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Neuroscience, Cognitive Science

Anand Gopalakrishnan, Aleksandar Stanić, Jürgen Schmidhuber, Michael Mozer

Current state-of-the-art synchrony-based models encode object bindings with complex-valued activations and compute with real-valued weights in feedforward architectures. We argue for the computational advantages of a recurrent architecture with complex-valued weights. We propose a fully convolutional autoencoder, SynCx, that performs iterative constraint satisfaction: at each iteration, a hidden layer bottleneck encodes statistically regular configurations of features in particular phase relationships; over iterations, local constraints propagate and the model converges to a globally consistent configuration of phase assignments. Binding is achieved simply by the matrix-vector product operation between complex-valued weights and activations, without the need for additional mechanisms that have been incorporated into current synchrony-based models. SynCx outperforms or is strongly competitive with current models for unsupervised object discovery. SynCx also avoids certain systematic grouping errors of current models, such as the inability to separate similarly colored objects without additional supervision.

Multimodal Models

Thomas Sutter, Yang Meng, Andrea Agostini, Daphné Chopard, Norbert Fortin, Julia Vogt, Babak Shahbaba, Stephan Mandt

Variational Autoencoders for multimodal data hold promise for many tasks in data analysis, such as representation learning, conditional generation, and imputation.Current architectures either share the encoder output, decoder input, or both across modalities to learn a shared representation. Such architectures impose hard constraints on the model. In this work, we show that a better latent representation can be obtained by replacing these hard constraints with a soft constraint. We propose a new mixture-of-experts prior, softly guiding each modality's latent representation towards a shared aggregate posterior.This approach results in a superior latent representation and allows each encoding to preserve information better from its uncompressed original features. In extensive experiments on multiple benchmark datasets and two challenging real-world datasets, we show improved learned latent representations and imputation of missing data modalities compared to existing methods.

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

Miguel A. Carreira-Perpinan, Kuat Gazizov

We propose a new model for dimensionality reduction, the PCA tree, which works like a regular autoencoder, having explicit projection and reconstruction mappings. The projection is effected by a sparse oblique tree, having hard, hyperplane splits using few features and linear leaves. The reconstruction mapping is a set of local linear mappings. Thus, rather than producing a global map as in t-SNE and other methods, which often leads to distortions, it produces a hierarchical set of local PCAs. The use of a sparse oblique tree and PCA makes the overall model interpretable and very fast to project or reconstruct new points. Joint optimization of all the parameters in the tree is a nonconvex nondifferentiable problem. We propose an algorithm that is guaranteed to decrease the error monotonically and which scales to large datasets without any approximation. In experiments, we show PCA trees are able to identify a wealth of low-dimensional and cluster structure in image and document datasets.

Huaijin Wu, Xinyu Ye, Junchi Yan

Molecule generation ideally in its 3-D form has enjoyed wide applications in material, chemistry, life science, etc. We propose the first quantum parametric circuit for 3-D molecule generation for its potential quantum advantage especially considering the arrival of Noisy Intermediate-Scale Quantum (NISQ) era. We choose the Variational AutoEncoder (VAE) scheme for its simplicity and one-shot generation ability, which we believe is more quantum-friendly compared with the auto-regressive generative models or diffusion models as used in classic approaches. Specifically, we present a quantum encoding scheme designed for 3-D molecules with qubits complexity $\mathcal{O}(C\log n)$ ($n$ is the number of atoms) and adopt a von Mises-Fisher (vMF) distributed latent space to meet the inherent coherence of the quantum system. We further design to encode conditions into quantum circuits for property-specified generation. Experimentally, our model could generate plausible 3-D molecules and achieve competitive quantitative performance with significantly reduced circuit parameters compared with their classic counterparts. The source code will be released upon publication.

Deep Learning · Autoencoders

Yura Perugachi Diaz, Arwin Gansekoele, Sandjai Bhulai

Neural image compression has made a great deal of progress. State-of-the-art models are based on variational autoencoders and are outperforming classical models. Neural compression models learn to encode an image into a quantized latent representation that can be efficiently sent to the decoder, which decodes the quantized latent into a reconstructed image. While these models have proven successful in practice, they lead to sub-optimal results due to imperfect optimization and limitations in the encoder and decoder capacity. Recent work shows how to use stochastic Gumbel annealing (SGA) to refine the latents of pre-trained neural image compression models. We extend this idea by introducing SGA+, which contains three different methods that build upon SGA.We show how our method improves the overall compression performance in terms of the R-D trade-off, compared to its predecessors. Additionally, we show how refinement of the latents with our best-performing method improves the compression performance on both the Tecnick and CLIC dataset. Our method is deployed for a pre-trained hyperprior and for a more flexible model.Further, we give a detailed analysis of our proposed methods and show that they are less sensitive to hyperparameter choices. Finally, we show how each method can be extended to three- instead of two-class rounding.

Probabilistic Methods · Bayesian Models and Methods

Matthew Dowling, Yuan Zhao, Memming Park

State-space graphical models and the variational autoencoder framework provide a principled apparatus for learning dynamical systems from data. State-of-the-art probabilistic approaches are often able to scale to large problems at the cost of flexibility of the variational posterior or expressivity of the dynamics model. However, those consolidations can be detrimental if the ultimate goal is to learn a generative model capable of explaining the spatiotemporal structure of the data and making accurate forecasts. We introduce a low-rank structured variational autoencoding framework for nonlinear Gaussian state-space graphical models capable of capturing dense covariance structures that are important for learning dynamical systems with predictive capabilities. Our inference algorithm exploits the covariance structures that arise naturally from sample based approximate Gaussian message passing and low-rank amortized posterior updates -- effectively performing approximate variational smoothing with time complexity scaling linearly in the state dimensionality. In comparisons with other deep state-space model architectures our approach consistently demonstrates the ability to learn a more predictive generative model. Furthermore, when applied to neural physiological recordings, our approach is able to learn a dynamical system capable of forecasting population spiking and behavioral correlates from a small portion of single trials.

Deep Learning · Algorithms

Chia-Hsiang Kao, Bharath Hariharan

Despite its widespread use in neural networks, error backpropagation has faced criticism for its lack of biological plausibility, suffering from issues such as the backward locking problem and the weight transport problem. These limitations have motivated researchers to explore more biologically plausible learning algorithms that could potentially shed light on how biological neural systems adapt and learn. Inspired by the counter-current exchange mechanisms observed in biological systems, we propose counter-current learning (CCL), a biologically plausible framework for credit assignment in deep learning. This framework employs a feedforward network to process input data and a feedback network to process targets, with each network enhancing the other through anti-parallel signal propagation. By leveraging the more informative signals from the bottom layer of the feedback network to guide the updates of the top layer of the feedforward network and vice versa, CCL enables the simultaneous transformation of source inputs to target outputs and the dynamic mutual influence of these transformations.Experimental results on MNIST, FashionMNIST, CIFAR10, CIFAR100, and STL-10 datasets using multi-layer perceptrons and convolutional neural networks demonstrate that CCL achieves comparable performance to other biological plausible algorithms while offering a more biologically realistic learning mechanism. Furthermore, we showcase the applicability of our approach to an autoencoder task, underscoring its potential for unsupervised representation learning.Our work presents a promising direction for biologically inspired and plausible learning algorithms, offering insights into the mechanisms of learning and adaptation in neural networks.

Generative Models

Ismail Alkhouri, Shijun Liang, Evan Bell, Qing Qu, Rongrong Wang, Saiprasad Ravishankar

Recently, Deep Image Prior (DIP) has emerged as an effective unsupervised one-shot learner, delivering competitive results across various image recovery problems. This method only requires the noisy measurements and a forward operator, relying solely on deep networks initialized with random noise to learn and restore the structure of the data. However, DIP is notorious for its vulnerability to overfitting due to the overparameterization of the network. Building upon insights into the impact of the DIP input and drawing inspiration from the gradual denoising process in cutting-edge diffusion models, we introduce Autoencoding Sequential DIP (aSeqDIP) for image reconstruction. This method progressively denoises and reconstructs the image through a sequential optimization of network weights. This is achieved using an input-adaptive DIP objective, combined with an autoencoding regularization term. Compared to diffusion models, our method does not require training data and outperforms other DIP-based methods in mitigating noise overfitting while maintaining a similar number of parameter updates as Vanilla DIP. Through extensive experiments, we validate the effectiveness of our method in various image reconstruction tasks, such as MRI and CT reconstruction, as well as in image restoration tasks like image denoising, inpainting, and non-linear deblurring.

Computer Vision

Yunlu Chen, Francisco Vicente Carrasco, Christian Häne, Giljoo Nam, Jean-Charles Bazin, Fernando D De la Torre

We introduce a doubly hierarchical generative representation for strand-based 3D hairstyle geometry that progresses from coarse, low-pass filtered guide hair to densely populated hair strands rich in high-frequency details. We employ the Discrete Cosine Transform (DCT) to separate low-frequency structural curves from high-frequency curliness and noise, avoiding the Gibbs' oscillation issues associated with the standard Fourier transform in open curves. Unlike the guide hair sampled from the scalp UV map grids which may lose capturing details of the hairstyle in existing methods, our method samples optimal sparse guide strands by utilising $k$-medoids clustering centres from low-pass filtered dense strands, which more accurately retain the hairstyle's inherent characteristics. The proposed variational autoencoder-based generation network, with an architecture inspired by geometric deep learning and implicit neural representations, facilitates flexible, off-the-grid guide strand modelling and enables the completion of dense strands in any quantity and density, drawing on principles from implicit neural representations. Empirical evaluations confirm the capacity of the model to generate convincing guide hair and dense strands, complete with nuanced high-frequency details.

Computational Biology

Xiangzhe Kong, Yinjun Jia, Wenbing Huang, Yang Liu

Peptide design plays a pivotal role in therapeutics, allowing brand new possibility to leverage target binding sites that are previously undruggable. Most existing methods are either inefficient or only concerned with the target-agnostic design of 1D sequences. In this paper, we propose a generative model for full-atom Peptide design with Geometric LAtent Diffusion (PepGLAD) given the binding site. We first establish a benchmark consisting of both 1D sequences and 3D structures from Protein Data Bank (PDB) and literature for systematic evaluation. We then identify two major challenges of leveraging current diffusion-based models for peptide design: the full-atom geometry and the variable binding geometry. To tackle the first challenge, PepGLAD derives a variational autoencoder that first encodes full-atom residues of variable size into fixed-dimensional latent representations, and then decodes back to the residue space after conducting the diffusion process in the latent space. For the second issue, PepGLAD explores a receptor-specific affine transformation to convert the 3D coordinates into a shared standard space, enabling better generalization ability across different binding shapes. Experimental Results show that our method not only improves diversity and binding affinity significantly in the task of sequence-structure co-design, but also excels at recovering reference structures for binding conformation generation.

Generative Models · Diffusion models

Tim Salimans, Thomas Mensink, Jonathan Heek, Emiel Hoogeboom

We present a new method for making diffusion models faster to sample. The method distills many-step diffusion models into few-step models by matching conditional expectations of the clean data given noisy data along the sampling trajectory. Our approach extends recently proposed one-step methods to the multi-step case, and provides a new perspective by interpreting these approaches in terms of moment matching. By using up to 8 sampling steps, we obtain distilled models that outperform not only their one-step versions but also their original many-step teacher models, obtaining new state-of-the-art results on the Imagenet dataset. We also show promising results on a large text-to-image model where we achieve fast generation of high resolution images directly in image space, without needing autoencoders or upsamplers.

Interpretability

Dan Braun, Jordan Taylor, Nicholas Goldowsky-Dill, Lee Sharkey

Identifying the features learned by neural networks is a core challenge in mechanistic interpretability. Sparse autoencoders (SAEs), which learn a sparse, overcomplete dictionary that reconstructs a network's internal activations, have been used to identify these features. However, SAEs may learn more about the structure of the datatset than the computational structure of the network. There is therefore only indirect reason to believe that the directions found in these dictionaries are functionally important to the network. We propose end-to-end (e2e) sparse dictionary learning, a method for training SAEs that ensures the features learned are functionally important by minimizing the KL divergence between the output distributions of the original model and the model with SAE activations inserted. Compared to standard SAEs, e2e SAEs offer a Pareto improvement: They explain more network performance, require fewer total features, and require fewer simultaneously active features per datapoint, all with no cost to interpretability. We explore geometric and qualitative differences between e2e SAE features and standard SAE features. E2e dictionary learning brings us closer to methods that can explain network behavior concisely and accurately. We release our library for training e2e SAEs and reproducing our analysis athttps://github.com/ApolloResearch/e2e_sae.

Physical Models · Physics

Parsa Esmati, Amirhossein Dadashzadeh, Vahid Ardakani, Nicolas Larrosa, Nicolò Grilli

Current approaches using sequential networks have shown promise in estimating field variables for dynamical systems, but they are often limited by high rollout errors. The unresolved issue of rollout error accumulation results in unreliable estimations as the network predicts further into the future, with each step's error compounding and leading to an increase in inaccuracy. Here, we introduce the State-Exchange Attention (SEA) module, a novel transformer-based module enabling information exchange between encoded fields through multi-head cross-attention. The cross-field multidirectional information exchange design enables all state variables in the system to exchange information with one another, capturing physical relationships and symmetries between fields. Additionally, we introduce an efficient ViT-like mesh autoencoder to generate spatially coherent mesh embeddings for a large number of meshing cells. The SEA integrated transformer demonstrates the state-of-the-art rollout error compared to other competitive baselines. Specifically, we outperform PbGMR-GMUS Transformer-RealNVP and GMR-GMUS Transformer, with a reduction in error of 88% and 91%, respectively. Furthermore, we demonstrate that the SEA module alone can reduce errors by 97% for state variables that are highly dependent on other states of the system. The repository for this work is available at: https://github.com/ParsaEsmati/SEA

Deep Learning · Autoencoders

Sifei Liu, Shalini De Mello, Jan Kautz

In this paper, we introduce Cosine Autoencoder (CosAE), a novel, generic Autoencoder that seamlessly leverages the classic Fourier series with a feed-forward neural network. CosAE represents an input image as a series of 2D Cosine time series, each defined by a tuple of learnable frequency and Fourier coefficients. This method stands in contrast to a conventional Autoencoder that often sacrifices detail in their reduced-resolution bottleneck latent spaces. CosAE, however, encodes frequency coefficients, i.e., the amplitudes and phases, in its bottleneck. This encoding enables extreme spatial compression, e.g., $64\times$ downsampled feature maps in the bottleneck, without losing detail upon decoding. We showcase the advantage of CosAE via extensive experiments on flexible-resolution super-resolution and blind image restoration, two highly challenging tasks that demand the restoration network to effectively generalize to complex and even unknown image degradations. Our method surpasses state-of-the-art approaches, highlighting its capability to learn a generalizable representation for image restoration. The project page is maintained at [https://sifeiliu.net/CosAE-page/](https://sifeiliu.net/CosAE-page/).

Generative Models · Diffusion models

Seyedmorteza Sadat, Jakob Buhmann, Derek Bradley, Otmar Hilliges, Romann M Weber

Advances in latent diffusion models (LDMs) have revolutionized high-resolution image generation, but the design space of the autoencoder that is central to these systems remains underexplored. In this paper, we introduce LiteVAE, a new autoencoder design for LDMs, which leverages the 2D discrete wavelet transform to enhance scalability and computational efficiency over standard variational autoencoders (VAEs) with no sacrifice in output quality. We investigate the training methodologies and the decoder architecture of LiteVAE and propose several enhancements that improve the training dynamics and reconstruction quality. Our base LiteVAE model matches the quality of the established VAEs in current LDMs with a six-fold reduction in encoder parameters, leading to faster training and lower GPU memory requirements, while our larger model outperforms VAEs of comparable complexity across all evaluated metrics (rFID, LPIPS, PSNR, and SSIM).

Computational Biology

Jiayu Su, David A Knowles, Raúl Rabadán

The success of machine learning models relies heavily on effectively representing high-dimensional data. However, ensuring data representations capture human-understandable concepts remains difficult, often requiring the incorporation of prior knowledge and decomposition of data into multiple subspaces. Traditional linear methods fall short in modeling more than one space, while more expressive deep learning approaches lack interpretability. Here, we introduce Supervised Independent Subspace Principal Component Analysis ($\texttt{sisPCA}$), a PCA extension designed for multi-subspace learning. Leveraging the Hilbert-Schmidt Independence Criterion (HSIC), $\texttt{sisPCA}$ incorporates supervision and simultaneously ensures subspace disentanglement. We demonstrate $\texttt{sisPCA}$'s connections with autoencoders and regularized linear regression and showcase its ability to identify and separate hidden data structures through extensive applications, including breast cancer diagnosis from image features, learning aging-associated DNA methylation changes, and single-cell analysis of malaria infection. Our results reveal distinct functional pathways associated with malaria colonization, underscoring the essentiality of explainable representation in high-dimensional data analysis.

Multimodal Models

Liyi Chen, Ying Sun, Shengzhe Zhang, Yuyang Ye, Wei Wu, Hui Xiong

Recently, multi-modal entity alignment has emerged as a pivotal endeavor for the integration of Multi-Modal Knowledge Graphs (MMKGs) originating from diverse data sources. Existing works primarily focus on fully depicting entity features by designing various modality encoders or fusion approaches. However, uncertain correspondences between inter-modal or intra-modal cues, such as weak inter-modal associations, description diversity, and modality absence, still severely hinder the effective exploration of aligned entity similarities. To this end, in this paper, we propose a novel Tackling uncertain correspondences method for Multi-modal Entity Alignment (TMEA). Specifically, to handle diverse attribute knowledge descriptions, we design alignment-augmented abstract representation that incorporates the large language model and in-context learning into attribute alignment and filtering for generating and embedding the attribute abstract. In order to mitigate the influence of the modality absence, we propose to unify all modality features into a shared latent subspace and generate pseudo features via variational autoencoders according to existing modal features. Then, we develop an inter-modal commonality enhancement mechanism based on cross-attention with orthogonal constraints, to address weak semantic associations between modalities. Extensive experiments on two real-world datasets validate the effectiveness of TMEA with a clear improvement over competitive baselines.

Neuroscience, Cognitive Science

Jaivardhan Kapoor, Auguste Schulz, Julius Vetter, Felix Pei, Richard Gao, Jakob H Macke

Modern datasets in neuroscience enable unprecedented inquiries into the relationship between complex behaviors and the activity of many simultaneously recorded neurons. While latent variable models can successfully extract low-dimensional embeddings from such recordings, using them to generate realistic spiking data, especially in a behavior-dependent manner, still poses a challenge. Here, we present Latent Diffusion for Neural Spiking data (LDNS), a diffusion-based generative model with a low-dimensional latent space: LDNS employs an autoencoder with structured state-space (S4) layers to project discrete high-dimensional spiking data into continuous time-aligned latents. On these inferred latents, we train expressive (conditional) diffusion models, enabling us to sample neural activity with realistic single-neuron and population spiking statistics. We validate LDNS on synthetic data, accurately recovering latent structure, firing rates, and spiking statistics. Next, we demonstrate its flexibility by generating variable-length data that mimics human cortical activity during attempted speech. We show how to equip LDNS with an expressive observation model that accounts for single-neuron dynamics not mediated by the latent state, further increasing the realism of generated samples. Finally, conditional LDNS trained on motor cortical activity during diverse reaching behaviors can generate realistic spiking data given reach direction or unseen reach trajectories. In summary, LDNS simultaneously enables inference of low-dimensional latents and realistic conditional generation of neural spiking datasets, opening up further possibilities for simulating experimentally testable hypotheses.

Deep Learning · Representation Learning

Yinzhu Jin, Aman Shrivastava, Tom Fletcher

In this work, we introduce a new approach to model group actions in autoencoders. Diverging from prior research in this domain, we propose to learn the group actions on the latent space rather than strictly on the data space. This adaptation enhances the versatility of our model, enabling it to learn a broader range of scenarios prevalent in the real world, where groups can act on latent factors. Our method allows a wide flexibility in the encoder and decoder architectures and does not require group-specific layers. In addition, we show that our model theoretically serves as a superset of methods that learn group actions on the data space. We test our approach on five image datasets with diverse groups acting on them and demonstrate superior performance to recently proposed methods for modeling group actions.

Reinforcement Learning · Multi-agent

Tao Jiang, Lei Yuan, Lihe Li, Cong Guan, Zongzhang Zhang, Yang Yu

The shift in dynamics results in significant performance degradation of policies trained in the source domain when deployed in a different target domain, posing a challenge for the practical application of reinforcement learning (RL) in real-world scenarios. Domain transfer methods aim to bridge this dynamics gap through techniques such as domain adaptation or domain calibration. While domain adaptation involves refining the policy through extensive interactions in the target domain, it may not be feasible for sensitive fields like healthcare and autonomous driving. On the other hand, offline domain calibration utilizes only static data from the target domain to adjust the physics parameters of the source domain (e.g., a simulator) to align with the target dynamics, enabling the direct deployment of the trained policy without sacrificing performance, which emerges as the most promising for policy deployment. However, existing techniques primarily rely on evolution algorithms for calibration, resulting in low sample efficiency.To tackle this issue, we propose a novel framework Madoc (\textbf{M}ulti-\textbf{a}gent \textbf{do}main \textbf{c}alibration). Firstly, we formulate a bandit RL objective to match the target trajectory distribution by learning a couple of classifiers. We then address the challenge of a large domain parameter space by modeling domain calibration as a cooperative multi-agent reinforcement learning (MARL) problem. Specifically, we utilize a Variational Autoencoder (VAE) to automatically cluster physics parameters with similar effects on the dynamics, grouping them into distinct agents. These grouped agents train calibration policies coordinately to adjust multiple parameters using MARL.Our empirical evaluation on 21 offline locomotion tasks in D4RL and NeoRL benchmarks showcases the superior performance of our method compared to strong existing offline model-based RL, offline domain calibration, and hybrid offline-and-online RL baselines.