论文检索

Deep Learning · Graph Neural Networks

Wei Huang, Hanchen Wang, Dong Wen, SHAOZHEN MA, Wenjie Zhang, Xuemin Lin

Graph Edit Distance (GED) is a fundamental graph similarity metric widely used in various applications. However, computing GED is an NP-hard problem. Recent state-of-the-art hybrid GED solver has shown promising performance by formulating GED as a bipartite graph matching problem, then leveraging a generative diffusion model to predict node matching between two graphs, from which both the GED and its corresponding edit path can be extracted using a traditional algorithm. However, such methods typically rely heavily on ground-truth supervision, where the ground-truth node matchings are often costly to obtain in real-world scenarios. In this paper, we propose GEDRanker, a novel unsupervised GAN-based framework for GED computation. Specifically, GEDRanker consists of a matching-based GED solver and introduces an interpretable preference-aware discriminator. By leveraging preference signals over different node matchings derived from edit path lengths, the discriminator can guide the matching-based solver toward generating high-quality node matching without the need for ground-truth supervision. Extensive experiments on benchmark datasets demonstrate that our GEDRanker enables the matching-based GED solver to achieve near-optimal solution quality without any ground-truth supervision.

Social Aspects · Accountability, Transparency and Interpretability

Dipkamal Bhusal, Michael Clifford, Sara Rampazzi, Nidhi Rastogi

Interpreting deep neural networks through concept-based explanations offers a bridge between low-level features and high-level human-understandable semantics. However, existing automatic concept discovery methods often fail to align these extracted concepts with the model’s true decision-making process, thereby compromising explanation faithfulness. In this work, we propose FACE (Faithful Automatic Concept Extraction), a novel framework that combines Non-negative Matrix Factorization (NMF) with a Kullback-Leibler (KL) divergence regularization term to ensure alignment between the model’s original and concept-based predictions. Unlike prior methods that operate solely on encoder activations, FACE incorporates classifier supervision during concept learning, enforcing predictive consistency and enabling faithful explanations. We provide theoretical guarantees showing that minimizing the KL divergence bounds the deviation in predictive distributions, thereby promoting faithful local linearity in the learned concept space. Systematic evaluations on ImageNet, COCO, and CelebA datasets demonstrate that FACE outperforms existing methods across faithfulness and sparsity metrics.

Computer Vision · Image and Video Generation

Donghoon Ahn, Jiwon Kang, Sanghyun Lee, Minjae Kim, Wooseok Jang, Jaewon Min, Sangwu Lee, Sayak Paul, Seungryong Kim

Recent guidance methods in diffusion models steer reverse sampling by perturbing the model to construct an implicit weak model and guide generation away from it. Among these approaches, attention perturbation has demonstrated strong empirical performance in unconditional scenarios where classifier-free guidance is not applicable. However, existing attention perturbation methods lack principled approaches for determining where perturbations should be applied, particularly in Diffusion Transformer (DiT) architectures where quality-relevant computations are distributed across layers. In this paper, we investigate the granularity of attention perturbations, ranging from the layer level down to individual attention heads, and discover that specific heads govern distinct visual concepts such as structure, style, and texture quality. Building on this insight, we propose ``HeadHunter", a systematic framework for iteratively selecting attention heads that align with user-centric objectives, enabling fine-grained control over generation quality and visual attributes. In addition, we introduce SoftPAG, which linearly interpolates each selected head’s attention map toward an identity matrix, providing a continuous knob to tune perturbation strength and suppress artifacts. Our approach not only mitigates the oversmoothing issues of existing layer-level perturbation but also enables targeted manipulation of specific visual styles through compositional head selection. We validate our method on modern large-scale DiT-based text-to-image models including Stable Diffusion 3 and FLUX.1, demonstrating superior performance in both general quality enhancement and style-specific guidance. Our work provides the first head-level analysis of attention perturbation in diffusion models, uncovering interpretable specialization within attention layers and enabling practical design of effective perturbation strategies.

Computer Vision · Segmentation

Md Mostafijur Rahman, Radu Marculescu

U‑shaped networks output logits at multiple spatial scales, each capturing a different blend of coarse context and fine detail. Yet, training still treats these logits in isolation—either supervising only the final, highest‑resolution logits or applying deep supervision with identical loss weights at every scale—without exploring *mixed‑scale* combinations. Consequently, the decoder output misses the complementary cues that arise only when coarse and fine predictions are fused. To address this issue, we introduce LoMix ($\underline{Lo}$gits $\underline{Mix}$ing), a Neural Architecture Search (NAS)‑inspired, differentiable plug-and-play module that **generates** new mixed‑scale outputs and **learns** how exactly each of them should guide the training process. More precisely, LoMix mixes the multi-scale decoder logits with four lightweight fusion operators: addition, multiplication, concatenation, and attention-based weighted fusion, yielding a rich set of synthetic “mutant’’ maps. Every original or mutant map is given a softplus loss weight that is co‑optimized with network parameters, mimicking a one‑step architecture search that automatically discovers the most useful scales, mixtures, and operators. Plugging LoMix into recent U-shaped architectures (i.e., PVT‑V2‑B2 backbone with EMCAD decoder) on Synapse 8‑organ dataset improves DICE by +4.2\% over single‑output supervision, +2.2\% over deep supervision, and +1.5\% over equally weighted additive fusion, all with **zero** inference overhead. When training data are scarce (e.g., one or two labeled scans, 5\% of the trainset), the advantage grows to +9.23\%, underscoring LoMix’s data efficiency. Across four benchmarks and diverse U-shaped networks, LoMiX improves DICE by up to +13.5\% over single-output supervision, confirming that learnable weighted mixed‑scale fusion generalizes broadly while remaining data efficient, fully interpretable, and overhead-free at inference. Our implementation is available at https://github.com/SLDGroup/LoMix.

Applications · Neuroscience, Cognitive Science

Hyunmo Kang, Abdulkadir Canatar, SueYeon Chung

Understanding representational similarity between neural recordings and computational models is essential for neuroscience, yet remains challenging to measure reliably due to the constraints on the number of neurons that can be recorded simultaneously. In this work, we apply tools from Random Matrix Theory to investigate how such limitations affect similarity measures, focusing on Centered Kernel Alignment (CKA) and Canonical Correlation Analysis (CCA). We propose an analytical framework for representational similarity analysis that relates measured similarities to the spectral properties of the underlying representations. We demonstrate that neural similarities are systematically underestimated under finite neuron sampling, mainly due to eigenvector delocalization. To overcome this, we introduce a denoising method to infer population-level similarity, enabling accurate analysis even with small neuron samples. Theoretical predictions are validated on synthetic and real datasets, offering practical strategies for interpreting neural data under finite sampling constraints.

Social Aspects · Accountability, Transparency and Interpretability

Johanna Vielhaben, Dilyara Bareeva, Jim Berend, Wojciech Samek, Nils Strodthoff

Measuring the alignment between representations lets us understand similarities between the feature spaces of different models, such as Vision Transformers trained under diverse paradigms. However, traditional measures for representational alignment yield only scalar values that obscure how these spaces agree in terms of learned features. To address this, we combine alignment analysis with concept discovery, allowing a fine-grained breakdown of alignment into individual concepts. This approach reveals both universal concepts across models and each representation’s internal concept structure. We introduce a new definition of concepts as non-linear manifolds, hypothesizing they better capture the geometry of the feature space. A sanity check demonstrates the advantage of this manifold-based definition over linear baselines for concept-based alignment. Finally, our alignment analysis of four different ViTs shows that increased supervision tends to reduce semantic organization in learned representations.

Applications · Health

Silas Ruhrberg Estévez, Nicolás Astorga, Mihaela van der Schaar

There is growing interest in using machine learning (ML) to support clinical diagnosis, but most approaches rely on static, fully observed datasets and fail to reflect the sequential, resource-aware reasoning clinicians use in practice. Diagnosis remains complex and error prone, especially in high-pressure or resource-limited settings, underscoring the need for frameworks that help clinicians make timely and cost-effective decisions. We propose ACTMED (Adaptive Clinical Test selection via Model-based Experimental Design), a diagnostic framework that integrates Bayesian Experimental Design (BED) with large language models (LLMs) to better emulate real-world diagnostic reasoning. At each step, ACTMED selects the test expected to yield the greatest reduction in diagnostic uncertainty for a given patient. LLMs act as flexible simulators, generating plausible patient state distributions and supporting belief updates without requiring structured, task-specific training data. Clinicians can remain in the loop; reviewing test suggestions, interpreting intermediate outputs, and applying clinical judgment throughout. We evaluate ACTMED on real-world datasets and show it can optimize test selection to improve diagnostic accuracy, interpretability, and resource use. This represents a step toward transparent, adaptive, and clinician-aligned diagnostic systems that generalize across settings with reduced reliance on domain-specific data.

Applications

Chengpeng Li, Zhengyang Tang, Ziniu Li, Mingfeng Xue, Keqin Bao, Tian Ding, Ruoyu Sun, Benyou Wang, Xiang Wang, Junyang Lin 等

Large reasoning models (LRMs) like OpenAI-o1 have shown impressive capabilities in natural language reasoning. However, these models frequently demonstrate inefficiencies or inaccuracies when tackling complex mathematical operations. While integrating computational tools such as Code Interpreters (CIs) offers a promising solution, it introduces a critical challenge: a conflict between the model's internal, probabilistic reasoning and the external, deterministic knowledge provided by the CI, which often leads models to unproductive deliberation. To overcome this, we introduce CoRT (Code-Optimized Reasoning Training), a post-training framework designed to teach LRMs to effectively utilize CIs. We propose **Hint-Engineering**, a new data synthesis strategy that strategically injects diverse hints at optimal points within reasoning paths. This approach generates high-quality, code-integrated reasoning data specifically tailored to optimize LRM-CI interaction. Using this method, we have synthesized 30 high-quality samples to post-train models ranging from 1.5B to 32B parameters through supervised fine-tuning. CoRT further refines the multi-round interleaving of external CI usage and internal thinking by employing rejection sampling and reinforcement learning. Our experimental evaluations demonstrate CoRT's effectiveness, yielding absolute improvements of 4\% and 8\% on DeepSeek-R1-Distill-Qwen-32B and DeepSeek-R1-Distill-Qwen-1.5B, respectively, across five challenging mathematical reasoning datasets. Moreover, CoRT significantly enhances efficiency, reducing token usage by approximately 30\% for the 32B model and 50\% for the 1.5B model compared to pure natural language reasoning baselines. The models and code are available at: [this url](https://github.com/ChengpengLi1003/CoRT).

Applications · Language, Speech and Dialog

Umberto Cappellazzo, Minsu Kim, Pingchuan Ma, Honglie Chen, Xubo Liu, Stavros Petridis, Maja Pantic

Large language models (LLMs) have recently shown strong potential in audio-visual speech recognition (AVSR), but their high computational demands and sensitivity to token granularity limit their practicality in resource-constrained settings. Token compression methods can reduce inference cost, but they require fixing a compression rate in advance and produce a single fixed-length output, offering no flexibility to balance information density and efficiency at inference time. Matryoshka representation learning (MRL) addresses this by enabling a single model to operate across multiple token granularities, allowing compression rates to be adjusted dynamically. However, current MRL-based methods treat each scale independently during training, limiting cross-scale generalization, robustness at high compression, and interpretability. To overcome these limitations, we propose MoME (Mixture of Matryoshka Experts), a novel framework that integrates sparse Mixture-of-Experts (MoE) into MRL-based LLMs for AVSR. MoME augments a frozen LLM with top-k routed and shared experts, allowing dynamic capacity allocation across scales and modalities. A shared router promotes consistent expert activation across granularities, enabling compressed sequences to benefit from representations learned at lower compression. Experiments on LRS2 and LRS3 demonstrate that MoME achieves state-of-the-art performance across AVSR, ASR, and VSR tasks, while requiring significantly fewer parameters and maintaining robustness under noise. MoME unifies the adaptability of MRL with the efficiency of MoE, offering a scalable and interpretable solution for resource-aware speech recognition.

Deep Learning · Robustness

Chenxu Niu, Jie Zhang, Yanbing Liu, Yunpeng Li, Jinta Weng, Yue Hu

Backdoor attacks pose a significant threat to large language models (LLMs) by embedding malicious triggers that manipulate model behavior. However, existing defenses primarily rely on prior knowledge of backdoor triggers or targets and offer only superficial mitigation strategies, thus struggling to fundamentally address the inherent reliance on unreliable features. To address these limitations, we propose a novel defense strategy, \textit{RepGuard}, that strengthens LLM resilience by adaptively separating abnormal features from useful semantic representations, rendering the defense agnostic to specific trigger patterns. Specifically, we first introduce a dual-perspective feature localization strategy that integrates local consistency and sample-wise deviation metrics to identify suspicious backdoor patterns. Based on this identification, an adaptive mask generation mechanism is applied to isolate backdoor-targeted shortcut features by decomposing hidden representations into independent spaces, while preserving task-relevant semantics. With a multi-objective optimization framework, our method can inherently mitigates backdoor attacks. Across \textit{Target Refusal} and \textit{Jailbreak} tasks under four types of attacks, RepGuard consistently reduced the attack success rate on poisoned data by nearly 80\% on average, while maintaining near-original task performance on clean data. Extensive experiments demonstrate that RepGuard provides a scalable and interpretable solution for safeguarding LLMs against sophisticated backdoor threats.

Social Aspects · Accountability, Transparency and Interpretability

Jaehyun Park, Konyul Park, Daehun Kim, Junseo Park, Jun Won Choi

In autonomous driving, transparency in the decision-making of perception models is critical, as even a single misperception can be catastrophic. Yet with multi-sensor inputs, it is difficult to determine how each modality contributes to a prediction because sensor information becomes entangled within the fusion network. We introduce Layer-Wise Modality Decomposition (LMD), a post-hoc, model-agnostic interpretability method that disentangles modality-specific information across all layers of a pretrained fusion model. To our knowledge, LMD is the first approach to attribute the predictions of a perception model to individual input modalities in a sensor-fusion system for autonomous driving. We evaluate LMD on pretrained fusion models under camera–radar, camera–LiDAR, and camera–radar–LiDAR settings for autonomous driving. Its effectiveness is validated using structured perturbation-based metrics and modality-wise visual decompositions, demonstrating practical applicability to interpreting high-capacity multimodal architectures. Code is available at https://github.com/detxter-jvb/Layer-Wise-Modality-Decomposition.

Computer Vision · Vision Models & Multimodal

Dmitry Lvov, Ilya Pershin

Predicting human eye movements during goal-directed visual search is critical for enhancing interactive AI systems. In medical imaging, such prediction can support radiologists in interpreting complex data, such as chest X-rays. Many existing methods rely on generic vision--language models and saliency-based features, which can limit their ability to capture fine-grained clinical semantics and integrate domain knowledge effectively. We present \textbf{LogitGaze-Med}, a state-of-the-art multimodal transformer framework that unifies (1) domain-specific visual encoders (e.g., CheXNet), (2) textual embeddings of diagnostic labels, and (3) semantic priors extracted via the logit-lens from an instruction-tuned medical vision--language model (LLaVA-Med). By directly predicting continuous fixation coordinates and dwell durations, our model generates clinically meaningful scanpaths. Experiments on the GazeSearch dataset and synthetic scanpaths generated from MIMIC-CXR and validated by experts demonstrate that LogitGaze-Med improves scanpath similarity metrics by 20--30\% over competitive baselines and yields over 5\% gains in downstream pathology classification when incorporating predicted fixations as additional training data.

Deep Learning · Graph Neural Networks

Tian Qiu, Wenda Li, Zunlei Feng, Jie Lei, Tao Wang, Yi Gao, Mingli Song, Yang Gao

Fraudulent activities have caused substantial negative social impacts and are exhibiting emerging characteristics such as intelligence and industrialization, posing challenges of high-order interactions, intricate dependencies, and the sparse yet concealed nature of fraudulent entities. Existing graph fraud detectors are limited by their narrow "receptive fields", as they focus only on the relations between an entity and its neighbors while neglecting longer-range structural associations hidden between entities. To address this issue, we propose a novel fraud detector based on Graph Path Aggregation (GPA). It operates through variable-length path sampling, semantic-associated path encoding, path interaction and aggregation, and aggregation-enhanced fraud detection. To further facilitate interpretable association analysis, we synthesize G-Internet, the first benchmark dataset in the field of internet fraud detection. Extensive experiments across datasets in multiple fraud scenarios demonstrate that the proposed GPA outperforms mainstream fraud detectors by up to +15% in Average Precision (AP). Additionally, GPA exhibits enhanced robustness to noisy labels and provides excellent interpretability by uncovering implicit fraudulent patterns across broader contexts. Code is available at https://github.com/horrible-dong/GPA.

Theory · Game Theory

Yatong Chen, Safwan Hossain, Yiling Chen

We examine hypothesis testing within a principal-agent framework, where a strategic agent, holding private beliefs about the effectiveness of a product, submits data to a principal who decides on approval. The principal employs a hypothesis testing rule, aiming to pick a p-value threshold that balances false positives and false negatives while anticipating the agent’s incentive to maximize expected profitability. Building on prior work, we develop a game-theoretic model that captures how the agent’s participation and reporting behavior respond to the principal’s statistical decision rule. Despite the complexity of the interaction, we show that the principal's errors exhibit clear monotonic behavior when segmented by an efficiently computable critical p-value threshold, leading to an interpretable characterization of their optimal p-value threshold. We empirically validate our model and these insights using publicly available data on drug approvals. Overall, our work offers a comprehensive perspective on strategic interactions within the hypothesis testing framework, providing technical and regulatory insights.

Applications · Genetics, Cell Biology, etc

Jiayi Fan, Jingyuan Yang, Shuangge Ma, Mengyun Wu

Accurate network estimation serves as the cornerstone for understanding complex systems across scientific domains, from decoding gene regulatory networks in systems biology to identifying social relationship patterns in computational sociology. Modern applications demand methods that simultaneously address two critical challenges: capturing nonlinear dependencies between variables and reconstructing inherent hierarchical structures where higher-level entities coordinate lower-level components (e.g., functional pathways organizing gene clusters). Traditional Gaussian graphical models fundamentally fail in these aspects due to their restrictive linear assumptions and flat network representations. We propose NNBLNet, a neural network-based learning framework for bi-level network inference. The core innovation lies in hierarchical selection layers that enforce structural consistency between high-level coordinator groups and their constituent low-level connections via adaptive sparsity constraints. This architecture is integrated with a compositional neural network architecture that learn cross-level association patterns through constrained nonlinear transformations, explicitly preserving hierarchical dependencies while overcoming the representational limitations of linear methods. Crucially, we establish formal theoretical guarantees for the consistent recovery of both high-level connections and their internal low-level structures under general statistical regimes. Extensive validation demonstrates NNBLNet's effectiveness across synthetic and real-world scenarios, achieving superior F1 scores compared to competitive methods and particularly beneficial for complex systems analysis through its interpretable bi-level structure discovery.

Optimization

Zhiqin Zhang, Yining Ma, Zhiguang Cao, Hoong Chuin Lau

Neural combinatorial optimization (NCO) has achieved remarkable performance, yet its learned model representations and decision rationale remain a black box. This impedes both academic research and practical deployment, since researchers and stakeholders require deeper insights into NCO models. In this paper, we take the first critical step towards interpreting NCO models by investigating their representations through various probing tasks. Moreover, we introduce a novel probing tool named Coefficient Significance Probing (CS-Probing) to enable deeper analysis of NCO representations by examining the coefficients and statistical significance during probing. Extensive experiments and analysis reveal that NCO models encode low-level information essential for solution construction, while capturing high-level knowledge to facilitate better decisions. Using CS-Probing, we find that prevalent NCO models impose varying inductive biases on their learned representations, uncover direct evidence related to model generalization, and identify key embedding dimensions associated with specific knowledge. These insights can be potentially translated into practice, for example, with minor code modifications, we improve the generalization of the analyzed model. Our work represents a first systematic attempt to interpret black-box NCO models, showcasing probing as a promising tool for analyzing their internal mechanisms and revealing insights for the NCO community. The source code is publicly available.

General Machine Learning · Representation Learning

Louis Bethune, David Vigouroux, Yilun Du, Rufin VanRullen, Thomas Serre, Victor Boutin

What is the shortest path between two data points lying in a high-dimensional space? While the answer is trivial in Euclidean geometry, it becomes significantly more complex when the data lies on a curved manifold—requiring a Riemannian metric to describe the space's local curvature. Estimating such a metric, however, remains a major challenge in high dimensions. In this work, we propose a method for deriving Riemannian metrics directly from pretrained Energy-Based Models (EBMs)—a class of generative models that assign low energy to high-density regions. These metrics define spatially varying distances, enabling the computation of geodesics—shortest paths that follow the data manifold’s intrinsic geometry. We introduce two novel metrics derived from EBMs and show that they produce geodesics that remain closer to the data manifold and exhibit lower curvature distortion, as measured by alignment with ground-truth trajectories. We evaluate our approach on increasingly complex datasets: synthetic datasets with known data density, rotated character images with interpretable geometry, and high-resolution natural images embedded in a pretrained VAE latent space. Our results show that EBM-derived metrics consistently outperform established baselines, especially in high-dimensional settings. Our work is the first to derive Riemannian metrics from EBMs, enabling data-aware geodesics and unlocking scalable, geometry-driven learning for generative modeling and simulation.

Applications · Neuroscience, Cognitive Science

Zhongju Yuan, Geraint Wiggins, Dick Botteldooren

Today’s deep learning architectures are primarily based on perceptron models, which do not capture the oscillatory dynamics characteristic of biological neurons. Although oscillatory systems have recently gained attention for their closer resemblance to neural behavior, they still fall short of modeling the intricate spatio-temporal interactions observed in natural neural circuits. In this paper, we propose a bio-inspired oscillatory state system (BioOSS) designed to emulate the wave-like propagation dynamics critical to neural processing, particularly in the prefrontal cortex (PFC), where complex activity patterns emerge. BioOSS comprises two interacting populations of neurons: p neurons, which represent simplified membrane-potential-like units inspired by pyramidal cells in cortical columns, and o neurons, which govern propagation velocities and modulate the lateral spread of activity. Through local interactions, these neurons produce wave-like propagation patterns. The model incorporates trainable parameters for damping and propagation speed, enabling flexible adaptation to task-specific spatio-temporal structures. We evaluate BioOSS on both synthetic and real-world tasks, demonstrating superior performance and enhanced interpretability compared to alternative architectures.

Applications · Neuroscience, Cognitive Science

Matthew Bull, Po-Chen Kuo, Andrew Smith, Michael Buice

The modern connectivist framing of neural computation emphasizes the primacy of synaptic communication at the risk of neglecting the influence of the surrounding neuromodulatory environment --- a neuron's 'biophysical context.' Decades of experimental work has established two views of neuromodulatory (NMs) influence: 1) NMs significantly alter circuit dynamics and 2) NMs gate synaptic plasticity, acting as a 'third factor' in learning. Here, we unify these perspectives, proposing that neuromodulation via volume transmission implements a powerful computational principle: context factorization. We derive an endogenously neuromodulated Recurrent Neural Network (e-nmRNN) from a rate reduction of NM release, showing how NM concentrations dynamically factorize network connectivity. This framework reveals how multiplicative NM gating distinctly influences dynamical regimes compared to additive input. Crucially, this context factorization enables targeted online credit assignment: learning rules derived for the e-nmRNN are naturally gated by NM concentrations, localizing updates to relevant contexts. We demonstrate that e-nmRNN dynamics can learn to approximate gradient descent, facilitating rapid in-context adaptation akin to meta-learning. Empirically, e-nmRNNs achieve strong compositional generalization in sequence-to-sequence tasks, outperforming baselines and exhibiting greater hyperparameter robustness. Furthermore, when trained on complex multitasking benchmarks, e-nmRNNs develop emergent properties mirroring biological observations, including modularity, cell-type specialization based on NM release, and distinct neuromodulatory timescales encoding task context. The model's interpretability allows us to reverse engineer these emergent structures. Notably, in reinforcement learning tasks, the e-nmRNN learns to encode context and signals like Reward Prediction Error (RPE) within its neuromodulator dynamics, demonstrating a mechanism for RPE-gated online credit assignment essential for learning how to learn. By bridging biophysical mechanisms with computational principles and empirical validation, our work presents e-nmRNNs as a performant, interpretable model for understanding the computational role of neuromodulation in flexible and compositional learning.

Applications · Everything Else

Henry Pinkard, Leyla Kabuli, Eric Markley, Tiffany Chien, Jiantao Jiao, Laura Waller

Imaging systems have traditionally been designed to mimic the human eye and produce visually interpretable measurements. Modern imaging systems, however, process raw measurements computationally before or instead of human viewing. As a result, the information content of raw measurements matters more than their visual interpretability. Despite the importance of measurement information content, current approaches for evaluating imaging system performance do not quantify it: they instead either use alternative metrics that assess specific aspects of measurement quality or assess measurements indirectly with performance on secondary tasks. We developed the theoretical foundations and a practical method to directly quantify mutual information between noisy measurements and unknown objects. By fitting probabilistic models to measurements and their noise characteristics, our method estimates information by upper bounding its true value. By applying gradient-based optimization to these estimates, we also developed a technique for designing imaging systems called Information-Driven Encoder Analysis Learning (IDEAL). Our information estimates accurately captured system performance differences across four imaging domains (color photography, radio astronomy, lensless imaging, and microscopy). Systems designed with IDEAL matched the performance of those designed with end-to-end optimization, the prevailing approach that jointly optimizes hardware and image processing algorithms. These results establish mutual information as a universal performance metric for imaging systems that enables both computationally efficient design optimization and evaluation in real-world conditions. A video summary of this work can be found at: https://waller-lab.github.io/EncodingInformationWebsite/