Causal discovery from observational data is a fundamental task in artificial intelligence, with far-reaching implications for decision-making, predictions, and interventions. Despite significant advances, existing methods can be broadly categorized as constraint-based or score-based approaches. Constraint-based methods offer rigorous causal discovery but are often hindered by small sample sizes, while score-based methods provide flexible optimization but typically forgo explicit conditional independence testing. This work explores a third avenue: developing differentiable d-separation scores, obtained through a percolation theory using soft logic. This enables the implementation of a new type of causal discovery method: gradient-based optimization of conditional independence constraints. Empirical evaluations demonstrate the robust performance of our approach in low-sample regimes, surpassing traditional constraint-based and score-based baselines on a real-world dataset.

Distinguishing cause and effect from bivariate observational data is a foundational problem in many disciplines, but challenging without additional assumptions. Additive noise models (ANMs) are widely used to enable sample-efficient bivariate causal discovery. However, conventional ANM-based methods fail when unobserved mediators corrupt the causal relationship between variables. This paper makes three key contributions: first, we rigorously characterize why standard ANM approaches break down in the presence of unmeasured mediators. Second, we demonstrate that prior solutions for hidden mediation are brittle in finite sample settings, limiting their practical utility. To address these gaps, we propose Bivariate Denoising Diffusion (BiDD) for causal discovery, a method designed to handle latent noise introduced by unmeasured mediators. Unlike prior methods that infer directionality through mean squared error loss comparisons, our approach introduces a novel independence test statistic: during the noising and denoising processes for each variable, we condition on the other variable as input and evaluate the independence of the predicted noise relative to this input. We prove asymptotic consistency of BiDD under the ANM, and conjecture that it performs well under hidden mediation. Experiments on synthetic and real-world data demonstrate consistent performance, outperforming existing methods in mediator-corrupted settings while maintaining strong performance in mediator-free settings.

We study generalized smoothness in nonconvex optimization, focusing on $(L_0, L_1)$-smoothness and anisotropic smoothness. The former was empirically derived from practical neural network training examples, while the latter arises naturally in the analysis of nonlinearly preconditioned gradient methods. We introduce a new sufficient condition that encompasses both notions, reveals their close connection, and holds in key applications such as phase retrieval and matrix factorization. Leveraging tools from dynamical systems theory, we then show that nonlinear preconditioning--including gradient clipping--preserves the saddle point avoidance property of classical gradient descent. Crucially, the assumptions required for this analysis are actually satisfied in these applications, unlike in classical results that rely on restrictive Lipschitz smoothness conditions. We further analyze a perturbed variant that efficiently attains second-order stationarity with only logarithmic dependence on dimension, matching similar guarantees of classical gradient methods.

We present a novel deep neural network architecture for unsupervised subspace clustering. This architecture is built upon deep auto-encoders, which non-linearly map the input data into a latent space. Our key idea is to introduce a novel self-expressive layer between the encoder and the decoder to mimic the self-expressiveness property that has proven effective in traditional subspace clustering. Being differentiable, our new self-expressive layer provides a simple but effective way to learn pairwise affinities between all data points through a standard back-propagation procedure. Being nonlinear, our neural-network based method is able to cluster data points having complex (often nonlinear) structures. We further propose pre-training and fine-tuning strategies that let us effectively learn the parameters of our subspace clustering networks. Our experiments show that the proposed method significantly outperforms the state-of-the-art unsupervised subspace clustering methods.

A large body of recent work focuses on methods for extracting low-dimensional latent structure from multi-neuron spike train data. Most such methods employ either linear latent dynamics or linear mappings from latent space to log spike rates. Here we propose a doubly nonlinear latent variable model that can identify low-dimensional structure underlying apparently high-dimensional spike train data. We introduce the Poisson Gaussian-Process Latent Variable Model (P-GPLVM), which consists of Poisson spiking observations and two underlying Gaussian processes--one governing a temporal latent variable and another governing a set of nonlinear tuning curves. The use of nonlinear tuning curves enables discovery of low-dimensional latent structure even when spike responses exhibit high linear dimensionality (e.g., as found in hippocampal place cell codes). To learn the model from data, we introduce the decoupled Laplace approximation, a fast approximate inference method that allows us to efficiently optimize the latent path while marginalizing over tuning curves. We show that this method outperforms previous Laplace-approximation-based inference methods in both the speed of convergence and accuracy. We apply the model to spike trains recorded from hippocampal place cells and show that it compares favorably to a variety of previous methods for latent structure discovery, including variational auto-encoder (VAE) based methods that parametrize the nonlinear mapping from latent space to spike rates with a deep neural network.

Decoding sensory stimuli from neural signals can be used to reveal how we sense our physical environment, and is valuable for the design of brain-machine interfaces. However, existing linear techniques for neural decoding may not fully reveal or exploit the fidelity of the neural signal. Here we develop a new approximate Bayesian method for decoding natural images from the spiking activity of populations of retinal ganglion cells (RGCs). We sidestep known computational challenges with Bayesian inference by exploiting artificial neural networks developed for computer vision, enabling fast nonlinear decoding that incorporates natural scene statistics implicitly. We use a decoder architecture that first linearly reconstructs an image from RGC spikes, then applies a convolutional autoencoder to enhance the image. The resulting decoder, trained on natural images and simulated neural responses, significantly outperforms linear decoding, as well as simple point-wise nonlinear decoding. These results provide a tool for the assessment and optimization of retinal prosthesis technologies, and reveal that the retina may provide a more accurate representation of the visual scene than previously appreciated.

Reservoir expansion can improve online independent component analysis (ICA) under nonlinear mixing, yet top-$n$ whitening may discard injected features. We formalize this bottleneck as \emph{reservoir subspace injection} (RSI): injected features help only if they enter the retained eigenspace without displacing passthrough directions. RSI diagnostics (IER, SSO, $ρ_x$) identify a failure mode in our top-$n$ setting: stronger injection increases IER but crowds out passthrough energy ($ρ_x: 1.00\!\rightarrow\!0.77$), degrading SI-SDR by up to $2.2$\,dB. A guarded RSI controller preserves passthrough retention and recovers mean performance to within $0.1$\,dB of baseline $1/N$ scaling. With passthrough preserved, RE-OICA improves over vanilla online ICA by $+1.7$\,dB under nonlinear mixing and achieves positive SI-SDR$_{\mathrm{sc}}$ on the tested super-Gaussian benchmark ($+0.6$\,dB).

Using the method of auxiliary coordinates, we derive a training algorithm that works by alternating steps that train an auxiliary embeddingwith steps that train the mapping.

BEACON introduces several novel ideas to the design of implicit communication and efficient exploration.