We employ a unified framework for computing the information capacity of biological signaling systems using Fisher Information. By deriving closed-form or easily computable information capacity formulas, we quantify how well different signaling models, including binomial, multinomial, Poisson, Gaussian, and Gamma distributions, can discriminate among input signals. These expressions clarify how key features such as signal range, noise scaling, pathway length, and receivers' diversity shape the theoretical limits of sensing. In particular, we show how signal-to-noise ratio and fold-change sensitivity arise naturally within the Fisher formalism, and how signal degradation in cascades imposes linear information loss. Our results provide intuitive, analytically grounded tools to benchmark and guide the analysis of real signaling systems, without requiring computationally expensive mutual information estimation. While motivated by cellular communication, the framework generalizes to any system where noisy input-output relationships constrain transmission fidelity, including synthetic biology, sensor networks, and engineered communication channels.
Ensuring the trustworthiness of large language models (LLMs) is crucial. Most studies concentrate on fully pre-trained LLMs to better understand and improve LLMs' trustworthiness. In this paper, to reveal the untapped potential of pre-training, we pioneer the exploration of LLMs' trustworthiness during this period, focusing on five key dimensions: reliability, privacy, toxicity, fairness, and robustness. To begin with, we apply linear probing to LLMs. The high probing accuracy suggests that \textit{LLMs in early pre-training can already distinguish concepts in each trustworthiness dimension}. Therefore, to further uncover the hidden possibilities of pre-training, we extract steering vectors from a LLM's pre-training checkpoints to enhance the LLM's trustworthiness. Finally, inspired by~\citet{choi2023understanding} that mutual information estimation is bounded by linear probing accuracy, we also probe LLMs with mutual information to investigate the dynamics of trustworthiness during pre-training. We are the first to observe a similar two-phase phenomenon: fitting and compression~\citep{shwartz2017opening}. This research provides an initial exploration of trustworthiness modeling during LLM pre-training, seeking to unveil new insights and spur further developments in the field. We will make our code publicly accessible at \url{https://github.com/ChnQ/TracingLLM}.
Recent advances in large language models (LLMs) have promoted generative error correction (GER) for automatic speech recognition (ASR), which leverages the rich linguistic knowledge and powerful reasoning ability of LLMs to improve recognition results. The latest work proposes a GER benchmark with HyPoradise dataset to learn the mapping from ASR N-best hypotheses to ground-truth transcription by efficient LLM finetuning, which shows great effectiveness but lacks specificity on noise-robust ASR. In this work, we extend the benchmark to noisy conditions and investigate if we can teach LLMs to perform denoising for GER just like what robust ASR do}, where one solution is introducing noise information as a conditioner into LLM. However, directly incorporating noise embeddings from audio encoder could harm the LLM tuning due to cross-modality gap. To this end, we propose to extract a language-space noise embedding from the N-best list to represent the noise conditions of source speech, which can promote the denoising process in GER. Furthermore, in order to enhance its representation ability of audio noise, we design a knowledge distillation (KD) approach via mutual information estimation to distill the real noise information in audio embeddings to our language embedding. Experiments on various latest LLMs demonstrate our approach achieves a new breakthrough with up to 53.9% correction improvement in terms of word error rate while with limited training data. Analysis shows that our language-space noise embedding can well represent the noise conditions of source speech, under which off-the-shelf LLMs show strong ability of language-space denoising.
The pointwise mutual information profile, or simply profile, is the distribution of pointwise mutual information for a given pair of random variables. One of its important properties is that its expected value is precisely the mutual information between these random variables. In this paper, we analytically describe the profiles of multivariate normal distributions and introduce a novel family of distributions, Bend and Mix Models, for which the profile can be accurately estimated using Monte Carlo methods. We then show how Bend and Mix Models can be used to study the limitations of existing mutual information estimators, investigate the behavior of neural critics used in variational estimators, and understand the effect of experimental outliers on mutual information estimation. Finally, we show how Bend and Mix Models can be used to obtain model-based Bayesian estimates of mutual information, suitable for problems with available domain expertise in which uncertainty quantification is necessary.
In this work we present a new method for the estimation of Mutual Information (MI) between random variables. Our approach is based on an original interpretation of the Girsanov theorem, which allows us to use score-based diffusion models to estimate the Kullback Leibler divergence between two densities as a difference between their score functions. As a by-product, our method also enables the estimation of the entropy of random variables. Armed with such building blocks, we present a general recipe to measure MI, which unfolds in two directions: one uses conditional diffusion process, whereas the other uses joint diffusion processes that allow simultaneous modelling of two random variables. Our results, which derive from a thorough experimental protocol over all the variants of our approach, indicate that our method is more accurate than the main alternatives from the literature, especially for challenging distributions. Furthermore, our methods pass MI self-consistency tests, including data processing and additivity under independence, which instead are a pain-point of existing methods.
Recently, contrastive learning has become a key component in fine-tuning code search models for software development efficiency and effectiveness. It pulls together positive code snippets while pushing negative samples away given search queries. Among contrastive learning, InfoNCE is the most widely used loss function due to its better performance. However, the following problems in negative samples of InfoNCE may deteriorate its representation learning: 1) The existence of false negative samples in large code corpora due to duplications. 2). The failure to explicitly differentiate between the potential relevance of negative samples. As an example, a bubble sorting algorithm example is less ``negative'' than a file saving function for the quick sorting algorithm query. In this paper, we tackle the above problems by proposing a simple yet effective Soft-InfoNCE loss that inserts weight terms into InfoNCE. In our proposed loss function, we apply three methods to estimate the weights of negative pairs and show that the vanilla InfoNCE loss is a special case of Soft-InfoNCE. Theoretically, we analyze the effects of Soft-InfoNCE on controlling the distribution of learnt code representations and on deducing a more precise mutual information estimation. We furthermore discuss the superiority of proposed loss functions with other design alternatives. Extensive experiments demonstrate the effectiveness of Soft-InfoNCE and weights estimation methods under state-of-the-art code search models on a large-scale public dataset consisting of six programming languages. Source code is available at \url{https://github.com/Alex-HaochenLi/Soft-InfoNCE}.
Zero-shot skeleton-based action recognition aims to recognize actions of unseen categories after training on data of seen categories. The key is to build the connection between visual and semantic space from seen to unseen classes. Previous studies have primarily focused on encoding sequences into a singular feature vector, with subsequent mapping the features to an identical anchor point within the embedded space. Their performance is hindered by 1) the ignorance of the global visual/semantic distribution alignment, which results in a limitation to capture the true interdependence between the two spaces. 2) the negligence of temporal information since the frame-wise features with rich action clues are directly pooled into a single feature vector. We propose a new zero-shot skeleton-based action recognition method via mutual information (MI) estimation and maximization. Specifically, 1) we maximize the MI between visual and semantic space for distribution alignment; 2) we leverage the temporal information for estimating the MI by encouraging MI to increase as more frames are observed. Extensive experiments on three large-scale skeleton action datasets confirm the effectiveness of our method. Code: https://github.com/YujieOuO/SMIE.
Estimating mutual information accurately is pivotal across diverse applications, from machine learning to communications and biology, enabling us to gain insights into the inner mechanisms of complex systems. Yet, dealing with high-dimensional data presents a formidable challenge, due to its size and the presence of intricate relationships. Recently proposed neural methods employing variational lower bounds on the mutual information have gained prominence. However, these approaches suffer from either high bias or high variance, as the sample size and the structure of the loss function directly influence the training process. In this paper, we propose a novel class of discriminative mutual information estimators based on the variational representation of the $f$-divergence. We investigate the impact of the permutation function used to obtain the marginal training samples and present a novel architectural solution based on derangements. The proposed estimator is flexible since it exhibits an excellent bias/variance trade-off. The comparison with state-of-the-art neural estimators, through extensive experimentation within established reference scenarios, shows that our approach offers higher accuracy and lower complexity.
Computing optimal transport (OT) for general high-dimensional data has been a long-standing challenge. Despite much progress, most of the efforts including neural network methods have been focused on the static formulation of the OT problem. The current work proposes to compute the dynamic OT between two arbitrary distributions $P$ and $Q$ by optimizing a flow model, where both distributions are only accessible via finite samples. Our method learns the dynamic OT by finding an invertible flow that minimizes the transport cost. The trained optimal transport flow subsequently allows for performing many downstream tasks, including infinitesimal density ratio estimation (DRE) and domain adaptation by interpolating distributions in the latent space. The effectiveness of the proposed model on high-dimensional data is demonstrated by strong empirical performance on OT baselines, image-to-image translation, and high-dimensional DRE.
Mutual information (MI) is a fundamental quantity in information theory and machine learning. However, direct estimation of MI is intractable, even if the true joint probability density for the variables of interest is known, as it involves estimating a potentially high-dimensional log partition function. In this work, we present a unifying view of existing MI bounds from the perspective of importance sampling, and propose three novel bounds based on this approach. Since accurate estimation of MI without density information requires a sample size exponential in the true MI, we assume either a single marginal or the full joint density information is known. In settings where the full joint density is available, we propose Multi-Sample Annealed Importance Sampling (AIS) bounds on MI, which we demonstrate can tightly estimate large values of MI in our experiments. In settings where only a single marginal distribution is known, we propose Generalized IWAE (GIWAE) and MINE-AIS bounds. Our GIWAE bound unifies variational and contrastive bounds in a single framework that generalizes InfoNCE, IWAE, and Barber-Agakov bounds. Our MINE-AIS method improves upon existing energy-based methods such as MINE-DV and MINE-F by directly optimizing a tighter lower bound on MI. MINE-AIS uses MCMC sampling to estimate gradients for training and Multi-Sample AIS for evaluating the bound. Our methods are particularly suitable for evaluating MI in deep generative models, since explicit forms of the marginal or joint densities are often available. We evaluate our bounds on estimating the MI of VAEs and GANs trained on the MNIST and CIFAR datasets, and showcase significant gains over existing bounds in these challenging settings with high ground truth MI.
The rise of mobile AI accelerators allows latency-sensitive applications to execute lightweight Deep Neural Networks (DNNs) on the client side. However, critical applications require powerful models that edge devices cannot host and must therefore offload requests, where the high-dimensional data will compete for limited bandwidth. This work proposes shifting away from focusing on executing shallow layers of partitioned DNNs. Instead, it advocates concentrating the local resources on variational compression optimized for machine interpretability. We introduce a novel framework for resource-conscious compression models and extensively evaluate our method in an environment reflecting the asymmetric resource distribution between edge devices and servers. Our method achieves 60% lower bitrate than a state-of-the-art SC method without decreasing accuracy and is up to 16x faster than offloading with existing codec standards.
Self-supervised sequential recommendation significantly improves recommendation performance by maximizing mutual information with well-designed data augmentations. However, the mutual information estimation is based on the calculation of Kullback Leibler divergence with several limitations, including asymmetrical estimation, the exponential need of the sample size, and training instability. Also, existing data augmentations are mostly stochastic and can potentially break sequential correlations with random modifications. These two issues motivate us to investigate an alternative robust mutual information measurement capable of modeling uncertainty and alleviating KL divergence limitations. To this end, we propose a novel self-supervised learning framework based on Mutual WasserStein discrepancy minimization MStein for the sequential recommendation. We propose the Wasserstein Discrepancy Measurement to measure the mutual information between augmented sequences. Wasserstein Discrepancy Measurement builds upon the 2-Wasserstein distance, which is more robust, more efficient in small batch sizes, and able to model the uncertainty of stochastic augmentation processes. We also propose a novel contrastive learning loss based on Wasserstein Discrepancy Measurement. Extensive experiments on four benchmark datasets demonstrate the effectiveness of MStein over baselines. More quantitative analyses show the robustness against perturbations and training efficiency in batch size. Finally, improvements analysis indicates better representations of popular users or items with significant uncertainty. The source code is at https://github.com/zfan20/MStein.
We introduce an information-theoretic quantity with similar properties to mutual information that can be estimated from data without making explicit assumptions on the underlying distribution. This quantity is based on a recently proposed matrix-based entropy that uses the eigenvalues of a normalized Gram matrix to compute an estimate of the eigenvalues of an uncentered covariance operator in a reproducing kernel Hilbert space. We show that a difference of matrix-based entropies (DiME) is well suited for problems involving the maximization of mutual information between random variables. While many methods for such tasks can lead to trivial solutions, DiME naturally penalizes such outcomes. We compare DiME to several baseline estimators of mutual information on a toy Gaussian dataset. We provide examples of use cases for DiME, such as latent factor disentanglement and a multiview representation learning problem where DiME is used to learn a shared representation among views with high mutual information.
Probability density estimation from observed data constitutes a central task in statistics. Recent advancements in machine learning offer new tools but also pose new challenges. The big data era demands analysis of long-range spatial and long-term temporal dependencies in large collections of raw data, rendering neural networks an attractive solution for density estimation. In this paper, we exploit the concept of copula to explicitly build an estimate of the probability density function associated to any observed data. In particular, we separate univariate marginal distributions from the joint dependence structure in the data, the copula itself, and we model the latter with a neural network-based method referred to as copula density neural estimation (CODINE). Results show that the novel learning approach is capable of modeling complex distributions and it can be applied for mutual information estimation and data generation.
The pretasks are mainly built on mutual information estimation, which requires data augmentation to construct positive samples with similar semantics to learn invariant signals and negative samples with dissimilar semantics in order to empower representation discriminability. However, an appropriate data augmentation configuration depends heavily on lots of empirical trials such as choosing the compositions of data augmentation techniques and the corresponding hyperparameter settings. We propose an augmentation-free graph contrastive learning method, invariant-discriminative graph contrastive learning (iGCL), that does not intrinsically require negative samples. iGCL designs the invariant-discriminative loss (ID loss) to learn invariant and discriminative representations. On the one hand, ID loss learns invariant signals by directly minimizing the mean square error between the target samples and positive samples in the representation space. On the other hand, ID loss ensures that the representations are discriminative by an orthonormal constraint forcing the different dimensions of representations to be independent of each other. This prevents representations from collapsing to a point or subspace. Our theoretical analysis explains the effectiveness of ID loss from the perspectives of the redundancy reduction criterion, canonical correlation analysis, and information bottleneck principle. The experimental results demonstrate that iGCL outperforms all baselines on 5 node classification benchmark datasets. iGCL also shows superior performance for different label ratios and is capable of resisting graph attacks, which indicates that iGCL has excellent generalization and robustness. The source code is available at https://github.com/lehaifeng/T-GCN/tree/master/iGCL.
Deep neural networks (DNNs) are found to be vulnerable to adversarial noise. They are typically misled by adversarial samples to make wrong predictions. To alleviate this negative effect, in this paper, we investigate the dependence between outputs of the target model and input adversarial samples from the perspective of information theory, and propose an adversarial defense method. Specifically, we first measure the dependence by estimating the mutual information (MI) between outputs and the natural patterns of inputs (called natural MI) and MI between outputs and the adversarial patterns of inputs (called adversarial MI), respectively. We find that adversarial samples usually have larger adversarial MI and smaller natural MI compared with those w.r.t. natural samples. Motivated by this observation, we propose to enhance the adversarial robustness by maximizing the natural MI and minimizing the adversarial MI during the training process. In this way, the target model is expected to pay more attention to the natural pattern that contains objective semantics. Empirical evaluations demonstrate that our method could effectively improve the adversarial accuracy against multiple attacks.
Unsupervised domain adaptation approaches have recently succeeded in various medical image segmentation tasks. The reported works often tackle the domain shift problem by aligning the domain-invariant features and minimizing the domain-specific discrepancies. That strategy works well when the difference between a specific domain and between different domains is slight. However, the generalization ability of these models on diverse imaging modalities remains a significant challenge. This paper introduces UDA-VAE++, an unsupervised domain adaptation framework for cardiac segmentation with a compact loss function lower bound. To estimate this new lower bound, we develop a novel Structure Mutual Information Estimation (SMIE) block with a global estimator, a local estimator, and a prior information matching estimator to maximize the mutual information between the reconstruction and segmentation tasks. Specifically, we design a novel sequential reparameterization scheme that enables information flow and variance correction from the low-resolution latent space to the high-resolution latent space. Comprehensive experiments on benchmark cardiac segmentation datasets demonstrate that our model outperforms previous state-of-the-art qualitatively and quantitatively. The code is available at https://github.com/LOUEY233/Toward-Mutual-Information}{https://github.com/LOUEY233/Toward-Mutual-Information
Graph neural networks (GNNs) have become a powerful tool for processing graph-structured data but still face challenges in effectively aggregating and propagating information between layers, which limits their performance. We tackle this problem with the kernel regression (KR) approach, using KR loss as the primary loss in self-supervised settings or as a regularization term in supervised settings. We show substantial performance improvements compared to state-of-the-art in both scenarios on multiple transductive and inductive node classification datasets, especially for deep networks. As opposed to mutual information (MI), KR loss is convex and easy to estimate in high-dimensional cases, even though it indirectly maximizes the MI between its inputs. Our work highlights the potential of KR to advance the field of graph representation learning and enhance the performance of GNNs. The code to reproduce our experiments is available at https://github.com/Anonymous1252022/KR_for_GNNs
Density ratio estimation (DRE) is a fundamental machine learning technique for comparing two probability distributions. However, existing methods struggle in high-dimensional settings, as it is difficult to accurately compare probability distributions based on finite samples. In this work we propose DRE-\infty, a divide-and-conquer approach to reduce DRE to a series of easier subproblems. Inspired by Monte Carlo methods, we smoothly interpolate between the two distributions via an infinite continuum of intermediate bridge distributions. We then estimate the instantaneous rate of change of the bridge distributions indexed by time (the "time score") -- a quantity defined analogously to data (Stein) scores -- with a novel time score matching objective. Crucially, the learned time scores can then be integrated to compute the desired density ratio. In addition, we show that traditional (Stein) scores can be used to obtain integration paths that connect regions of high density in both distributions, improving performance in practice. Empirically, we demonstrate that our approach performs well on downstream tasks such as mutual information estimation and energy-based modeling on complex, high-dimensional datasets.
Density ratio estimation serves as an important technique in the unsupervised machine learning toolbox. However, such ratios are difficult to estimate for complex, high-dimensional data, particularly when the densities of interest are sufficiently different. In our work, we propose to leverage an invertible generative model to map the two distributions into a common feature space prior to estimation. This featurization brings the densities closer together in latent space, sidestepping pathological scenarios where the learned density ratios in input space can be arbitrarily inaccurate. At the same time, the invertibility of our feature map guarantees that the ratios computed in feature space are equivalent to those in input space. Empirically, we demonstrate the efficacy of our approach in a variety of downstream tasks that require access to accurate density ratios such as mutual information estimation, targeted sampling in deep generative models, and classification with data augmentation.