ML, bridging the gap between deep learning's predictive power and the intrinsic transparency of symbolic models.

General Machine Learning · Supervised Learning

Corinna Cortes, Anqi Mao, Mehryar Mohri, Yutao Zhong

Class imbalance remains a major challenge in machine learning, especially in multi-class problems with long-tailed distributions. Existing methods, such as data resampling, cost-sensitive techniques, and logistic loss modifications, though popular and often effective, lack solid theoretical foundations. As an example, we demonstrate that cost-sensitive methods are not Bayes-consistent. This paper introduces a novel theoretical framework for analyzing generalization in imbalanced classification. We propose a new class-imbalanced margin loss function for both binary and multi-class settings, prove its strong $H$-consistency, and derive corresponding learning guarantees based on empirical loss and a new notion of class-sensitive Rademacher complexity. Leveraging these theoretical results, we devise novel and general learning algorithms, IMMAX (*Imbalanced Margin Maximization*), which incorporate confidence margins and are applicable to various hypothesis sets. While our focus is theoretical, we also present extensive empirical results demonstrating the effectiveness of our algorithms compared to existing baselines.

Theory · Learning Theory

Anqi Mao, Mehryar Mohri, Yutao Zhong

The problem of learning to defer with multiple experts consists of optimally assigning input instances to experts, balancing the trade-off between their accuracy and computational cost. This is a critical challenge in natural language generation, but also in other fields such as image processing, and medical diagnostics. Recent studies have proposed surrogate loss functions to optimize deferral, but challenges remain in ensuring their consistency properties. This paper introduces novel surrogate loss functions and efficient algorithms with strong theoretical learning guarantees. We address open questions regarding realizable $H$-consistency, $H$-consistency bounds, and Bayes-consistency for both single-stage (jointly learning predictor and deferral function) and two-stage (learning only the deferral function with a fixed expert) learning scenarios. For single-stage deferral, we introduce a family of new realizable $H$-consistent surrogate losses and further prove $H$-consistency for a selected member. For two-stage deferral, we derive new surrogate losses that achieve realizable $H$-consistency, $H$-consistency bounds, and Bayes-consistency for the two-expert scenario and, under natural assumptions, multiple-expertscenario. Additionally, we provide enhanced theoretical guarantees under low-noise assumptions for both scenarios. Finally, we report the results of experiments using our proposed surrogate losses, comparing their performance against existing baselines.

Deep Learning · Graph Neural Networks

Haofei Yu, Zhaochen Hong, Zirui Cheng, Kunlun Zhu, Keyang Xuan, Jinwei Yao, Tao Feng, Jiaxuan You

Large Language Models (LLMs) have demonstrated remarkable potential in scientific domains, yet a fundamental question remains unanswered: Can we simulate human research communities with LLMs? Addressing this question can deepen our understanding of the processes behind idea brainstorming and inspire the automatic discovery of novel scientific insights. In this work, we propose ResearchTown, a multi-agent framework for research community simulation. Within this framework, the human research community is simplified as an agent-data graph, where researchers and papers are represented as agent-type and data-type nodes, respectively, and connected based on their collaboration relationships. We also introduce TextGNN, a text-based inference framework that models various research activities (e.g., paper reading, paper writing, and review writing) as special forms of a unified message-passing process on the agent-data graph. To evaluate the quality of the research community simulation, we present ResearchBench, a benchmark that uses a node-masking prediction task for scalable and objective assessment based on similarity. Our experiments reveal three key findings: (1) ResearchTown can provide a realistic simulation of collaborative research activities, including paper writing and review writing; (2) ResearchTown can maintain robust simulation with multiple researchers and diverse papers; (3) ResearchTown can generate interdisciplinary research ideas that potentially inspire pioneering research directions.

General Machine Learning · Supervised Learning

Anqi Mao, Mehryar Mohri, Yutao Zhong

In applications with significant class imbalance or asymmetric costs, metrics such as the $F_\beta$-measure, AM measure, Jaccard similarity coefficient, and weighted accuracy offer more suitable evaluation criteria than standard binary classification loss. However, optimizing these metrics present significant computational and statistical challenges. Existing approaches often rely on the characterization of the Bayes-optimal classifier, and use threshold-based methods that first estimate class probabilities and then seek an optimal threshold. This leads to algorithms that are not tailored to restricted hypothesis sets and lack finite-sample performance guarantees. In this work, we introduce principled algorithms for optimizing generalized metrics, supported by $H$-consistency and finite-sample generalization bounds. Our approach reformulates metric optimization as a generalized cost-sensitive learning problem, enabling the design of novel surrogate loss functions with provable $H$-consistency guarantees. Leveraging this framework, we develop new algorithms, METRO (*Metric Optimization*), with strong theoretical performance guarantees. We report the results of experiments demonstrating the effectiveness of our methods compared to prior baselines.

General Machine Learning · Supervised Learning

Mingyang Wu, Li Lin, Wenbin Zhang, Xin Wang, Zhenhuan Yang, Shu Hu

The Area Under the ROC Curve (AUC) is a key metric for classification, especially under class imbalance, with growing research focus on optimizing AUC over accuracy in applications like medical image analysis and deepfake detection. This leads to fairness in AUC optimization becoming crucial as biases can impact protected groups. While various fairness mitigation techniques exist, fairness considerations in AUC optimization remain in their early stages, with most research focusing on improving AUC fairness under theassumption of clean protected groups. However, these studies often overlook the impact of noisy protected groups, leading to fairness violations in practice. To address this, we propose the first robust AUC fairness approach under noisy protected groups with fairness theoretical guarantees using distributionally robust optimization. Extensive experiments on tabular and image datasets show that our method outperforms state-of-the-art approaches in preserving AUC fairness. The code is in https://github.com/Purdue-M2/AUC_Fairness_with_Noisy_Groups.

Reinforcement Learning

Arman Sharifi Kolarijani, Tolga Ok, Peyman Mohajerin Esfahani, Mohamad Amin Sharifi Kolarijani

In this paper, we provide a novel algorithm for solving planning and learning problems of Markov decision processes. The proposed algorithm follows a policy iteration-type update by using a rank-one approximation of the transition probability matrix in the policy evaluation step. This rank-one approximation is closely related to the stationary distribution of the corresponding transition probability matrix, which is approximated using the power method. We provide theoretical guarantees for the convergence of the proposed algorithm to optimal (action-)value function with the same rate and computational complexity as the value iteration algorithm in the planning problem and as the Q-learning algorithm in the learning problem. Through our extensive numerical simulations, however, we show that the proposed algorithm consistently outperforms first-order algorithms and their accelerated versions for both planning and learning problems.

Reinforcement Learning · Batch/Offline

Dongsu Lee, Minhae Kwon

The goal of offline reinforcement learning (RL) is to extract the best possible policy from the previously collected dataset considering the *out-of-distribution* (OOD) sample issue. Offline model-based RL (MBRL) is a captivating solution capable of alleviating such issues through a \textit{state-action transition augmentation} with a learned dynamic model. Unfortunately, offline MBRL methods have been observed to fail in sparse rewarded and long-horizon environments for a long time. In this work, we propose a novel MBRL method, dubbed Temporal Distance-Aware Transition Augmentation (TempDATA), that generates additional transitions in a geometrically structured representation space, instead of state space. For comprehending long-horizon behaviors efficiently, our main idea is to learn state abstraction, which captures a *temporal distance* from both *trajectory and transition levels* of state space. Our experiments empirically confirm that TempDATA outperforms previous offline MBRL methods and achieves matching or surpassing the performance of diffusion-based trajectory augmentation and goal-conditioned RL on the D4RL AntMaze, FrankaKitchen, CALVIN, and pixel-based FrankaKitchen.

Applications · Health / Medicine

Justin Lee, Behnaz Moradi-Jamei, Heman Shakeri

Modeling the evolution of high-dimensional systems from limited snapshot observations at irregular time points poses a significant challenge in quantitative biology and related fields. Traditional approaches often rely on dimensionality reduction techniques, which can oversimplify the dynamics and fail to capture critical transient behaviors in non-equilibrium systems. We present Multi-Marginal Stochastic Flow Matching (MMSFM), a novel extension of simulation-free score and flow matching methods to the multi-marginal setting, enabling the alignment of high-dimensional data measured at non-equidistant time points without reducing dimensionality. The use of measure-valued splines enhances robustness to irregular snapshot timing, and score matching prevents overfitting in high-dimensional spaces. We validate our framework on several synthetic and benchmark datasets and apply it to single-cell perturbation data from melanoma cell lines and gene expression data collected at uneven time points.

General Machine Learning · Sequential, Network, and Time Series Modeling

Samidha Verma, Arushi Goyal, Ananya Mathur, Ankit Anand, Sayan Ranu

Graph Edit Distance (GED) is a widely used metric for measuring similarity between two graphs. Computing the optimal GED is NP-hard, leading to the development of various neural and non-neural heuristics. While neural methods have achieved improved approximation quality compared to non-neural approaches, they face significant challenges: (1) They require large amounts of ground truth data, which is itself NP-hard to compute. (2) They operate as black boxes, offering limited interpretability. (3) They lack cross-domain generalization, necessitating expensive retraining for each new dataset. We address these limitations with GRAIL, introducing a paradigm shift in this domain. Instead of training a neural model to predict GED, GRAIL employs a novel combination of large language models (LLMs) and automated prompt tuning to generate a *program* that is used to compute GED. This shift from predicting GED to generating programs imparts various advantages, including end-to-end interpretability and an autonomous self-evolutionary learning mechanism without ground-truth supervision. Extensive experiments on seven datasets confirm that GRAIL not only surpasses state-of-the-art GED approximation methods in prediction quality but also achieves robust cross-domain generalization across diverse graph distributions.

Deep Learning · Graph Neural Networks

Federico Errica, Henrik Christiansen, Viktor Zaverkin, Takashi Maruyama, Mathias Niepert, Francesco Alesiani

Long-range interactions are essential for the correct description of complex systems in many scientific fields. The price to pay for including them in the calculations, however, is a dramatic increase in the overall computational costs. Recently, deep graph networks have been employed as efficient, data-driven models for predicting properties of complex systems represented as graphs. These models rely on a message passing strategy that should, in principle, capture long-range information without explicitly modeling the corresponding interactions. In practice, most deep graph networks cannot really model long-range dependencies due to the intrinsic limitations of (synchronous) message passing, namely oversmoothing, oversquashing, and underreaching. This work proposes a general framework that \textit{learns to mitigate} these limitations: within a variational inference framework, we endow message passing architectures with the ability to adapt their depth and filter messages along the way. With theoretical and empirical arguments, we show that this strategy better captures long-range interactions, by competing with the state of the art on five node and graph prediction datasets.

Applications · Computer Vision

Yuanhuiyi Lyu, Xu Zheng, Lutao Jiang, Yibo Yan, Xin Zou, Huiyu Zhou, Linfeng Zhang, Xuming Hu

Recent text-to-image generative models, e.g., Stable Diffusion V3 and Flux, have achieved notable progress. However, these models are strongly restricted to their limited knowledge, a.k.a., their own fixed parameters, that are trained with closed datasets. This leads to significant hallucinations or distortions when facing fine-grained and unseen novel real-world objects, e.g., the appearance of the Tesla Cybertruck. To this end, we present **the first** real-object-based retrieval-augmented generation framework (**RealRAG**), which augments fine-grained and unseen novel object generation by learning and retrieving real-world images to overcome the knowledge gaps of generative models. Specifically, to integrate missing memory for unseen novel object generation, we train a reflective retriever by **self-reflective contrastive learning**, which injects the generator's knowledge into the sef-reflective negatives, ensuring that the retrieved augmented images compensate for the model's missing knowledge. Furthermore, the real-object-based framework integrates fine-grained visual knowledge for the generative models, tackling the distortion problem and improving the realism for fine-grained object generation. Our Real-RAG is superior in its modular application to **all types** of state-of-the-art text-to-image generative models and also delivers **remarkable** performance boosts with all of them, such as a **gain of *16.18\%* FID score** with the auto-regressive model on the Stanford Car benchmark.

Optimization · Everything Else

Ke Ren, Peyman Mohajerin Esfahani, Angelos Georghiou

We study inverse optimization (IO), where the goal is to use a parametric optimization program as the hypothesis class to infer relationships between input-decision pairs. Most of the literature focuses on learning only the objective function, as learning the constraint function (i.e., feasible regions) leads to nonconvex training programs. Motivated by this, we focus on learning feasible regions for known linear objectives, and introduce two training losses along with a hypothesis class to parameterize the constraint function. Our hypothesis class surpasses the previous objective-only method by naturally capturing discontinuous behaviors in input-decision pairs. We introduce a customized block coordinate descent algorithm with a smoothing technique to solve the training problems, while for further restricted hypothesis classes, we reformulate the training optimization as a tractable convex program or mixed integer linear program. Synthetic experiments and two power system applications including comparisons with state-of-the-art approaches showcase and validate the proposed approach.

Deep Learning · Other Representation Learning

Haorun Cai, Han-Jia Ye

Deep tabular models have demonstrated remarkable success on i.i.d. data, excelling in a variety of structured data tasks. However, their performance often deteriorates under temporal distribution shifts, where trends and periodic patterns are present in the evolving data distribution over time.In this paper, we explore the underlying reasons for this failure in capturing temporal dependencies. We begin by investigating the training protocol, revealing a key issue in how the data is split for model training and validation.While existing approaches typically use temporal ordering for splitting, we show that even a random split significantly improves model performance. By accounting for reducing training lag and validation bias to achieve better generalization ability, our proposed splitting protocol offers substantial improvements across a variety of methods.Furthermore, we analyses how temporal data affects deep tabular representations, uncovering that these models often fail to capture crucial periodic and trend information. To address this gap, we introduce a plug-and-play temporal embedding based on Fourier series expansion to learn and incorporate temporal patterns, offering an adaptive approach to handle temporal shifts.Our experiments demonstrate that this temporal embedding, combined with the improved splitting strategy, provides a more effective and robust framework for learning from temporal tabular data.

Reinforcement Learning

Alessio Russo, Aldo Pacchiano

We study the policy evaluation problem in an online multi-reward multi-policy discounted setting, where multiple reward functions must be evaluated simultaneously for different policies. We adopt an $(\epsilon,\delta)$-PAC perspective to achieve $\epsilon$-accurate estimates with high confidence across finite or convex sets of rewards, a setting that has not been investigated in the literature. Building on prior work on Multi-Reward Best Policy Identification, we adapt the MR-NaS exploration scheme to jointly minimize sample complexity for evaluating different policies across different reward sets. Our approach leverages an instance-specific lower bound revealing how the sample complexity scales with a measure of value deviation, guiding the design of an efficient exploration policy. Although computing this bound entails a hard non-convex optimization, we propose an efficient convex approximation that holds for both finite and convex reward sets. Experiments in tabular domains demonstrate the effectiveness of this adaptive exploration scheme.

Applications

Ya Jiang, Chuxiong Wu, Massieh Kordi Boroujeny, Brian Mark, Kai Zeng

Watermarking for large language models (LLMs) offers a promising approach to identifying AI-generated text. Existing approaches, however, either compromise the distribution of original generated text by LLMs or are limited to embedding zero-bit information that only allows for watermark detection but ignores identification. We present StealthInk, a stealthy multi-bit watermarking scheme that preserves the original text distribution while enabling the embedding of provenance data, such as userID, TimeStamp, and modelID, within LLM-generated text. This enhances fast traceability without requiring access to the language model's API or prompts. We derive a lower bound on the number of tokens necessary for watermark detection at a fixed equal error rate, which provides insights on how to enhance the capacity. Comprehensive empirical evaluations across diverse tasks highlight the stealthiness, detectability, and resilience of StealthInk, establishing it as an effective solution for LLM watermarking applications.

Deep Learning · Graph Neural Networks

GUOGUO AI, Guansong Pang, Hezhe Qiao, YuanGao, Hui Yan

Graph Transformers (GTs) have demonstrated remarkable performance in graph representation learning over popular graph neural networks (GNNs). However, self-attention, the core module of GTs, preserves only low-frequency signals in graph features, leading to ineffectiveness in capturing other important signals like high-frequency ones. Some recent GT models help alleviate this issue, but their flexibility and expressiveness are still limited since the filters they learn are fixed on predefined graph spectrum or spectral order. To tackle this challenge, we propose a Graph Fourier Kolmogorov-Arnold Transformer (GrokFormer), a novel GT model that learns highly expressive spectral filters with adaptive graph spectrum and spectral order through a Fourier series modeling over learnable activation functions. We demonstrate theoretically and empirically that the proposed GrokFormer filter offers better expressiveness than other spectral methods. Comprehensive experiments on 10 real-world node classification datasets across various domains, scales, and graph properties, as well as 5 graph classification datasets, show that GrokFormer outperforms state-of-the-art GTs and GNNs. Our code is available at https://github.com/GGA23/GrokFormer.