Daily Papers

Recurrent neural networks (RNNs) provide a powerful approach in neuroscience to infer latent dynamics in neural populations and to generate hypotheses about the neural computations underlying behavior. However, past work has focused on relatively simple, input-driven, and largely deterministic behaviors - little is known about the mechanisms that would allow RNNs to generate the richer, spontaneous, and potentially stochastic behaviors observed in natural settings. Modeling with Hidden Markov Models (HMMs) has revealed a segmentation of natural behaviors into discrete latent states with stochastic transitions between them, a type of dynamics that may appear at odds with the continuous state spaces implemented by RNNs. Here we first show that RNNs can replicate HMM emission statistics and then reverse-engineer the trained networks to uncover the mechanisms they implement. In the absence of inputs, the activity of trained RNNs collapses towards a single fixed point. When driven by stochastic input, trajectories instead exhibit noise-sustained dynamics along closed orbits. Rotation along these orbits modulates the emission probabilities and is governed by transitions between regions of slow, noise-driven dynamics connected by fast, deterministic transitions. The trained RNNs develop highly structured connectivity, with a small set of "kick neurons" initiating transitions between these regions. This mechanism emerges during training as the network shifts into a regime of stochastic resonance, enabling it to perform probabilistic computations. Analyses across multiple HMM architectures - fully connected, cyclic, and linear-chain - reveal that this solution generalizes through the modular reuse of the same dynamical motif, suggesting a compositional principle by which RNNs can emulate complex discrete latent dynamics.

Training recurrent neural networks (RNNs) is a high-dimensional process that requires updating numerous parameters. Therefore, it is often difficult to pinpoint the underlying learning mechanisms. To address this challenge, we propose to gain mechanistic insights into the phenomenon of abrupt learning by studying RNNs trained to perform diverse short-term memory tasks. In these tasks, RNN training begins with an initial search phase. Following a long period of plateau in accuracy, the values of the loss function suddenly drop, indicating abrupt learning. Analyzing the neural computation performed by these RNNs reveals geometric restructuring (GR) in their phase spaces prior to the drop. To promote these GR events, we introduce a temporal consistency regularization that accelerates (bioplausible) training, facilitates attractor formation, and enables efficient learning in strongly connected networks. Our findings offer testable predictions for neuroscientists and emphasize the need for goal-agnostic secondary mechanisms to facilitate learning in biological and artificial networks.

RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly for applications in drug discovery, remains a challenge due to the complexity of RNA structures and interactions. While foundational models in biology have demonstrated success in modeling several biomolecules, especially proteins, achieving similar breakthroughs for RNA has proven more difficult. Current RNA models have yet to match the performance observed in the protein domain, leaving an important gap in computational biology. In this work, we present ChaRNABERT, a suite of sample and parameter-efficient RNA foundational models, that through a learnable tokenization process, are able to reach state-of-the-art performance on several tasks in established benchmarks. We extend its testing in relevant downstream tasks such as RNA-protein and aptamer-protein interaction prediction. Weights and inference code for ChaRNABERT-8M will be provided for academic research use. The other models will be available upon request.

Instruction fine-tuning (IFT) elicits instruction following capabilities and steers the behavior of large language models (LLMs) via supervised learning. However, existing models trained on open-source IFT datasets only have the ability to follow instructions from users, and often fail to follow complex role and rules specified by developers, a.k.a. system prompts. The ability to follow these roles and rules is essential for deployment, as it ensures that the model safely interacts with users within developer defined guidelines. To improve such role and rule following ability, we propose \model, an automated data generation pipeline that generates diverse roles and rules from existing IFT instructions, along with corresponding responses. This data can then be used to train models that follow complex system prompts. The models are evaluated on our newly created benchmarks for role and rule following ability, as well as standard instruction-following benchmarks and general NLP tasks. Our framework significantly improves role and rule following capability in LLMs, as evidenced by over 25% increase in pass-rate on rule adherence, i.e. following all requirements, in our experiments with the Alpaca and Ultrachat datasets. Moreover, our models achieves this increase without any regression on popular instruction following benchmarks.

RNN-like language models are getting renewed attention from NLP researchers in recent years and several models have made significant progress, which demonstrates performance comparable to traditional transformers. However, due to the recurrent nature of RNNs, this kind of language model can only store information in a set of fixed-length state vectors. As a consequence, they still suffer from forgetfulness though after a lot of improvements and optimizations, when given complex instructions or prompts. As the prompted generation is the main and most concerned function of LMs, solving the problem of forgetting in the process of generation is no wonder of vital importance. In this paper, focusing on easing the prompt forgetting during generation, we proposed an architecture to teach the model memorizing prompt during generation by synthetic gradient. To force the model to memorize the prompt, we derive the states that encode the prompt, then transform it into model parameter modification using low-rank gradient approximation, which hard-codes the prompt into model parameters temporarily. We construct a dataset for experiments, and the results have demonstrated the effectiveness of our method in solving the problem of forgetfulness in the process of prompted generation. We will release all the code upon acceptance.

Recurrent neural networks (RNNs) are widely used throughout neuroscience as models of local neural activity. Many properties of single RNNs are well characterized theoretically, but experimental neuroscience has moved in the direction of studying multiple interacting areas, and RNN theory needs to be likewise extended. We take a constructive approach towards this problem, leveraging tools from nonlinear control theory and machine learning to characterize when combinations of stable RNNs will themselves be stable. Importantly, we derive conditions which allow for massive feedback connections between interacting RNNs. We parameterize these conditions for easy optimization using gradient-based techniques, and show that stability-constrained "networks of networks" can perform well on challenging sequential-processing benchmark tasks. Altogether, our results provide a principled approach towards understanding distributed, modular function in the brain.

This abstract explores an RNN-based approach to online handwritten recognition problem. Our method uses data from an accelerometer and a gyroscope mounted on a handheld pen-like device to train and run a character pre-diction model. We have built a dataset of timestamped gyroscope and accelerometer data gathered during the manual process of handwriting Latin characters, labeled with the character being written; in total, the dataset con-sists of 1500 gyroscope and accelerometer data sequenc-es for 8 characters of the Latin alphabet from 6 different people, and 20 characters, each 1500 samples from Georgian alphabet from 5 different people. with each sequence containing the gyroscope and accelerometer data captured during the writing of a particular character sampled once every 10ms. We train an RNN-based neural network architecture on this dataset to predict the character being written. The model is optimized with categorical cross-entropy loss and RMSprop optimizer and achieves high accuracy on test data.

Mamba has recently garnered attention as an effective backbone for vision tasks. However, its underlying mechanism in visual domains remains poorly understood. In this work, we systematically investigate Mamba's representational properties and make three primary contributions. First, we theoretically analyze Mamba's relationship to Softmax and Linear Attention, confirming that it can be viewed as a low-rank approximation of Softmax Attention and thereby bridging the representational gap between Softmax and Linear forms. Second, we introduce a novel binary segmentation metric for activation map evaluation, extending qualitative assessments to a quantitative measure that demonstrates Mamba's capacity to model long-range dependencies. Third, by leveraging DINO for self-supervised pretraining, we obtain clearer activation maps than those produced by standard supervised approaches, highlighting Mamba's potential for interpretability. Notably, our model also achieves a 78.5 percent linear probing accuracy on ImageNet, underscoring its strong performance. We hope this work can provide valuable insights for future investigations of Mamba-based vision architectures.

The Arabic language is among the most popular languages in the world with a huge variety of dialects spoken in 22 countries. In this study, we address the problem of classifying 18 Arabic dialects of the QADI dataset of Arabic tweets. RNN models, Transformer models, and large language models (LLMs) via prompt engineering are created and tested. Among these, MARBERTv2 performed best with 65% accuracy and 64% F1-score. Through the use of state-of-the-art preprocessing techniques and the latest NLP models, this paper identifies the most significant linguistic issues in Arabic dialect identification. The results corroborate applications like personalized chatbots that respond in users' dialects, social media monitoring, and greater accessibility for Arabic communities.

3D Gaussian Splatting (3DGS) has shown its impressive power in novel view synthesis. However, creating relightable 3D assets, especially for objects with ill-defined shapes (e.g., fur), is still a challenging task. For these scenes, the decomposition between the light, geometry, and material is more ambiguous, as neither the surface constraints nor the analytical shading model hold. To address this issue, we propose RNG, a novel representation of relightable neural Gaussians, enabling the relighting of objects with both hard surfaces or fluffy boundaries. We avoid any assumptions in the shading model but maintain feature vectors, which can be further decoded by an MLP into colors, in each Gaussian point. Following prior work, we utilize a point light to reduce the ambiguity and introduce a shadow-aware condition to the network. We additionally propose a depth refinement network to help the shadow computation under the 3DGS framework, leading to better shadow effects under point lights. Furthermore, to avoid the blurriness brought by the alpha-blending in 3DGS, we design a hybrid forward-deferred optimization strategy. As a result, we achieve about 20times faster in training and about 600times faster in rendering than prior work based on neural radiance fields, with 60 frames per second on an RTX4090.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

This paper investigates the gap in representation powers of Recurrent Neural Networks (RNNs) and Transformers in the context of solving algorithmic problems. We focus on understanding whether RNNs, known for their memory efficiency in handling long sequences, can match the performance of Transformers, particularly when enhanced with Chain-of-Thought (CoT) prompting. Our theoretical analysis reveals that CoT improves RNNs but is insufficient to close the gap with Transformers. A key bottleneck lies in the inability of RNNs to perfectly retrieve information from the context, even with CoT: for several tasks that explicitly or implicitly require this capability, such as associative recall and determining if a graph is a tree, we prove that RNNs are not expressive enough to solve the tasks while Transformers can solve them with ease. Conversely, we prove that adopting techniques to enhance the in-context retrieval capability of RNNs, including Retrieval-Augmented Generation (RAG) and adding a single Transformer layer, can elevate RNNs to be capable of solving all polynomial-time solvable problems with CoT, hence closing the representation gap with Transformers.

RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA folding model. Understanding the specific local structures (i.e., "motifs") that contribute to undesignability is crucial for refining RNA folding models and determining the limits of RNA designability. Despite its importance, this problem has received very little attention, and previous efforts are neither scalable nor interpretable. We develop a new theoretical framework for motif (un-)designability, and design scalable and interpretable algorithms to identify minimal undesignable motifs within a given RNA secondary structure. Our approach establishes motif undesignability by searching for rival motifs, rather than exhaustively enumerating all (partial) sequences that could potentially fold into the motif. Furthermore, we exploit rotational invariance in RNA structures to detect, group, and reuse equivalent motifs and to construct a database of unique minimal undesignable motifs. To achieve that, we propose a loop-pair graph representation for motifs and a recursive graph isomorphism algorithm for motif equivalence. Our algorithms successfully identify 24 unique minimal undesignable motifs among 18 undesignable puzzles from the Eterna100 benchmark. Surprisingly, we also find over 350 unique minimal undesignable motifs and 663 undesignable native structures in the ArchiveII dataset, drawn from a diverse set of RNA families. Our source code is available at https://github.com/shanry/RNA-Undesign and our web server is available at http://linearfold.org/motifs.

This paper introduces a versatile paradigm for integrating multi-view reflectance (optional) and normal maps acquired through photometric stereo. Our approach employs a pixel-wise joint re-parameterization of reflectance and normal, considering them as a vector of radiances rendered under simulated, varying illumination. This re-parameterization enables the seamless integration of reflectance and normal maps as input data in neural volume rendering-based 3D reconstruction while preserving a single optimization objective. In contrast, recent multi-view photometric stereo (MVPS) methods depend on multiple, potentially conflicting objectives. Despite its apparent simplicity, our proposed approach outperforms state-of-the-art approaches in MVPS benchmarks across F-score, Chamfer distance, and mean angular error metrics. Notably, it significantly improves the detailed 3D reconstruction of areas with high curvature or low visibility.

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of folding into a target structure, little attention has been given to the identification of undesignable structures according to the minimum free energy (MFE) criterion under the Turner model. In this paper, we address this gap by first introducing mathematical theorems outlining sufficient conditions for recognizing undesignable structures, then proposing efficient algorithms, guided by these theorems, to verify the undesignability of RNA structures. Through the application of these theorems and algorithms to the Eterna100 puzzles, we demonstrate the ability to efficiently establish that 15 of the puzzles indeed fall within the category of undesignable structures. In addition, we provide specific insights from the study of undesignability, in the hope that it will enable more understanding of RNA folding and RNA design.

RNN-T models are widely used in ASR, which rely on the RNN-T loss to achieve length alignment between input audio and target sequence. However, the implementation complexity and the alignment-based optimization target of RNN-T loss lead to computational redundancy and a reduced role for predictor network, respectively. In this paper, we propose a novel model named CIF-Transducer (CIF-T) which incorporates the Continuous Integrate-and-Fire (CIF) mechanism with the RNN-T model to achieve efficient alignment. In this way, the RNN-T loss is abandoned, thus bringing a computational reduction and allowing the predictor network a more significant role. We also introduce Funnel-CIF, Context Blocks, Unified Gating and Bilinear Pooling joint network, and auxiliary training strategy to further improve performance. Experiments on the 178-hour AISHELL-1 and 10000-hour WenetSpeech datasets show that CIF-T achieves state-of-the-art results with lower computational overhead compared to RNN-T models.

In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly predict the RNA base-pairing matrix, and use an unrolled algorithm for constrained programming as the template for deep architectures to enforce constraints. With comprehensive experiments on benchmark datasets, we demonstrate the superior performance of E2Efold: it predicts significantly better structures compared to previous SOTA (especially for pseudoknotted structures), while being as efficient as the fastest algorithms in terms of inference time.

NeXML is a powerful and extensible exchange standard recently proposed to better meet the expanding needs for phylogenetic data and metadata sharing. Here we present the RNeXML package, which provides users of the R programming language with easy-to-use tools for reading and writing NeXML documents, including rich metadata, in a way that interfaces seamlessly with the extensive library of phylogenetic tools already available in the R ecosystem.

The scalability limitations of Transformers regarding sequence length have renewed interest in recurrent sequence models that are parallelizable during training. As a result, many novel recurrent architectures, such as S4, Mamba, and Aaren, have been proposed that achieve comparable performance. In this work, we revisit traditional recurrent neural networks (RNNs) from over a decade ago: LSTMs (1997) and GRUs (2014). While these models were slow due to requiring to backpropagate through time (BPTT), we show that by removing their hidden state dependencies from their input, forget, and update gates, LSTMs and GRUs no longer need to BPTT and can be efficiently trained in parallel. Building on this, we introduce minimal versions (minLSTMs and minGRUs) that (1) use significantly fewer parameters than their traditional counterparts and (2) are fully parallelizable during training (175x faster for a sequence of length 512). Lastly, we show that these stripped-down versions of decade-old RNNs match the empirical performance of recent sequence models.

Self-attention performs well in long context but has quadratic complexity. Existing RNN layers have linear complexity, but their performance in long context is limited by the expressive power of their hidden state. We propose a new class of sequence modeling layers with linear complexity and an expressive hidden state. The key idea is to make the hidden state a machine learning model itself, and the update rule a step of self-supervised learning. Since the hidden state is updated by training even on test sequences, our layers are called Test-Time Training (TTT) layers. We consider two instantiations: TTT-Linear and TTT-MLP, whose hidden state is a linear model and a two-layer MLP respectively. We evaluate our instantiations at the scale of 125M to 1.3B parameters, comparing with a strong Transformer and Mamba, a modern RNN. Both TTT-Linear and TTT-MLP match or exceed the baselines. Similar to Transformer, they can keep reducing perplexity by conditioning on more tokens, while Mamba cannot after 16k context. With preliminary systems optimization, TTT-Linear is already faster than Transformer at 8k context and matches Mamba in wall-clock time. TTT-MLP still faces challenges in memory I/O, but shows larger potential in long context, pointing to a promising direction for future research.

Linear RNNs with gating recently demonstrated competitive performance compared to Transformers in language modeling. Although their linear compute scaling in sequence length offers theoretical runtime advantages over Transformers, realizing these benefits in practice requires optimized custom kernels, as Transformers rely on the highly efficient Flash Attention kernels (Dao, 2024). Leveraging the chunkwise-parallel formulation of linear RNNs, Flash Linear Attention (FLA) (Yang & Zhang, 2024) shows that linear RNN kernels are faster than Flash Attention, by parallelizing over chunks of the input sequence. However, since the chunk size of FLA is limited, many intermediate states must be materialized in GPU memory. This leads to low arithmetic intensity and causes high memory consumption and IO cost, especially for long-context pre-training. In this work, we present Tiled Flash Linear Attention (TFLA), a novel kernel algorithm for linear RNNs, that enables arbitrary large chunk sizes and high arithmetic intensity by introducing an additional level of sequence parallelization within each chunk. First, we apply TFLA to the xLSTM with matrix memory, the mLSTM (Beck et al., 2024). Second, we propose an mLSTM variant with sigmoid input gate and reduced computation for even faster kernel runtimes at equal language modeling performance. In our speed benchmarks, we show that our new mLSTM kernels based on TFLA outperform highly optimized Flash Attention, Linear Attention and Mamba kernels, setting a new state of the art for efficient long-context sequence modeling primitives.

This paper explores the potential of recurrent neural networks (RNNs) and other subquadratic architectures as competitive alternatives to transformer-based models in low-resource language modeling scenarios. We utilize HGRN2 (Qin et al., 2024), a recently proposed RNN-based architecture, and comparatively evaluate its effectiveness against transformer-based baselines and other subquadratic architectures (LSTM, xLSTM, Mamba). Our experimental results show that BABYHGRN, our HGRN2 language model, outperforms transformer-based models in both the 10M and 100M word tracks of the challenge, as measured by their performance on the BLiMP, EWoK, GLUE and BEAR benchmarks. Further, we show the positive impact of knowledge distillation. Our findings challenge the prevailing focus on transformer architectures and indicate the viability of RNN-based models, particularly in resource-constrained environments.

In this paper, we propose a novel neural network model called RNN Encoder-Decoder that consists of two recurrent neural networks (RNN). One RNN encodes a sequence of symbols into a fixed-length vector representation, and the other decodes the representation into another sequence of symbols. The encoder and decoder of the proposed model are jointly trained to maximize the conditional probability of a target sequence given a source sequence. The performance of a statistical machine translation system is empirically found to improve by using the conditional probabilities of phrase pairs computed by the RNN Encoder-Decoder as an additional feature in the existing log-linear model. Qualitatively, we show that the proposed model learns a semantically and syntactically meaningful representation of linguistic phrases.

Transfer RNAs (tRNAs) are universal adaptors of the genetic code, yet their evolutionary dynamics across photosynthetic eukaryotes remain underexplored. Here, we present the largest comparative re-analysis integrating the PlantRNA database with published data to explore tRNA gene evolution. We find that tRNA gene repertoires have been deeply shaped by ecological transitions, genome architecture, and translational demands. Terrestrialization marks a major shift in tRNA evolution, characterized by the loss of selenoproteins and their dedicated selenocysteine tRNAs in land plants compared to algae. Patterns of intron prevalence, position, and structure diverged among lineages, with extensive intron loss occurring around the origin of land plants. Organellar genomes exhibit divergent trajectories: mitochondrial tRNA sets are highly labile due to recurrent gene losses, imports, and horizontal transfers, whereas plastid repertoires are comparatively stable with lineage-specific exceptions. In parallel, angiosperm nuclear tRNA genes exhibit reinforced cis-regulatory elements, consistent with increased and developmentally complex translational demands, and their copy number correlates tightly with codon usage and amino acid composition. Finally, conserved yet family-biased clustering of nuclear tRNA genes reveals contrasting organizational principles in plants versus metazoans. Together, these findings establish tRNA gene evolution as a major determinant of translational capacity and a key driver of photosynthetic diversification.

Transcriptomic foundation models (TFMs) have recently emerged as powerful tools for analyzing gene expression in cells and tissues, supporting key tasks such as cell-type annotation, batch correction, and perturbation prediction. However, the diversity of model implementations and training strategies across recent TFMs, though promising, makes it challenging to isolate the contribution of individual design choices or evaluate their potential synergies. This hinders the field's ability to converge on best practices and limits the reproducibility of insights across studies. We present BMFM-RNA, an open-source, modular software package that unifies diverse TFM pretraining and fine-tuning objectives within a single framework. Leveraging this capability, we introduce a novel training objective, whole cell expression decoder (WCED), which captures global expression patterns using an autoencoder-like CLS bottleneck representation. In this paper, we describe the framework, supported input representations, and training objectives. We evaluated four model checkpoints pretrained on CELLxGENE using combinations of masked language modeling (MLM), WCED and multitask learning. Using the benchmarking capabilities of BMFM-RNA, we show that WCED-based models achieve performance that matches or exceeds state-of-the-art approaches like scGPT across more than a dozen datasets in both zero-shot and fine-tuning tasks. BMFM-RNA, available as part of the biomed-multi-omics project ( https://github.com/BiomedSciAI/biomed-multi-omic ), offers a reproducible foundation for systematic benchmarking and community-driven exploration of optimal TFM training strategies, enabling the development of more effective tools to leverage the latest advances in AI for understanding cell biology.

The RNA structure-function relationship has recently garnered significant attention within the deep learning community, promising to grow in importance as nucleic acid structure models advance. However, the absence of standardized and accessible benchmarks for deep learning on RNA 3D structures has impeded the development of models for RNA functional characteristics. In this work, we introduce a set of seven benchmarking datasets for RNA structure-function prediction, designed to address this gap. Our library builds on the established Python library rnaglib, and offers easy data distribution and encoding, splitters and evaluation methods, providing a convenient all-in-one framework for comparing models. Datasets are implemented in a fully modular and reproducible manner, facilitating for community contributions and customization. Finally, we provide initial baseline results for all tasks using a graph neural network. Source code: https://github.com/cgoliver/rnaglib Documentation: https://rnaglib.org

While Transformers and other sequence-parallelizable neural network architectures seem like the current state of the art in sequence modeling, they specifically lack state-tracking capabilities. These are important for time-series tasks and logical reasoning. Traditional RNNs like LSTMs and GRUs, as well as modern variants like sLSTM do have these capabilities at the cost of strictly sequential processing. While this is often seen as a strong limitation, we show how fast these networks can get with our hardware-optimization FlashRNN in Triton and CUDA, optimizing kernels to the register level on modern GPUs. We extend traditional RNNs with a parallelization variant that processes multiple RNNs of smaller hidden state in parallel, similar to the head-wise processing in Transformers. To enable flexibility on different GPU variants, we introduce a new optimization framework for hardware-internal cache sizes, memory and compute handling. It models the hardware in a setting using polyhedral-like constraints, including the notion of divisibility. This speeds up the solution process in our ConstrINT library for general integer constraint satisfaction problems (integer CSPs). We show that our kernels can achieve 50x speed-ups over a vanilla PyTorch implementation and allow 40x larger hidden sizes compared to our Triton implementation. Our open-source kernels and the optimization library are released here to boost research in the direction of state-tracking enabled RNNs and sequence modeling: https://github.com/NX-AI/flashrnn

Dynamical systems (DS) theory is fundamental for many areas of science and engineering. It can provide deep insights into the behavior of systems evolving in time, as typically described by differential or recursive equations. A common approach to facilitate mathematical tractability and interpretability of DS models involves decomposing nonlinear DS into multiple linear DS separated by switching manifolds, i.e. piecewise linear (PWL) systems. PWL models are popular in engineering and a frequent choice in mathematics for analyzing the topological properties of DS. However, hand-crafting such models is tedious and only possible for very low-dimensional scenarios, while inferring them from data usually gives rise to unnecessarily complex representations with very many linear subregions. Here we introduce Almost-Linear Recurrent Neural Networks (AL-RNNs) which automatically and robustly produce most parsimonious PWL representations of DS from time series data, using as few PWL nonlinearities as possible. AL-RNNs can be efficiently trained with any SOTA algorithm for dynamical systems reconstruction (DSR), and naturally give rise to a symbolic encoding of the underlying DS that provably preserves important topological properties. We show that for the Lorenz and R\"ossler systems, AL-RNNs discover, in a purely data-driven way, the known topologically minimal PWL representations of the corresponding chaotic attractors. We further illustrate on two challenging empirical datasets that interpretable symbolic encodings of the dynamics can be achieved, tremendously facilitating mathematical and computational analysis of the underlying systems.

Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D geometry and conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. Under the hood, gRNAde is a multi-state Graph Neural Network that generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. [2010], gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent ribozyme. Open source code: https://github.com/chaitjo/geometric-rna-design

The RNN-Transducer (RNN-T) framework for speech recognition has been growing in popularity, particularly for deployed real-time ASR systems, because it combines high accuracy with naturally streaming recognition. One of the drawbacks of RNN-T is that its loss function is relatively slow to compute, and can use a lot of memory. Excessive GPU memory usage can make it impractical to use RNN-T loss in cases where the vocabulary size is large: for example, for Chinese character-based ASR. We introduce a method for faster and more memory-efficient RNN-T loss computation. We first obtain pruning bounds for the RNN-T recursion using a simple joiner network that is linear in the encoder and decoder embeddings; we can evaluate this without using much memory. We then use those pruning bounds to evaluate the full, non-linear joiner network.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

We explore the abilities of character recurrent neural network (char-RNN) for hashtag segmentation. Our approach to the task is the following: we generate synthetic training dataset according to frequent n-grams that satisfy predefined morpho-syntactic patterns to avoid any manual annotation. The active learning strategy limits the training dataset and selects informative training subset. The approach does not require any language-specific settings and is compared for two languages, which differ in inflection degree.

This study introduces PV-RNN, a novel variational RNN inspired by the predictive-coding ideas. The model learns to extract the probabilistic structures hidden in fluctuating temporal patterns by dynamically changing the stochasticity of its latent states. Its architecture attempts to address two major concerns of variational Bayes RNNs: how can latent variables learn meaningful representations and how can the inference model transfer future observations to the latent variables. PV-RNN does both by introducing adaptive vectors mirroring the training data, whose values can then be adapted differently during evaluation. Moreover, prediction errors during backpropagation, rather than external inputs during the forward computation, are used to convey information to the network about the external data. For testing, we introduce error regression for predicting unseen sequences as inspired by predictive coding that leverages those mechanisms. The model introduces a weighting parameter, the meta-prior, to balance the optimization pressure placed on two terms of a lower bound on the marginal likelihood of the sequential data. We test the model on two datasets with probabilistic structures and show that with high values of the meta-prior the network develops deterministic chaos through which the data's randomness is imitated. For low values, the model behaves as a random process. The network performs best on intermediate values, and is able to capture the latent probabilistic structure with good generalization. Analyzing the meta-prior's impact on the network allows to precisely study the theoretical value and practical benefits of incorporating stochastic dynamics in our model. We demonstrate better prediction performance on a robot imitation task with our model using error regression compared to a standard variational Bayes model lacking such a procedure.

Transformers are considered conceptually different compared to the previous generation of state-of-the-art NLP models - recurrent neural networks (RNNs). In this work, we demonstrate that decoder-only transformers can in fact be conceptualized as infinite multi-state RNNs - an RNN variant with unlimited hidden state size. We further show that pretrained transformers can be converted into finite multi-state RNNs by fixing the size of their hidden state. We observe that several existing transformers cache compression techniques can be framed as such conversion policies, and introduce a novel policy, TOVA, which is simpler compared to these policies. Our experiments with several long range tasks indicate that TOVA outperforms all other baseline policies, while being nearly on par with the full (infinite) model, and using in some cases only 1{8} of the original cache size. Our results indicate that transformer decoder LLMs often behave in practice as RNNs. They also lay out the option of mitigating one of their most painful computational bottlenecks - the size of their cache memory. We publicly release our code at https://github.com/schwartz-lab-NLP/TOVA.

Hierarchically gated linear RNN (HGRN,Qin et al. 2023) has demonstrated competitive training speed and performance in language modeling, while offering efficient inference. However, the recurrent state size of HGRN remains relatively small, which limits its expressiveness.To address this issue, inspired by linear attention, we introduce a simple outer-product-based state expansion mechanism so that the recurrent state size can be significantly enlarged without introducing any additional parameters. The linear attention form also allows for hardware-efficient training.Our extensive experiments verify the advantage of HGRN2 over HGRN1 in language modeling, image classification, and Long Range Arena.Our largest 3B HGRN2 model slightly outperforms Mamba and LLaMa Architecture Transformer for language modeling in a controlled experiment setting; and performs competitively with many open-source 3B models in downstream evaluation while using much fewer total training tokens.

Transformers have revolutionized almost all natural language processing (NLP) tasks but suffer from memory and computational complexity that scales quadratically with sequence length. In contrast, recurrent neural networks (RNNs) exhibit linear scaling in memory and computational requirements but struggle to match the same performance as Transformers due to limitations in parallelization and scalability. We propose a novel model architecture, Receptance Weighted Key Value (RWKV), that combines the efficient parallelizable training of Transformers with the efficient inference of RNNs. Our approach leverages a linear attention mechanism and allows us to formulate the model as either a Transformer or an RNN, which parallelizes computations during training and maintains constant computational and memory complexity during inference, leading to the first non-transformer architecture to be scaled to tens of billions of parameters. Our experiments reveal that RWKV performs on par with similarly sized Transformers, suggesting that future work can leverage this architecture to create more efficient models. This work presents a significant step towards reconciling the trade-offs between computational efficiency and model performance in sequence processing tasks.

Existing open-vocabulary image segmentation methods require a fine-tuning step on mask annotations and/or image-text datasets. Mask labels are labor-intensive, which limits the number of categories in segmentation datasets. As a result, the open-vocabulary capacity of pre-trained VLMs is severely reduced after fine-tuning. However, without fine-tuning, VLMs trained under weak image-text supervision tend to make suboptimal mask predictions when there are text queries referring to non-existing concepts in the image. To alleviate these issues, we introduce a novel recurrent framework that progressively filters out irrelevant texts and enhances mask quality without training efforts. The recurrent unit is a two-stage segmenter built upon a VLM with frozen weights. Thus, our model retains the VLM's broad vocabulary space and strengthens its segmentation capability. Experimental results show that our method outperforms not only the training-free counterparts, but also those fine-tuned with millions of additional data samples, and sets new state-of-the-art records for both zero-shot semantic and referring image segmentation tasks. Specifically, we improve the current record by 28.8, 16.0, and 6.9 mIoU on Pascal VOC, COCO Object, and Pascal Context.

Recurrent Neural Networks (RNNs) laid the foundation for sequence modeling, but their intrinsic sequential nature restricts parallel computation, creating a fundamental barrier to scaling. This has led to the dominance of parallelizable architectures like Transformers and, more recently, State Space Models (SSMs). While SSMs achieve efficient parallelization through structured linear recurrences, this linearity constraint limits their expressive power and precludes modeling complex, nonlinear sequence-wise dependencies. To address this, we present ParaRNN, a framework that breaks the sequence-parallelization barrier for nonlinear RNNs. Building on prior work, we cast the sequence of nonlinear recurrence relationships as a single system of equations, which we solve in parallel using Newton's iterations combined with custom parallel reductions. Our implementation achieves speedups of up to 665x over naive sequential application, allowing training nonlinear RNNs at unprecedented scales. To showcase this, we apply ParaRNN to adaptations of LSTM and GRU architectures, successfully training models of 7B parameters that attain perplexity comparable to similarly-sized Transformers and Mamba2 architectures. To accelerate research in efficient sequence modeling, we release the ParaRNN codebase as an open-source framework for automatic training-parallelization of nonlinear RNNs, enabling researchers and practitioners to explore new nonlinear RNN models at scale.

The benefit of transformers in large-scale 3D point cloud perception tasks, such as 3D object detection, is limited by their quadratic computation cost when modeling long-range relationships. In contrast, linear RNNs have low computational complexity and are suitable for long-range modeling. Toward this goal, we propose a simple and effective window-based framework built on LInear grOup RNN (i.e., perform linear RNN for grouped features) for accurate 3D object detection, called LION. The key property is to allow sufficient feature interaction in a much larger group than transformer-based methods. However, effectively applying linear group RNN to 3D object detection in highly sparse point clouds is not trivial due to its limitation in handling spatial modeling. To tackle this problem, we simply introduce a 3D spatial feature descriptor and integrate it into the linear group RNN operators to enhance their spatial features rather than blindly increasing the number of scanning orders for voxel features. To further address the challenge in highly sparse point clouds, we propose a 3D voxel generation strategy to densify foreground features thanks to linear group RNN as a natural property of auto-regressive models. Extensive experiments verify the effectiveness of the proposed components and the generalization of our LION on different linear group RNN operators including Mamba, RWKV, and RetNet. Furthermore, it is worth mentioning that our LION-Mamba achieves state-of-the-art on Waymo, nuScenes, Argoverse V2, and ONCE dataset. Last but not least, our method supports kinds of advanced linear RNN operators (e.g., RetNet, RWKV, Mamba, xLSTM and TTT) on small but popular KITTI dataset for a quick experience with our linear RNN-based framework.

Transformers achieve remarkable performance in several tasks but due to their quadratic complexity, with respect to the input's length, they are prohibitively slow for very long sequences. To address this limitation, we express the self-attention as a linear dot-product of kernel feature maps and make use of the associativity property of matrix products to reduce the complexity from Oleft(N^2right) to Oleft(Nright), where N is the sequence length. We show that this formulation permits an iterative implementation that dramatically accelerates autoregressive transformers and reveals their relationship to recurrent neural networks. Our linear transformers achieve similar performance to vanilla transformers and they are up to 4000x faster on autoregressive prediction of very long sequences.

While Transformer-based models have demonstrated remarkable language modeling performance, their high complexities result in high costs when processing long contexts. In contrast, recurrent neural networks (RNNs) such as linear attention and state space models have gained popularity due to their constant per-token complexities. However, these recurrent models struggle with tasks that require accurate recall of contextual information from long contexts, because all contextual information is compressed into a constant-size recurrent state. Previous works have shown that recall ability is positively correlated with the recurrent state size, yet directly training RNNs with larger recurrent states results in high training costs. In this paper, we introduce StateX, a training pipeline for efficiently expanding the states of pre-trained RNNs through post-training. For two popular classes of RNNs, linear attention and state space models, we design post-training architectural modifications to scale up the state size with no or negligible increase in model parameters. Experiments on models up to 1.3B parameters demonstrate that StateX efficiently enhances the recall and in-context learning ability of RNNs without incurring high post-training costs or compromising other capabilities.

The advent of Transformers marked a significant breakthrough in sequence modelling, providing a highly performant architecture capable of leveraging GPU parallelism. However, Transformers are computationally expensive at inference time, limiting their applications, particularly in low-resource settings (e.g., mobile and embedded devices). Addressing this, we (1) begin by showing that attention can be viewed as a special Recurrent Neural Network (RNN) with the ability to compute its many-to-one RNN output efficiently. We then (2) show that popular attention-based models such as Transformers can be viewed as RNN variants. However, unlike traditional RNNs (e.g., LSTMs), these models cannot be updated efficiently with new tokens, an important property in sequence modelling. Tackling this, we (3) introduce a new efficient method of computing attention's many-to-many RNN output based on the parallel prefix scan algorithm. Building on the new attention formulation, we (4) introduce Aaren, an attention-based module that can not only (i) be trained in parallel (like Transformers) but also (ii) be updated efficiently with new tokens, requiring only constant memory for inferences (like traditional RNNs). Empirically, we show Aarens achieve comparable performance to Transformers on 38 datasets spread across four popular sequential problem settings: reinforcement learning, event forecasting, time series classification, and time series forecasting tasks while being more time and memory-efficient.

One essential advantage of recurrent neural networks (RNNs) over transformer-based language models is their linear computational complexity concerning the sequence length, which makes them much faster in handling long sequences during inference. However, most publicly available RNNs (e.g., Mamba and RWKV) are trained on sequences with less than 10K tokens, and their effectiveness in longer contexts remains largely unsatisfying so far. In this paper, we study the cause of the inability to process long context for RNNs and suggest critical mitigations. We examine two practical concerns when applying state-of-the-art RNNs to long contexts: (1) the inability to extrapolate to inputs longer than the training length and (2) the upper bound of memory capacity. Addressing the first concern, we first investigate *state collapse* (SC), a phenomenon that causes severe performance degradation on sequence lengths not encountered during training. With controlled experiments, we attribute this to overfitting due to the recurrent state being overparameterized for the training length. For the second concern, we train a series of Mamba-2 models on long documents to empirically estimate the recurrent state capacity in language modeling and passkey retrieval. Then, three SC mitigation methods are proposed to improve Mamba-2's length generalizability, allowing the model to process more than 1M tokens without SC. We also find that the recurrent state capacity in passkey retrieval scales exponentially to the state size, and we empirically train a Mamba-2 370M with near-perfect passkey retrieval accuracy on 256K context length. This suggests a promising future for RNN-based long-context modeling.

Linear recurrent neural networks (RNNs) and state-space models (SSMs) such as Mamba have become promising alternatives to softmax-attention as sequence mixing layers in Transformer architectures. Current models, however, do not exhibit the full state-tracking expressivity of RNNs because they rely on channel-wise (i.e. diagonal) sequence mixing. In this paper, we investigate parameterizations of a large class of dense linear RNNs as fixed-points of parallelizable diagonal linear RNNs. The resulting models can naturally trade expressivity for efficiency at a fixed number of parameters and achieve state-of-the-art results on the state-tracking benchmarks A_5 and S_5, while matching performance on copying and other tasks.

State-space models (SSMs) and transformers dominate the language modeling landscape. However, they are constrained to a lower computational complexity than classical recurrent neural networks (RNNs), limiting their expressivity. In contrast, RNNs lack parallelization during training, raising fundamental questions about the trade off between parallelization and expressivity. We propose implicit SSMs, which iterate a transformation until convergence to a fixed point. Theoretically, we show that implicit SSMs implement the non-linear state-transitions of RNNs. Empirically, we find that only approximate fixed-point convergence suffices, enabling the design of a scalable training curriculum that largely retains parallelization, with full convergence required only for a small subset of tokens. Our approach demonstrates superior state-tracking capabilities on regular languages, surpassing transformers and SSMs. We further scale implicit SSMs to natural language reasoning tasks and pretraining of large-scale language models up to 1.3B parameters on 207B tokens - representing, to our knowledge, the largest implicit model trained to date. Notably, our implicit models outperform their explicit counterparts on standard benchmarks.

In Recurrent Neural Networks (RNNs), encoding information in a suboptimal or erroneous way can impact the quality of representations based on later elements in the sequence and subsequently lead to wrong predictions and a worse model performance. In humans, challenging cases like garden path sentences (an instance of this being the infamous "The horse raced past the barn fell") can lead their language understanding astray. However, they are still able to correct their representation accordingly and recover when new information is encountered. Inspired by this, I propose an augmentation to standard RNNs in form of a gradient-based correction mechanism: This way I hope to enable such models to dynamically adapt their inner representation of a sentence, adding a way to correct deviations as soon as they occur. This could therefore lead to more robust models using more flexible representations, even during inference time. I conduct different experiments in the context of language modeling, where the impact of using such a mechanism is examined in detail. To this end, I look at modifications based on different kinds of time-dependent error signals and how they influence the model performance. Furthermore, this work contains a study of the model's confidence in its predictions during training and for challenging test samples and the effect of the manipulation thereof. Lastly, I also study the difference in behavior of these novel models compared to a standard LSTM baseline and investigate error cases in detail to identify points of future research. I show that while the proposed approach comes with promising theoretical guarantees and an appealing intuition, it is only able to produce minor improvements over the baseline due to challenges in its practical application and the efficacy of the tested model variants.

Recurrent Neural Network (RNN) inference exhibits low hardware utilization due to the strict data dependencies across time-steps. Batching multiple requests can increase throughput. However, RNN batching requires a large amount of padding since the batched input sequences may largely differ in length. Schemes that dynamically update the batch every few time-steps avoid padding. However, they require executing different RNN layers in a short timespan, decreasing energy efficiency. Hence, we propose E-BATCH, a low-latency and energy-efficient batching scheme tailored to RNN accelerators. It consists of a runtime system and effective hardware support. The runtime concatenates multiple sequences to create large batches, resulting in substantial energy savings. Furthermore, the accelerator notifies it when the evaluation of a sequence is done, so that a new sequence can be immediately added to a batch, thus largely reducing the amount of padding. E-BATCH dynamically controls the number of time-steps evaluated per batch to achieve the best trade-off between latency and energy efficiency for the given hardware platform. We evaluate E-BATCH on top of E-PUR and TPU. In E-PUR, E-BATCH improves throughput by 1.8x and energy-efficiency by 3.6x, whereas in TPU, it improves throughput by 2.1x and energy-efficiency by 1.6x, over the state-of-the-art.

In this article, we propose a new counter-based implementation of John von Neumann's middle-square random number generator (RNG). Several rounds of squaring are applied to a counter to produce a random output. We discovered that four rounds are sufficient to provide satisfactory data. Two versions of the RNG are presented, a 4-round version with 32-bit output and a 5-round version with 64-bit output. Both pass stringent tests of randomness and may be the fastest counter-based generators.

Transformers have become the cornerstone of modern large-scale language models; however, their dependence on softmax attention poses a major computational bottleneck, particularly in long-context settings. In this work, rather than following prevalent approaches such as linear attention (or SSMs) and local attention, we introduce an intermediate design called \rat between recurrence and attention mechanisms. It partitions the input into chunks, applies a simple linear recurrence within each chunk to capture local dependencies, and then performs softmax attention across chunks to model long-range interactions. By adjusting the size of the chunk, \rat enables flexible trade-offs, combining the strengths of RNN and attention. Empirically, with a chunk size of 16, the \rat layer achieves a \(7\times\) improvement in training speed with 100K token sequences and \(9\times\) in generation at 4K sequence length, while maintaining similar or sometimes even better accuracy compared to standard attention. We demonstrate this by training 1.3B parameter models from scratch and performing large-scale evaluations, including short- and long-context benchmarks, as well as supervised fine-tuning~(SFT). We further propose a hybrid architecture that interleaves \rat with local attention. By combining efficient long-range modeling with strong local interactions, this hybrid design not only improves inference speed and reduces cache memory usage compared to attention, but also consistently enhances performance, for example, achieving an average 1 point gain in commonsense reasoning tasks, up to 4 points on code tasks, and a 1 point Rouge-L increase in a summarization SFT task. Code is available at https://github.com/CLAIRE-Labo/RAT

Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the high variability caused by disease heterogeneity, makes it challenging to integrate snRNA-seq data from multiple sources for precise analyses. To address these challenges, we present scMamba, a pre-trained model designed to improve the quality and utility of snRNA-seq analysis, with a particular focus on neurodegenerative diseases. Inspired by the recent Mamba model, scMamba introduces a novel architecture that incorporates a linear adapter layer, gene embeddings, and bidirectional Mamba blocks, enabling efficient processing of snRNA-seq data while preserving information from the raw input. Notably, scMamba learns generalizable features of cells and genes through pre-training on snRNA-seq data, without relying on dimension reduction or selection of highly variable genes. We demonstrate that scMamba outperforms benchmark methods in various downstream tasks, including cell type annotation, doublet detection, imputation, and the identification of differentially expressed genes.

Long non-coding RNAs (lncRNAs) serve as crucial regulators in numerous biological processes. Although they share sequence similarities with messenger RNAs (mRNAs), lncRNAs perform entirely different roles, providing new avenues for biological research. The emergence of next-generation sequencing technologies has greatly advanced the detection and identification of lncRNA transcripts and deep learning-based approaches have been introduced to classify long non-coding RNAs (lncRNAs). These advanced methods have significantly enhanced the efficiency of identifying lncRNAs. However, many of these methods are devoid of robustness and accuracy due to the extended length of the sequences involved. To tackle this issue, we have introduced a novel pre-trained bidirectional encoder representation called LoRA-BERT. LoRA-BERT is designed to capture the importance of nucleotide-level information during sequence classification, leading to more robust and satisfactory outcomes. In a comprehensive comparison with commonly used sequence prediction tools, we have demonstrated that LoRA-BERT outperforms them in terms of accuracy and efficiency. Our results indicate that, when utilizing the transformer model, LoRA-BERT achieves state-of-the-art performance in predicting both lncRNAs and mRNAs for human and mouse species. Through the utilization of LoRA-BERT, we acquire valuable insights into the traits of lncRNAs and mRNAs, offering the potential to aid in the comprehension and detection of diseases linked to lncRNAs in humans.

Single-cell RNA sequencing (scRNA-seq) data are often confounded by technical or biological batch effects. Existing deep learning models mitigate these effects but often discard batch-specific information, potentially losing valuable biological insights. We propose a Mixed Effects Deep Learning (MEDL) autoencoder framework that separately models batch-invariant (fixed effects) and batch-specific (random effects) components. By decoupling batch-invariant biological states from batch variations, our framework integrates both into predictive models. Our approach also generates 2D visualizations of how the same cell appears across batches, enhancing interpretability. Retaining both fixed and random effect latent spaces improves classification accuracy. We applied our framework to three datasets spanning the cardiovascular system (Healthy Heart), Autism Spectrum Disorder (ASD), and Acute Myeloid Leukemia (AML). With 147 batches in the Healthy Heart dataset, far exceeding typical numbers, we tested our framework's ability to handle many batches. In the ASD dataset, our approach captured donor heterogeneity between autistic and healthy individuals. In the AML dataset, it distinguished donor heterogeneity despite missing cell types and diseased donors exhibiting both healthy and malignant cells. These results highlight our framework's ability to characterize fixed and random effects, enhance batch effect visualization, and improve prediction accuracy across diverse datasets.

Due to the recurrent structure of RNN, the long information propagation path poses limitations in capturing long-term dependencies, gradient explosion/vanishing issues, and inefficient sequential execution. Based on this, we propose a novel paradigm called Parallel Gated Network (PGN) as the new successor to RNN. PGN directly captures information from previous time steps through the designed Historical Information Extraction (HIE) layer and leverages gated mechanisms to select and fuse it with the current time step information. This reduces the information propagation path to O(1), effectively addressing the limitations of RNN. To enhance PGN's performance in long-range time series forecasting tasks, we propose a novel temporal modeling framework called Temporal PGN (TPGN). TPGN incorporates two branches to comprehensively capture the semantic information of time series. One branch utilizes PGN to capture long-term periodic patterns while preserving their local characteristics. The other branch employs patches to capture short-term information and aggregate the global representation of the series. TPGN achieves a theoretical complexity of O(L), ensuring efficiency in its operations. Experimental results on five benchmark datasets demonstrate the state-of-the-art (SOTA) performance and high efficiency of TPGN, further confirming the effectiveness of PGN as the new successor to RNN in long-range time series forecasting. The code is available in this repository: https://github.com/Water2sea/TPGN.

The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures based on structure-contextualised modelling. The alignment enables free and bidirectional mappings between sequences and structures by utilising the flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capacity of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs only solved up to 3% of the puzzles due to the oversight of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of genome downstream tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.

Mispronunciation Detection and Diagnosis (MDD) systems, leveraging Automatic Speech Recognition (ASR), face two main challenges in Mandarin Chinese: 1) The two-stage models create an information gap between the phoneme or tone classification stage and the MDD stage. 2) The scarcity of Mandarin MDD datasets limits model training. In this paper, we introduce a stateless RNN-T model for Mandarin MDD, utilizing HuBERT features with pitch embedding through a Pitch Fusion Block. Our model, trained solely on native speaker data, shows a 3% improvement in Phone Error Rate and a 7% increase in False Acceptance Rate over the state-of-the-art baseline in non-native scenarios

Ribonucleic acid (RNA) plays a variety of crucial roles in fundamental biological processes. Recently, RNA has become an interesting drug target, emphasizing the need to improve our understanding of its structures and functions. Over the years, sequencing technologies have produced an enormous amount of unlabeled RNA data, which hides important knowledge and potential. Motivated by the successes of protein language models, we introduce RiboNucleic Acid Language Model (RiNALMo) to help unveil the hidden code of RNA. RiNALMo is the largest RNA language model to date with 650 million parameters pre-trained on 36 million non-coding RNA sequences from several available databases. RiNALMo is able to extract hidden knowledge and capture the underlying structure information implicitly embedded within the RNA sequences. RiNALMo achieves state-of-the-art results on several downstream tasks. Notably, we show that its generalization capabilities can overcome the inability of other deep learning methods for secondary structure prediction to generalize on unseen RNA families. The code has been made publicly available on https://github.com/lbcb-sci/RiNALMo.

We introduce the concept of multiple temporal perspectives, a novel approach applicable to Recurrent Neural Network (RNN) architectures for enhancing their understanding of sequential data. This method involves maintaining diverse temporal views of previously encountered text, significantly enriching the language models' capacity to interpret context. To show the efficacy of this approach, we incorporate it into the Receptance Weighted Key Value (RWKV) architecture, addressing its inherent challenge of retaining all historical information within a single hidden state. Notably, this improvement is achieved with a minimal increase in the number of parameters --even as little as 0.04% of the original number of parameters. Further, the additional parameters necessary for the multiple temporal perspectives are fine-tuned with minimal computational overhead, avoiding the need for a full pre-training. The resulting model maintains linear computational complexity during prompt inference, ensuring consistent efficiency across various sequence lengths. The empirical results and ablation studies included in our research validate the effectiveness of our approach, showcasing improved performance across multiple benchmarks. The code, model weights and datasets are open-sourced at: https://github.com/RazvanDu/TemporalRNNs.

Computational efficiency and robustness are essential in process modeling, optimization, and control for real-world engineering applications. While neural network-based approaches have gained significant attention in recent years, conventional neural networks often fail to address these two critical aspects simultaneously or even independently. Inspired by natural physical systems and established literature, input convex architectures are known to enhance computational efficiency in optimization tasks, whereas Lipschitz-constrained architectures improve robustness. However, combining these properties within a single model requires careful review, as inappropriate methods for enforcing one property can undermine the other. To overcome this, we introduce a novel network architecture, termed Input Convex Lipschitz Recurrent Neural Networks (ICLRNNs). This architecture seamlessly integrates the benefits of convexity and Lipschitz continuity, enabling fast and robust neural network-based modeling and optimization. The ICLRNN outperforms existing recurrent units in both computational efficiency and robustness. Additionally, it has been successfully applied to practical engineering scenarios, such as modeling and control of chemical process and the modeling and real-world solar irradiance prediction for solar PV system planning at LHT Holdings in Singapore. Source code is available at https://github.com/killingbear999/ICLRNN.

Our previously proposed MossFormer has achieved promising performance in monaural speech separation. However, it predominantly adopts a self-attention-based MossFormer module, which tends to emphasize longer-range, coarser-scale dependencies, with a deficiency in effectively modelling finer-scale recurrent patterns. In this paper, we introduce a novel hybrid model that provides the capabilities to model both long-range, coarse-scale dependencies and fine-scale recurrent patterns by integrating a recurrent module into the MossFormer framework. Instead of applying the recurrent neural networks (RNNs) that use traditional recurrent connections, we present a recurrent module based on a feedforward sequential memory network (FSMN), which is considered "RNN-free" recurrent network due to the ability to capture recurrent patterns without using recurrent connections. Our recurrent module mainly comprises an enhanced dilated FSMN block by using gated convolutional units (GCU) and dense connections. In addition, a bottleneck layer and an output layer are also added for controlling information flow. The recurrent module relies on linear projections and convolutions for seamless, parallel processing of the entire sequence. The integrated MossFormer2 hybrid model demonstrates remarkable enhancements over MossFormer and surpasses other state-of-the-art methods in WSJ0-2/3mix, Libri2Mix, and WHAM!/WHAMR! benchmarks.

A recurrent neural network (RNN) is a widely used deep-learning network for dealing with sequential data. Imitating a dynamical system, an infinite-width RNN can approximate any open dynamical system in a compact domain. In general, deep networks with bounded widths are more effective than wide networks in practice; however, the universal approximation theorem for deep narrow structures has yet to be extensively studied. In this study, we prove the universality of deep narrow RNNs and show that the upper bound of the minimum width for universality can be independent of the length of the data. Specifically, we show that a deep RNN with ReLU activation can approximate any continuous function or L^p function with the widths d_x+d_y+2 and max{d_x+1,d_y}, respectively, where the target function maps a finite sequence of vectors in R^{d_x} to a finite sequence of vectors in R^{d_y}. We also compute the additional width required if the activation function is tanh or more. In addition, we prove the universality of other recurrent networks, such as bidirectional RNNs. Bridging a multi-layer perceptron and an RNN, our theory and proof technique can be an initial step toward further research on deep RNNs.

We show that both an LSTM and a unitary-evolution recurrent neural network (URN) can achieve encouraging accuracy on two types of syntactic patterns: context-free long distance agreement, and mildly context-sensitive cross serial dependencies. This work extends recent experiments on deeply nested context-free long distance dependencies, with similar results. URNs differ from LSTMs in that they avoid non-linear activation functions, and they apply matrix multiplication to word embeddings encoded as unitary matrices. This permits them to retain all information in the processing of an input string over arbitrary distances. It also causes them to satisfy strict compositionality. URNs constitute a significant advance in the search for explainable models in deep learning applied to NLP.

The leading approaches in language modeling are all obsessed with TV shows of my youth - namely Transformers and Sesame Street. Transformers this, Transformers that, and over here a bonfire worth of GPU-TPU-neuromorphic wafer scale silicon. We opt for the lazy path of old and proven techniques with a fancy crypto inspired acronym: the Single Headed Attention RNN (SHA-RNN). The author's lone goal is to show that the entire field might have evolved a different direction if we had instead been obsessed with a slightly different acronym and slightly different result. We take a previously strong language model based only on boring LSTMs and get it to within a stone's throw of a stone's throw of state-of-the-art byte level language model results on enwik8. This work has undergone no intensive hyperparameter optimization and lived entirely on a commodity desktop machine that made the author's small studio apartment far too warm in the midst of a San Franciscan summer. The final results are achievable in plus or minus 24 hours on a single GPU as the author is impatient. The attention mechanism is also readily extended to large contexts with minimal computation. Take that Sesame Street.

State-of-the-art solutions in the areas of "Language Modelling & Generating Text", "Speech Recognition", "Generating Image Descriptions" or "Video Tagging" have been using Recurrent Neural Networks as the foundation for their approaches. Understanding the underlying concepts is therefore of tremendous importance if we want to keep up with recent or upcoming publications in those areas. In this work we give a short overview over some of the most important concepts in the realm of Recurrent Neural Networks which enables readers to easily understand the fundamentals such as but not limited to "Backpropagation through Time" or "Long Short-Term Memory Units" as well as some of the more recent advances like the "Attention Mechanism" or "Pointer Networks". We also give recommendations for further reading regarding more complex topics where it is necessary.

Recurrent neural network (RNN) and connectionist temporal classification (CTC) have showed successes in many sequence labeling tasks with the strong ability of dealing with the problems where the alignment between the inputs and the target labels is unknown. Residual network is a new structure of convolutional neural network and works well in various computer vision tasks. In this paper, we take advantage of the architectures mentioned above to create a new network for handwritten digit string recognition. First we design a residual network to extract features from input images, then we employ a RNN to model the contextual information within feature sequences and predict recognition results. At the top of this network, a standard CTC is applied to calculate the loss and yield the final results. These three parts compose an end-to-end trainable network. The proposed new architecture achieves the highest performances on ORAND-CAR-A and ORAND-CAR-B with recognition rates 89.75% and 91.14%, respectively. In addition, the experiments on a generated captcha dataset which has much longer string length show the potential of the proposed network to handle long strings.

Semantic parsing of large-scale 3D point clouds is an important research topic in computer vision and remote sensing fields. Most existing approaches utilize hand-crafted features for each modality independently and combine them in a heuristic manner. They often fail to consider the consistency and complementary information among features adequately, which makes them difficult to capture high-level semantic structures. The features learned by most of the current deep learning methods can obtain high-quality image classification results. However, these methods are hard to be applied to recognize 3D point clouds due to unorganized distribution and various point density of data. In this paper, we propose a 3DCNN-DQN-RNN method which fuses the 3D convolutional neural network (CNN), Deep Q-Network (DQN) and Residual recurrent neural network (RNN) for an efficient semantic parsing of large-scale 3D point clouds. In our method, an eye window under control of the 3D CNN and DQN can localize and segment the points of the object class efficiently. The 3D CNN and Residual RNN further extract robust and discriminative features of the points in the eye window, and thus greatly enhance the parsing accuracy of large-scale point clouds. Our method provides an automatic process that maps the raw data to the classification results. It also integrates object localization, segmentation and classification into one framework. Experimental results demonstrate that the proposed method outperforms the state-of-the-art point cloud classification methods.

We present a character-based model for joint segmentation and POS tagging for Chinese. The bidirectional RNN-CRF architecture for general sequence tagging is adapted and applied with novel vector representations of Chinese characters that capture rich contextual information and lower-than-character level features. The proposed model is extensively evaluated and compared with a state-of-the-art tagger respectively on CTB5, CTB9 and UD Chinese. The experimental results indicate that our model is accurate and robust across datasets in different sizes, genres and annotation schemes. We obtain state-of-the-art performance on CTB5, achieving 94.38 F1-score for joint segmentation and POS tagging.

Recent advances in recurrent neural network architectures, such as Mamba and RWKV, have enabled RNNs to match or exceed the performance of equal-size transformers in terms of language modeling perplexity and downstream evaluations, suggesting that future systems may be built on completely new architectures. In this paper, we examine if selected interpretability methods originally designed for transformer language models will transfer to these up-and-coming recurrent architectures. Specifically, we focus on steering model outputs via contrastive activation addition, on eliciting latent predictions via the tuned lens, and eliciting latent knowledge from models fine-tuned to produce false outputs under certain conditions. Our results show that most of these techniques are effective when applied to RNNs, and we show that it is possible to improve some of them by taking advantage of RNNs' compressed state.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6% increase in drug response prediction correlation, 9.6% improvement in single-cell drug classification AUC, and 1.1% average gain in gene perturbation prediction accuracy.

The performance of music source separation (MSS) models has been greatly improved in recent years thanks to the development of novel neural network architectures and training pipelines. However, recent model designs for MSS were mainly motivated by other audio processing tasks or other research fields, while the intrinsic characteristics and patterns of the music signals were not fully discovered. In this paper, we propose band-split RNN (BSRNN), a frequency-domain model that explictly splits the spectrogram of the mixture into subbands and perform interleaved band-level and sequence-level modeling. The choices of the bandwidths of the subbands can be determined by a priori knowledge or expert knowledge on the characteristics of the target source in order to optimize the performance on a certain type of target musical instrument. To better make use of unlabeled data, we also describe a semi-supervised model finetuning pipeline that can further improve the performance of the model. Experiment results show that BSRNN trained only on MUSDB18-HQ dataset significantly outperforms several top-ranking models in Music Demixing (MDX) Challenge 2021, and the semi-supervised finetuning stage further improves the performance on all four instrument tracks.

Foundation models for zero-shot time series forecasting face challenges in efficient long-horizon prediction and reproducibility, with existing synthetic-only approaches underperforming on challenging benchmarks. This paper presents TempoPFN, a univariate time series foundation model based on linear Recurrent Neural Networks (RNNs) pre-trained exclusively on synthetic data. The model uses a GatedDeltaProduct architecture with state-weaving for fully parallelizable training across sequence lengths, eliminating the need for windowing or summarization techniques while maintaining robust temporal state-tracking. Our comprehensive synthetic data pipeline unifies diverse generators, including stochastic differential equations, Gaussian processes, and audio synthesis, with novel augmentations. In zero-shot evaluations on the Gift-Eval benchmark, TempoPFN achieves top-tier competitive performance, outperforming all existing synthetic-only approaches and surpassing the vast majority of models trained on real-world data, while being more efficient than existing baselines by leveraging fully parallelizable training and inference. We open-source our complete data generation pipeline and training code, providing a reproducible foundation for future research.

Many methods have been proposed for removing batch effects and aligning single-cell RNA (scRNA) datasets. However, performance is typically evaluated based on multiple parameters and few datasets, creating challenges in assessing which method is best for aligning data at scale. Here, we introduce the K-Neighbors Intersection (KNI) score, a single score that both penalizes batch effects and measures accuracy at cross-dataset cell-type label prediction alongside carefully curated small (scMARK) and large (scREF) benchmarks comprising 11 and 46 human scRNA studies respectively, where we have standardized author labels. Using the KNI score, we evaluate and optimize approaches for cross-dataset single-cell RNA integration. We introduce Batch Adversarial single-cell Variational Inference (BA-scVI), as a new variant of scVI that uses adversarial training to penalize batch-effects in the encoder and decoder, and show this approach outperforms other methods. In the resulting aligned space, we find that the granularity of cell-type groupings is conserved, supporting the notion that whole-organism cell-type maps can be created by a single model without loss of information.

Linear Recurrent Neural Networks (linear RNNs) have emerged as competitive alternatives to Transformers for sequence modeling, offering efficient training and linear-time inference. However, existing architectures face a fundamental trade-off between expressivity and efficiency, dictated by the structure of their state-transition matrices. Diagonal matrices, used in models such as Mamba, GLA, or mLSTM, yield fast runtime but have limited expressivity. To address this, recent architectures such as DeltaNet and RWKV-7 adopted a diagonal plus rank-1 structure, which allows simultaneous token and channel mixing, improving associative recall and, as recently shown, state-tracking when allowing negative eigenvalues in the state-transition matrices. Building on the interpretation of DeltaNet's recurrence as performing one step of online gradient descent per token on an associative recall loss, we introduce DeltaProduct, which instead takes multiple (n_h) steps per token. This naturally leads to diagonal plus rank-n_h state-transition matrices, formed as products of n_h generalized Householder transformations, providing a tunable mechanism to balance expressivity and efficiency. We provide a detailed theoretical characterization of the state-tracking capability of DeltaProduct in finite precision, showing how it improves by increasing n_h. Our extensive experiments demonstrate that DeltaProduct outperforms DeltaNet in both state-tracking and language modeling, while also showing significantly improved length extrapolation capabilities.

Linear Recurrent Neural Networks (LRNNs) such as Mamba, RWKV, GLA, mLSTM, and DeltaNet have emerged as efficient alternatives to Transformers for long sequences. However, both Transformers and LRNNs struggle to perform state-tracking, which may impair performance in tasks such as code evaluation. In one forward pass, current architectures are unable to solve even parity, the simplest state-tracking task, which non-linear RNNs can handle effectively. Recently, Sarrof et al. (2024) demonstrated that the failure of LRNNs like Mamba to solve parity stems from restricting the value range of their diagonal state-transition matrices to [0, 1] and that incorporating negative values can resolve this issue. We extend this result to non-diagonal LRNNs such as DeltaNet. We prove that finite precision LRNNs with state-transition matrices having only positive eigenvalues cannot solve parity, while non-triangular matrices are needed to count modulo 3. Notably, we also prove that LRNNs can learn any regular language when their state-transition matrices are products of identity minus vector outer product matrices, each with eigenvalues in the range [-1, 1]. Our experiments confirm that extending the eigenvalue range of Mamba and DeltaNet to include negative values not only enables them to solve parity but consistently improves their performance on state-tracking tasks. We also show that state-tracking enabled LRNNs can be pretrained stably and efficiently at scale (1.3B parameters), achieving competitive performance on language modeling and showing promise on code and math tasks.

As a powerful tool for characterizing cellular subpopulations and cellular heterogeneity, single cell RNA sequencing (scRNA-seq) technology offers advantages of high throughput and multidimensional analysis. However, the process of data acquisition is often constrained by high cost and limited sample availability. To overcome these limitations, we propose a hybrid model based on Diffusion model and White-Box transformer that aims to generate synthetic and biologically plausible scRNA-seq data. Diffusion model progressively introduce noise into the data and then recover the original data through a denoising process, a forward and reverse process that is particularly suitable for generating complex data distributions. White-Box transformer is a deep learning architecture that emphasizes mathematical interpretability. By minimizing the encoding rate of the data and maximizing the sparsity of the representation, it not only reduces the computational burden, but also provides clear insight into underlying structure. Our White-Box Diffusion Transformer combines the generative capabilities of Diffusion model with the mathematical interpretability of White-Box transformer. Through experiments using six different single-cell RNA-Seq datasets, we visualize both generated and real data using t-SNE dimensionality reduction technique, as well as quantify similarity between generated and real data using various metrics to demonstrate comparable performance of White-Box Diffusion Transformer and Diffusion Transformer in generating scRNA-seq data alongside significant improvements in training efficiency and resource utilization. Our code is available at https://github.com/lingximamo/White-Box-Diffusion-Transformer

World models are a fundamental component in model-based reinforcement learning (MBRL). To perform temporally extended and consistent simulations of the future in partially observable environments, world models need to possess long-term memory. However, state-of-the-art MBRL agents, such as Dreamer, predominantly employ recurrent neural networks (RNNs) as their world model backbone, which have limited memory capacity. In this paper, we seek to explore alternative world model backbones for improving long-term memory. In particular, we investigate the effectiveness of Transformers and Structured State Space Sequence (S4) models, motivated by their remarkable ability to capture long-range dependencies in low-dimensional sequences and their complementary strengths. We propose S4WM, the first world model compatible with parallelizable SSMs including S4 and its variants. By incorporating latent variable modeling, S4WM can efficiently generate high-dimensional image sequences through latent imagination. Furthermore, we extensively compare RNN-, Transformer-, and S4-based world models across four sets of environments, which we have tailored to assess crucial memory capabilities of world models, including long-term imagination, context-dependent recall, reward prediction, and memory-based reasoning. Our findings demonstrate that S4WM outperforms Transformer-based world models in terms of long-term memory, while exhibiting greater efficiency during training and imagination. These results pave the way for the development of stronger MBRL agents.

Neural architecture search (NAS) has allowed for the automatic creation of new and effective neural network architectures, offering an alternative to the laborious process of manually designing complex architectures. However, traditional NAS algorithms are slow and require immense amounts of computing power. Recent research has investigated training-free NAS metrics for image classification architectures, drastically speeding up search algorithms. In this paper, we investigate training-free NAS metrics for recurrent neural network (RNN) and BERT-based transformer architectures, targeted towards language modeling tasks. First, we develop a new training-free metric, named hidden covariance, that predicts the trained performance of an RNN architecture and significantly outperforms existing training-free metrics. We experimentally evaluate the effectiveness of the hidden covariance metric on the NAS-Bench-NLP benchmark. Second, we find that the current search space paradigm for transformer architectures is not optimized for training-free neural architecture search. Instead, a simple qualitative analysis can effectively shrink the search space to the best performing architectures. This conclusion is based on our investigation of existing training-free metrics and new metrics developed from recent transformer pruning literature, evaluated on our own benchmark of trained BERT architectures. Ultimately, our analysis shows that the architecture search space and the training-free metric must be developed together in order to achieve effective results.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

Symmetries such as gauge invariance and anyonic symmetry play a crucial role in quantum many-body physics. We develop a general approach to constructing gauge invariant or anyonic symmetric autoregressive neural network quantum states, including a wide range of architectures such as Transformer and recurrent neural network (RNN), for quantum lattice models. These networks can be efficiently sampled and explicitly obey gauge symmetries or anyonic constraint. We prove that our methods can provide exact representation for the ground and excited states of the 2D and 3D toric codes, and the X-cube fracton model. We variationally optimize our symmetry incorporated autoregressive neural networks for ground states as well as real-time dynamics for a variety of models. We simulate the dynamics and the ground states of the quantum link model of U(1) lattice gauge theory, obtain the phase diagram for the 2D Z_2 gauge theory, determine the phase transition and the central charge of the SU(2)_3 anyonic chain, and also compute the ground state energy of the SU(2) invariant Heisenberg spin chain. Our approach provides powerful tools for exploring condensed matter physics, high energy physics and quantum information science.

In this paper we present an end-to-end speech recognition model with Transformer encoders that can be used in a streaming speech recognition system. Transformer computation blocks based on self-attention are used to encode both audio and label sequences independently. The activations from both audio and label encoders are combined with a feed-forward layer to compute a probability distribution over the label space for every combination of acoustic frame position and label history. This is similar to the Recurrent Neural Network Transducer (RNN-T) model, which uses RNNs for information encoding instead of Transformer encoders. The model is trained with the RNN-T loss well-suited to streaming decoding. We present results on the LibriSpeech dataset showing that limiting the left context for self-attention in the Transformer layers makes decoding computationally tractable for streaming, with only a slight degradation in accuracy. We also show that the full attention version of our model beats the-state-of-the art accuracy on the LibriSpeech benchmarks. Our results also show that we can bridge the gap between full attention and limited attention versions of our model by attending to a limited number of future frames.

Word embeddings improve generalization over lexical features by placing each word in a lower-dimensional space, using distributional information obtained from unlabeled data. However, the effectiveness of word embeddings for downstream NLP tasks is limited by out-of-vocabulary (OOV) words, for which embeddings do not exist. In this paper, we present MIMICK, an approach to generating OOV word embeddings compositionally, by learning a function from spellings to distributional embeddings. Unlike prior work, MIMICK does not require re-training on the original word embedding corpus; instead, learning is performed at the type level. Intrinsic and extrinsic evaluations demonstrate the power of this simple approach. On 23 languages, MIMICK improves performance over a word-based baseline for tagging part-of-speech and morphosyntactic attributes. It is competitive with (and complementary to) a supervised character-based model in low-resource settings.

We present a comprehensive study of deep bidirectional long short-term memory (LSTM) recurrent neural network (RNN) based acoustic models for automatic speech recognition (ASR). We study the effect of size and depth and train models of up to 8 layers. We investigate the training aspect and study different variants of optimization methods, batching, truncated backpropagation, different regularization techniques such as dropout and L_2 regularization, and different gradient clipping variants. The major part of the experimental analysis was performed on the Quaero corpus. Additional experiments also were performed on the Switchboard corpus. Our best LSTM model has a relative improvement in word error rate of over 14\% compared to our best feed-forward neural network (FFNN) baseline on the Quaero task. On this task, we get our best result with an 8 layer bidirectional LSTM and we show that a pretraining scheme with layer-wise construction helps for deep LSTMs. Finally we compare the training calculation time of many of the presented experiments in relation with recognition performance. All the experiments were done with RETURNN, the RWTH extensible training framework for universal recurrent neural networks in combination with RASR, the RWTH ASR toolkit.

In this work, we model abstractive text summarization using Attentional Encoder-Decoder Recurrent Neural Networks, and show that they achieve state-of-the-art performance on two different corpora. We propose several novel models that address critical problems in summarization that are not adequately modeled by the basic architecture, such as modeling key-words, capturing the hierarchy of sentence-to-word structure, and emitting words that are rare or unseen at training time. Our work shows that many of our proposed models contribute to further improvement in performance. We also propose a new dataset consisting of multi-sentence summaries, and establish performance benchmarks for further research.