SurvMamba: State Space Model with Multi-grained Multi-modal Interaction for Survival Prediction

Multi-modal learning that combines pathological images with genomic data has significantly enhanced the accuracy of survival prediction. Nevertheless, existing methods have not fully utilized the inherent hierarchical structure within both whole slide images (WSIs) and transcriptomic data, from which better intra-modal representations and inter-modal integration could be derived. Moreover, many existing studies attempt to improve multi-modal representations through attention mechanisms, which inevitably lead to high complexity when processing high-dimensional WSIs and transcriptomic data. Recently, a structured state space model named Mamba emerged as a promising approach for its superior performance in modeling long sequences with low complexity. In this study, we propose Mamba with multi-grained multi-modal interaction (SurvMamba) for survival prediction. SurvMamba is implemented with a Hierarchical Interaction Mamba (HIM) module that facilitates efficient intra-modal interactions at different granularities, thereby capturing more detailed local features as well as rich global representations. In addition, an Interaction Fusion Mamba (IFM) module is used for cascaded inter-modal interactive fusion, yielding more comprehensive features for survival prediction. Comprehensive evaluations on five TCGA datasets demonstrate that SurvMamba outperforms other existing methods in terms of performance and computational cost.

Associative Memories in the Feature Space

An autoassociative memory model is a function that, given a set of data points, takes as input an arbitrary vector and outputs the most similar data point from the memorized set. However, popular memory models fail to retrieve images even when the corruption is mild and easy to detect for a human evaluator. This is because similarities are evaluated in the raw pixel space, which does not contain any semantic information about the images. This problem can be easily solved by computing \emph{similarities} in an embedding space instead of the pixel space. We show that an effective way of computing such embeddings is via a network pretrained with a contrastive loss. As the dimension of embedding spaces is often significantly smaller than the pixel space, we also have a faster computation of similarity scores. We test this method on complex datasets such as CIFAR10 and STL10. An additional drawback of current models is the need of storing the whole dataset in the pixel space, which is often extremely large. We relax this condition and propose a class of memory models that only stores low-dimensional semantic embeddings, and uses them to retrieve similar, but not identical, memories. We demonstrate a proof of concept of this method on a simple task on the MNIST dataset.

Learning to Terminate in Object Navigation

This paper tackles the critical challenge of object navigation in autonomous navigation systems, particularly focusing on the problem of target approach and episode termination in environments with long optimal episode length in Deep Reinforcement Learning (DRL) based methods. While effective in environment exploration and object localization, conventional DRL methods often struggle with optimal path planning and termination recognition due to a lack of depth information. To overcome these limitations, we propose a novel approach, namely the Depth-Inference Termination Agent (DITA), which incorporates a supervised model called the Judge Model to implicitly infer object-wise depth and decide termination jointly with reinforcement learning. We train our judge model along with reinforcement learning in parallel and supervise the former efficiently by reward signal. Our evaluation shows the method is demonstrating superior performance, we achieve a 9.3% gain on success rate than our baseline method across all room types and gain 51.2% improvements on long episodes environment while maintaining slightly better Success Weighted by Path Length (SPL). Code and resources, visualization are available at: https://github.com/HuskyKingdom/DITA_acml2023

Incremental Predictive Coding: A Parallel and Fully Automatic Learning Algorithm

Neuroscience-inspired models, such as predictive coding, have the potential to play an important role in the future of machine intelligence. However, they are not yet used in industrial applications due to some limitations, such as the lack of efficiency. In this work, we address this by proposing incremental predictive coding (iPC), a variation of the original framework derived from the incremental expectation maximization algorithm, where every operation can be performed in parallel without external control. We show both theoretically and empirically that iPC is much faster than the original algorithm originally developed by Rao and Ballard, while maintaining performance comparable to backpropagation in image classification tasks. This work impacts several areas, has general applications in computational neuroscience and machine learning, and specific applications in scenarios where automatization and parallelization are important, such as distributed computing and implementations of deep learning models on analog and neuromorphic chips.

Predictive Coding beyond Gaussian Distributions

A large amount of recent research has the far-reaching goal of finding training methods for deep neural networks that can serve as alternatives to backpropagation (BP). A prominent example is predictive coding (PC), which is a neuroscience-inspired method that performs inference on hierarchical Gaussian generative models. These methods, however, fail to keep up with modern neural networks, as they are unable to replicate the dynamics of complex layers and activation functions. In this work, we solve this problem by generalizing PC to arbitrary probability distributions, enabling the training of architectures, such as transformers, that are hard to approximate with only Gaussian assumptions. We perform three experimental analyses. First, we study the gap between our method and the standard formulation of PC on multiple toy examples. Second, we test the reconstruction quality on variational autoencoders, where our method reaches the same reconstruction quality as BP. Third, we show that our method allows us to train transformer networks and achieve a performance comparable with BP on conditional language models. More broadly, this method allows neuroscience-inspired learning to be applied to multiple domains, since the internal distributions can be flexibly adapted to the data, tasks, and architectures used.

Bird-Eye Transformers for Text Generation Models

Transformers have become an indispensable module for text generation models since their great success in machine translation. Previous works attribute the~success of transformers to the query-key-value dot-product attention, which provides a robust inductive bias by the fully connected token graphs. However, we found that self-attention has a severe limitation. When predicting the (i+1)-th token, self-attention only takes the i-th token as an information collector, and it tends to give a high attention weight to those tokens similar to itself. Therefore, most of the historical information that occurred before the i-th token is not taken into consideration. Based on this observation, in this paper, we propose a new architecture, called bird-eye transformer(BET), which goes one step further to improve the performance of transformers by reweighting self-attention to encourage it to focus more on important historical information. We have conducted experiments on multiple text generation tasks, including machine translation (2 datasets) and language models (3 datasets). These experimental~results show that our proposed model achieves a better performance than the baseline transformer architectures on~all~datasets. The code is released at: \url{https://sites.google.com/view/bet-transformer/home}.

A Theoretical Framework for Inference and Learning in Predictive Coding Networks

Predictive coding (PC) is an influential theory in computational neuroscience, which argues that the cortex forms unsupervised world models by implementing a hierarchical process of prediction error minimization. PC networks (PCNs) are trained in two phases. First, neural activities are updated to optimize the network's response to external stimuli. Second, synaptic weights are updated to consolidate this change in activity -- an algorithm called \emph{prospective configuration}. While previous work has shown how in various limits, PCNs can be found to approximate backpropagation (BP), recent work has demonstrated that PCNs operating in this standard regime, which does not approximate BP, nevertheless obtain competitive training and generalization performance to BP-trained networks while outperforming them on tasks such as online, few-shot, and continual learning, where brains are known to excel. Despite this promising empirical performance, little is understood theoretically about the properties and dynamics of PCNs in this regime. In this paper, we provide a comprehensive theoretical analysis of the properties of PCNs trained with prospective configuration. We first derive analytical results concerning the inference equilibrium for PCNs and a previously unknown close connection relationship to target propagation (TP). Secondly, we provide a theoretical analysis of learning in PCNs as a variant of generalized expectation-maximization and use that to prove the convergence of PCNs to critical points of the BP loss function, thus showing that deep PCNs can, in theory, achieve the same generalization performance as BP, while maintaining their unique advantages.

Backpropagation at the Infinitesimal Inference Limit of Energy-Based Models: Unifying Predictive Coding, Equilibrium Propagation, and Contrastive Hebbian Learning

How the brain performs credit assignment is a fundamental unsolved problem in neuroscience. Many `biologically plausible' algorithms have been proposed, which compute gradients that approximate those computed by backpropagation (BP), and which operate in ways that more closely satisfy the constraints imposed by neural circuitry. Many such algorithms utilize the framework of energy-based models (EBMs), in which all free variables in the model are optimized to minimize a global energy function. However, in the literature, these algorithms exist in isolation and no unified theory exists linking them together. Here, we provide a comprehensive theory of the conditions under which EBMs can approximate BP, which lets us unify many of the BP approximation results in the literature (namely, predictive coding, equilibrium propagation, and contrastive Hebbian learning) and demonstrate that their approximation to BP arises from a simple and general mathematical property of EBMs at free-phase equilibrium. This property can then be exploited in different ways with different energy functions, and these specific choices yield a family of BP-approximating algorithms, which both includes the known results in the literature and can be used to derive new ones.

Predictive Coding: Towards a Future of Deep Learning beyond Backpropagation?

The backpropagation of error algorithm used to train deep neural networks has been fundamental to the successes of deep learning. However, it requires sequential backward updates and non-local computations, which make it challenging to parallelize at scale and is unlike how learning works in the brain. Neuroscience-inspired learning algorithms, however, such as \emph{predictive coding}, which utilize local learning, have the potential to overcome these limitations and advance beyond current deep learning technologies. While predictive coding originated in theoretical neuroscience as a model of information processing in the cortex, recent work has developed the idea into a general-purpose algorithm able to train neural networks using only local computations. In this survey, we review works that have contributed to this perspective and demonstrate the close theoretical connections between predictive coding and backpropagation, as well as works that highlight the multiple advantages of using predictive coding models over backpropagation-trained neural networks. Specifically, we show the substantially greater flexibility of predictive coding networks against equivalent deep neural networks, which can function as classifiers, generators, and associative memories simultaneously, and can be defined on arbitrary graph topologies. Finally, we review direct benchmarks of predictive coding networks on machine learning classification tasks, as well as its close connections to control theory and applications in robotics.

Universal Hopfield Networks: A General Framework for Single-Shot Associative Memory Models

A large number of neural network models of associative memory have been proposed in the literature. These include the classical Hopfield networks (HNs), sparse distributed memories (SDMs), and more recently the modern continuous Hopfield networks (MCHNs), which possesses close links with self-attention in machine learning. In this paper, we propose a general framework for understanding the operation of such memory networks as a sequence of three operations: similarity, separation, and projection. We derive all these memory models as instances of our general framework with differing similarity and separation functions. We extend the mathematical framework of Krotov et al (2020) to express general associative memory models using neural network dynamics with only second-order interactions between neurons, and derive a general energy function that is a Lyapunov function of the dynamics. Finally, using our framework, we empirically investigate the capacity of using different similarity functions for these associative memory models, beyond the dot product similarity measure, and demonstrate empirically that Euclidean or Manhattan distance similarity metrics perform substantially better in practice on many tasks, enabling a more robust retrieval and higher memory capacity than existing models.