Daily Papers

We investigate the possibility of forcing a self-supervised model trained using a contrastive predictive loss to extract slowly varying latent representations. Rather than producing individual predictions for each of the future representations, the model emits a sequence of predictions shorter than that of the upcoming representations to which they will be aligned. In this way, the prediction network solves a simpler task of predicting the next symbols, but not their exact timing, while the encoding network is trained to produce piece-wise constant latent codes. We evaluate the model on a speech coding task and demonstrate that the proposed Aligned Contrastive Predictive Coding (ACPC) leads to higher linear phone prediction accuracy and lower ABX error rates, while being slightly faster to train due to the reduced number of prediction heads.

This study examines the integration of Contrastive Predictive Coding (CPC) with Spiking Neural Networks (SNN). While CPC learns the predictive structure of data to generate meaningful representations, SNN mimics the computational processes of biological neural systems over time. In this study, the goal is to develop a predictive coding model with greater biological plausibility by processing inputs and outputs in a spike-based system. The proposed model was tested on the MNIST dataset and achieved a high classification rate in distinguishing positive sequential samples from non-sequential negative samples. The study demonstrates that CPC can be effectively combined with SNN, showing that an SNN trained for classification tasks can also function as an encoding mechanism. Project codes and detailed results can be accessed on our GitHub page: https://github.com/vnd-ogrenme/ongorusel-kodlama/tree/main/CPC_SNN

Predicting and reasoning about the future lie at the heart of many time-series questions. For example, goal-conditioned reinforcement learning can be viewed as learning representations to predict which states are likely to be visited in the future. While prior methods have used contrastive predictive coding to model time series data, learning representations that encode long-term dependencies usually requires large amounts of data. In this paper, we introduce a temporal difference version of contrastive predictive coding that stitches together pieces of different time series data to decrease the amount of data required to learn predictions of future events. We apply this representation learning method to derive an off-policy algorithm for goal-conditioned RL. Experiments demonstrate that, compared with prior RL methods, ours achieves 2 times median improvement in success rates and can better cope with stochastic environments. In tabular settings, we show that our method is about 20 times more sample efficient than the successor representation and 1500 times more sample efficient than the standard (Monte Carlo) version of contrastive predictive coding.

Predictive Coding (PC) is a theoretical framework in cognitive science suggesting that the human brain processes cognition through spatiotemporal prediction of the visual world. Existing studies have developed spatiotemporal prediction neural networks based on the PC theory, emulating its two core mechanisms: Correcting predictions from residuals and hierarchical learning. However, these models do not show the enhancement of prediction skills on real-world forecasting tasks and ignore the Precision Weighting mechanism of PC theory. The precision weighting mechanism posits that the brain allocates more attention to signals with lower precision, contributing to the cognitive ability of human brains. This work introduces the Cognitive Diffusion Probabilistic Models (CogDPM), which demonstrate the connection between diffusion probabilistic models and PC theory. CogDPM features a precision estimation method based on the hierarchical sampling capabilities of diffusion models and weight the guidance with precision weights estimated by the inherent property of diffusion models. We experimentally show that the precision weights effectively estimate the data predictability. We apply CogDPM to real-world prediction tasks using the United Kindom precipitation and ERA surface wind datasets. Our results demonstrate that CogDPM outperforms both existing domain-specific operational models and general deep prediction models by providing more proficient forecasting.

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.

Language models have achieved remarkable success in various natural language processing tasks. However, their application to time series data, a crucial component in many domains, remains limited. This paper proposes LiPCoT (Linear Predictive Coding based Tokenizer for time series), a novel tokenizer that encodes time series data into a sequence of tokens, enabling self-supervised learning of time series using existing Language model architectures such as BERT. Unlike traditional time series tokenizers that rely heavily on CNN encoder for time series feature generation, LiPCoT employs stochastic modeling through linear predictive coding to create a latent space for time series providing a compact yet rich representation of the inherent stochastic nature of the data. Furthermore, LiPCoT is computationally efficient and can effectively handle time series data with varying sampling rates and lengths, overcoming common limitations of existing time series tokenizers. In this proof-of-concept work, we present the effectiveness of LiPCoT in classifying Parkinson's disease (PD) using an EEG dataset from 46 participants. In particular, we utilize LiPCoT to encode EEG data into a small vocabulary of tokens and then use BERT for self-supervised learning and the downstream task of PD classification. We benchmark our approach against several state-of-the-art CNN-based deep learning architectures for PD detection. Our results reveal that BERT models utilizing self-supervised learning outperformed the best-performing existing method by 7.1% in precision, 2.3% in recall, 5.5% in accuracy, 4% in AUC, and 5% in F1-score highlighting the potential for self-supervised learning even on small datasets. Our work will inform future foundational models for time series, particularly for self-supervised learning.

Predictive coding networks are neuroscience-inspired models with roots in both Bayesian statistics and neuroscience. Training such models, however, is quite inefficient and unstable. In this work, we show how by simply changing the temporal scheduling of the update rule for the synaptic weights leads to an algorithm that is much more efficient and stable than the original one, and has theoretical guarantees in terms of convergence. The proposed algorithm, that we call incremental predictive coding (iPC) is also more biologically plausible than the original one, as it it fully automatic. In an extensive set of experiments, we show that iPC constantly performs better than the original formulation on a large number of benchmarks for image classification, as well as for the training of both conditional and masked language models, in terms of test accuracy, efficiency, and convergence with respect to a large set of hyperparameters.

Recent work has demonstrated the effectiveness of formulating decision making as a supervised learning problem on offline-collected trajectories. However, the benefits of performing sequence modeling on trajectory data is not yet clear. In this work we investigate if sequence modeling has the capability to condense trajectories into useful representations that can contribute to policy learning. To achieve this, we adopt a two-stage framework that first summarizes trajectories with sequence modeling techniques, and then employs these representations to learn a policy along with a desired goal. This design allows many existing supervised offline RL methods to be considered as specific instances of our framework. Within this framework, we introduce Goal-Conditioned Predicitve Coding (GCPC), an approach that brings powerful trajectory representations and leads to performant policies. We conduct extensive empirical evaluations on AntMaze, FrankaKitchen and Locomotion environments, and observe that sequence modeling has a significant impact on some decision making tasks. In addition, we demonstrate that GCPC learns a goal-conditioned latent representation about the future, which serves as an "implicit planner", and enables competitive performance on all three benchmarks.

While supervised learning has enabled great progress in many applications, unsupervised learning has not seen such widespread adoption, and remains an important and challenging endeavor for artificial intelligence. In this work, we propose a universal unsupervised learning approach to extract useful representations from high-dimensional data, which we call Contrastive Predictive Coding. The key insight of our model is to learn such representations by predicting the future in latent space by using powerful autoregressive models. We use a probabilistic contrastive loss which induces the latent space to capture information that is maximally useful to predict future samples. It also makes the model tractable by using negative sampling. While most prior work has focused on evaluating representations for a particular modality, we demonstrate that our approach is able to learn useful representations achieving strong performance on four distinct domains: speech, images, text and reinforcement learning in 3D environments.

Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support embodied, adaptable, and energy-efficient autonomous agents. A central theory in this domain is predictive coding, which posits that learning and behaviour are driven by hierarchical probabilistic inferences about the causes of sensory inputs. Biological realism constrains these networks to rely on simple local computations in the form of precision-weighted predictions and prediction errors. This can make this framework highly efficient, but its implementation comes with unique challenges on the software development side. Embedding such models in standard neural network libraries often becomes limiting, as these libraries' compilation and differentiation backends can force a conceptual separation between optimization algorithms and the systems being optimized. This critically departs from other biological principles such as self-monitoring, self-organisation, cellular growth and functional plasticity. In this paper, we introduce pyhgf: a Python package backed by JAX and Rust for creating, manipulating and sampling dynamic networks for predictive coding. We improve over other frameworks by enclosing the network components as transparent, modular and malleable variables in the message-passing steps. The resulting graphs can implement arbitrary computational complexities as beliefs propagation. But the transparency of core variables can also translate into inference processes that leverage self-organisation principles, and express structure learning, meta-learning or causal discovery as the consequence of network structural adaptation to surprising inputs. The code, tutorials and documentation are hosted at: https://github.com/ilabcode/pyhgf.

Automatic detection of phoneme or word-like units is one of the core objectives in zero-resource speech processing. Recent attempts employ self-supervised training methods, such as contrastive predictive coding (CPC), where the next frame is predicted given past context. However, CPC only looks at the audio signal's frame-level structure. We overcome this limitation with a segmental contrastive predictive coding (SCPC) framework that can model the signal structure at a higher level e.g. at the phoneme level. In this framework, a convolutional neural network learns frame-level representation from the raw waveform via noise-contrastive estimation (NCE). A differentiable boundary detector finds variable-length segments, which are then used to optimize a segment encoder via NCE to learn segment representations. The differentiable boundary detector allows us to train frame-level and segment-level encoders jointly. Typically, phoneme and word segmentation are treated as separate tasks. We unify them and experimentally show that our single model outperforms existing phoneme and word segmentation methods on TIMIT and Buckeye datasets. We analyze the impact of boundary threshold and when is the right time to include the segmental loss in the learning process.

Autoregressive Predictive Coding (APC), as a self-supervised objective, has enjoyed success in learning representations from large amounts of unlabeled data, and the learned representations are rich for many downstream tasks. However, the connection between low self-supervised loss and strong performance in downstream tasks remains unclear. In this work, we propose Vector-Quantized Autoregressive Predictive Coding (VQ-APC), a novel model that produces quantized representations, allowing us to explicitly control the amount of information encoded in the representations. By studying a sequence of increasingly limited models, we reveal the constituents of the learned representations. In particular, we confirm the presence of information with probing tasks, while showing the absence of information with mutual information, uncovering the model's preference in preserving speech information as its capacity becomes constrained. We find that there exists a point where phonetic and speaker information are amplified to maximize a self-supervised objective. As a byproduct, the learned codes for a particular model capacity correspond well to English phones.

Self-supervised learning methods overcome the key bottleneck for building more capable AI: limited availability of labeled data. However, one of the drawbacks of self-supervised architectures is that the representations that they learn are implicit and it is hard to extract meaningful information about the encoded world states, such as 3D structure of the visual scene encoded in a depth map. Moreover, in the visual domain such representations only rarely undergo evaluations that may be critical for downstream tasks, such as vision for autonomous cars. Herein, we propose a framework for evaluating visual representations for illumination invariance in the context of depth perception. We develop a new predictive coding-based architecture and a hybrid fully-supervised/self-supervised learning method. We propose a novel architecture that extends the predictive coding approach: PRedictive Lateral bottom-Up and top-Down Encoder-decoder Network (PreludeNet), which explicitly learns to infer and predict depth from video frames. In PreludeNet, the encoder's stack of predictive coding layers is trained in a self-supervised manner, while the predictive decoder is trained in a supervised manner to infer or predict the depth. We evaluate the robustness of our model on a new synthetic dataset, in which lighting conditions (such as overall illumination, and effect of shadows) can be be parametrically adjusted while keeping all other aspects of the world constant. PreludeNet achieves both competitive depth inference performance and next frame prediction accuracy. We also show how this new network architecture, coupled with the hybrid fully-supervised/self-supervised learning method, achieves balance between the said performance and invariance to changes in lighting. The proposed framework for evaluating visual representations can be extended to diverse task domains and invariance tests.

Learning meaningful and general representations from unannotated speech that are applicable to a wide range of tasks remains challenging. In this paper we propose to use autoregressive predictive coding (APC), a recently proposed self-supervised objective, as a generative pre-training approach for learning meaningful, non-specific, and transferable speech representations. We pre-train APC on large-scale unlabeled data and conduct transfer learning experiments on three speech applications that require different information about speech characteristics to perform well: speech recognition, speech translation, and speaker identification. Extensive experiments show that APC not only outperforms surface features (e.g., log Mel spectrograms) and other popular representation learning methods on all three tasks, but is also effective at reducing downstream labeled data size and model parameters. We also investigate the use of Transformers for modeling APC and find it superior to RNNs.

Self-supervised speech representations have been shown to be effective in a variety of speech applications. However, existing representation learning methods generally rely on the autoregressive model and/or observed global dependencies while generating the representation. In this work, we propose Non-Autoregressive Predictive Coding (NPC), a self-supervised method, to learn a speech representation in a non-autoregressive manner by relying only on local dependencies of speech. NPC has a conceptually simple objective and can be implemented easily with the introduced Masked Convolution Blocks. NPC offers a significant speedup for inference since it is parallelizable in time and has a fixed inference time for each time step regardless of the input sequence length. We discuss and verify the effectiveness of NPC by theoretically and empirically comparing it with other methods. We show that the NPC representation is comparable to other methods in speech experiments on phonetic and speaker classification while being more efficient.

PAQ8 is an open source lossless data compression algorithm that currently achieves the best compression rates on many benchmarks. This report presents a detailed description of PAQ8 from a statistical machine learning perspective. It shows that it is possible to understand some of the modules of PAQ8 and use this understanding to improve the method. However, intuitive statistical explanations of the behavior of other modules remain elusive. We hope the description in this report will be a starting point for discussions that will increase our understanding, lead to improvements to PAQ8, and facilitate a transfer of knowledge from PAQ8 to other machine learning methods, such a recurrent neural networks and stochastic memoizers. Finally, the report presents a broad range of new applications of PAQ to machine learning tasks including language modeling and adaptive text prediction, adaptive game playing, classification, and compression using features from the field of deep learning.

A demonstration of a real-time and continuous turn-taking prediction system is presented. The system is based on a voice activity projection (VAP) model, which directly maps dialogue stereo audio to future voice activities. The VAP model includes contrastive predictive coding (CPC) and self-attention transformers, followed by a cross-attention transformer. We examine the effect of the input context audio length and demonstrate that the proposed system can operate in real-time with CPU settings, with minimal performance degradation.

We propose a pre-training strategy called Multi-modal Multi-task Masked Autoencoders (MultiMAE). It differs from standard Masked Autoencoding in two key aspects: I) it can optionally accept additional modalities of information in the input besides the RGB image (hence "multi-modal"), and II) its training objective accordingly includes predicting multiple outputs besides the RGB image (hence "multi-task"). We make use of masking (across image patches and input modalities) to make training MultiMAE tractable as well as to ensure cross-modality predictive coding is indeed learned by the network. We show this pre-training strategy leads to a flexible, simple, and efficient framework with improved transfer results to downstream tasks. In particular, the same exact pre-trained network can be flexibly used when additional information besides RGB images is available or when no information other than RGB is available - in all configurations yielding competitive to or significantly better results than the baselines. To avoid needing training datasets with multiple modalities and tasks, we train MultiMAE entirely using pseudo labeling, which makes the framework widely applicable to any RGB dataset. The experiments are performed on multiple transfer tasks (image classification, semantic segmentation, depth estimation) and datasets (ImageNet, ADE20K, Taskonomy, Hypersim, NYUv2). The results show an intriguingly impressive capability by the model in cross-modal/task predictive coding and transfer.

The brain understands the external world through an internal model that generates predictions and refines them based on prediction errors. A complete prediction specifies what will happen, when it will happen, and with what probability, which we refer to as a "prediction object". Existing models typically capture only what and when, omit probabilities, and rely on biologically-implausible algorithms. Here we show that a single population of spiking neurons can jointly encode the prediction object through a biologically grounded learning mechanism. We implement a heterogeneous Izhikevich spiking reservoir with readouts trained by an error-modulated, attention-gated three-factor Hebbian rule and test it on a novel paradigm that controls both the timing and probability of upcoming stimuli. By integrating real-time learning of "when" with offline consolidation of "what", the model encodes the complete prediction object, firing at the correct times with magnitudes proportional to the probabilities. Critically, it rapidly adapts to changes in both stimulus timing and probability, an ability that global least-squares methods such as FORCE lack without explicit resets. During learning, the model self-organizes its readout weights into near-orthogonal subspaces for "what" and "when," showing that multiplexed encoding arises naturally from generic recurrent dynamics under local, error-gated modulation. These results challenge the view that "what" and "when" predictions require separate modules, suggesting instead that mixed selectivity within shared populations supports flexible predictive cognition. The model also predicts phase-specific neuromodulation and overlapping neural subspaces, offering a parsimonious alternative to hierarchical predictive-coding accounts.

We introduce a pretraining technique called Selfie, which stands for SELFie supervised Image Embedding. Selfie generalizes the concept of masked language modeling of BERT (Devlin et al., 2019) to continuous data, such as images, by making use of the Contrastive Predictive Coding loss (Oord et al., 2018). Given masked-out patches in an input image, our method learns to select the correct patch, among other "distractor" patches sampled from the same image, to fill in the masked location. This classification objective sidesteps the need for predicting exact pixel values of the target patches. The pretraining architecture of Selfie includes a network of convolutional blocks to process patches followed by an attention pooling network to summarize the content of unmasked patches before predicting masked ones. During finetuning, we reuse the convolutional weights found by pretraining. We evaluate Selfie on three benchmarks (CIFAR-10, ImageNet 32 x 32, and ImageNet 224 x 224) with varying amounts of labeled data, from 5% to 100% of the training sets. Our pretraining method provides consistent improvements to ResNet-50 across all settings compared to the standard supervised training of the same network. Notably, on ImageNet 224 x 224 with 60 examples per class (5%), our method improves the mean accuracy of ResNet-50 from 35.6% to 46.7%, an improvement of 11.1 points in absolute accuracy. Our pretraining method also improves ResNet-50 training stability, especially on low data regime, by significantly lowering the standard deviation of test accuracies across different runs.

This paper investigates the application of voice activity projection (VAP), a predictive turn-taking model for spoken dialogue, on multilingual data, encompassing English, Mandarin, and Japanese. The VAP model continuously predicts the upcoming voice activities of participants in dyadic dialogue, leveraging a cross-attention Transformer to capture the dynamic interplay between participants. The results show that a monolingual VAP model trained on one language does not make good predictions when applied to other languages. However, a multilingual model, trained on all three languages, demonstrates predictive performance on par with monolingual models across all languages. Further analyses show that the multilingual model has learned to discern the language of the input signal. We also analyze the sensitivity to pitch, a prosodic cue that is thought to be important for turn-taking. Finally, we compare two different audio encoders, contrastive predictive coding (CPC) pre-trained on English, with a recent model based on multilingual wav2vec 2.0 (MMS).

Standard multi-modal models assume the use of the same modalities in training and inference stages. However, in practice, the environment in which multi-modal models operate may not satisfy such assumption. As such, their performances degrade drastically if any modality is missing in the inference stage. We ask: how can we train a model that is robust to missing modalities? This paper seeks a set of good practices for multi-modal action recognition, with a particular interest in circumstances where some modalities are not available at an inference time. First, we study how to effectively regularize the model during training (e.g., data augmentation). Second, we investigate on fusion methods for robustness to missing modalities: we find that transformer-based fusion shows better robustness for missing modality than summation or concatenation. Third, we propose a simple modular network, ActionMAE, which learns missing modality predictive coding by randomly dropping modality features and tries to reconstruct them with the remaining modality features. Coupling these good practices, we build a model that is not only effective in multi-modal action recognition but also robust to modality missing. Our model achieves the state-of-the-arts on multiple benchmarks and maintains competitive performances even in missing modality scenarios. Codes are available at https://github.com/sangminwoo/ActionMAE.

We investigate the emergence of intuitive physics understanding in general-purpose deep neural network models trained to predict masked regions in natural videos. Leveraging the violation-of-expectation framework, we find that video prediction models trained to predict outcomes in a learned representation space demonstrate an understanding of various intuitive physics properties, such as object permanence and shape consistency. In contrast, video prediction in pixel space and multimodal large language models, which reason through text, achieve performance closer to chance. Our comparisons of these architectures reveal that jointly learning an abstract representation space while predicting missing parts of sensory input, akin to predictive coding, is sufficient to acquire an understanding of intuitive physics, and that even models trained on one week of unique video achieve above chance performance. This challenges the idea that core knowledge -- a set of innate systems to help understand the world -- needs to be hardwired to develop an understanding of intuitive physics.

Large Language Models have demonstrated remarkable abilities in reasoning and planning by breaking down complex problems into sequential steps. Despite their success in various domains like mathematical problem-solving and coding, LLMs face challenges in ensuring reliable and optimal planning due to their inherent myopic nature of autoregressive decoding. This paper revisits LLM reasoning from an optimal-control perspective, proposing a novel method, Predictive-Decoding, that leverages Model Predictive Control to enhance planning accuracy. By re-weighting LLM distributions based on foresight trajectories, Predictive-Decoding aims to mitigate early errors and promote non-myopic planning. Our experiments show significant improvements in a wide range of tasks for math, coding, and agents. Furthermore, Predictive-Decoding demonstrates computational efficiency, outperforming search baselines with reduced computational resources. This study provides insights into optimizing LLM planning capabilities.

Food security is a complex, multidimensional concept challenging to measure comprehensively. Effective anticipation, monitoring, and mitigation of food crises require timely and comprehensive global data. This paper introduces the Harmonized Food Insecurity Dataset (HFID), an open-source resource consolidating four key data sources: the Integrated Food Security Phase Classification (IPC)/Cadre Harmonis\'e (CH) phases, the Famine Early Warning Systems Network (FEWS NET) IPC-compatible phases, and the World Food Program's (WFP) Food Consumption Score (FCS) and reduced Coping Strategy Index (rCSI). Updated monthly and using a common reference system for administrative units, the HFID offers extensive spatial and temporal coverage. It serves as a vital tool for food security experts and humanitarian agencies, providing a unified resource for analyzing food security conditions and highlighting global data disparities. The scientific community can also leverage the HFID to develop data-driven predictive models, enhancing the capacity to forecast and prevent future food crises.

Predicting high-dimensional or extreme multilabels, such as in medical coding, requires both accuracy and interpretability. Existing works often rely on local interpretability methods, failing to provide comprehensive explanations of the overall mechanism behind each label prediction within a multilabel set. We propose a mechanistic interpretability module called DIctionary Label Attention (\method) that disentangles uninterpretable dense embeddings into a sparse embedding space, where each nonzero element (a dictionary feature) represents a globally learned medical concept. Through human evaluations, we show that our sparse embeddings are more human understandable than its dense counterparts by at least 50 percent. Our automated dictionary feature identification pipeline, leveraging large language models (LLMs), uncovers thousands of learned medical concepts by examining and summarizing the highest activating tokens for each dictionary feature. We represent the relationships between dictionary features and medical codes through a sparse interpretable matrix, enhancing the mechanistic and global understanding of the model's predictions while maintaining competitive performance and scalability without extensive human annotation.

In this work we present Ludwig, a flexible, extensible and easy to use toolbox which allows users to train deep learning models and use them for obtaining predictions without writing code. Ludwig implements a novel approach to deep learning model building based on two main abstractions: data types and declarative configuration files. The data type abstraction allows for easier code and sub-model reuse, and the standardized interfaces imposed by this abstraction allow for encapsulation and make the code easy to extend. Declarative model definition configuration files enable inexperienced users to obtain effective models and increase the productivity of expert users. Alongside these two innovations, Ludwig introduces a general modularized deep learning architecture called Encoder-Combiner-Decoder that can be instantiated to perform a vast amount of machine learning tasks. These innovations make it possible for engineers, scientists from other fields and, in general, a much broader audience to adopt deep learning models for their tasks, concretely helping in its democratization.

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.

Given the clinical notes written in electronic health records (EHRs), it is challenging to predict the diagnostic codes which is formulated as a multi-label classification task. The large set of labels, the hierarchical dependency, and the imbalanced data make this prediction task extremely hard. Most existing work built a binary prediction for each label independently, ignoring the dependencies between labels. To address this problem, we propose a two-stage framework to improve automatic ICD coding by capturing the label correlation. Specifically, we train a label set distribution estimator to rescore the probability of each label set candidate generated by a base predictor. This paper is the first attempt at learning the label set distribution as a reranking module for medical code prediction. In the experiments, our proposed framework is able to improve upon best-performing predictors on the benchmark MIMIC datasets. The source code of this project is available at https://github.com/MiuLab/ICD-Correlation.

Large language models such as GPT and Llama are trained with a next-token prediction loss. In this work, we suggest that training language models to predict multiple future tokens at once results in higher sample efficiency. More specifically, at each position in the training corpus, we ask the model to predict the following n tokens using n independent output heads, operating on top of a shared model trunk. Considering multi-token prediction as an auxiliary training task, we measure improved downstream capabilities with no overhead in training time for both code and natural language models. The method is increasingly useful for larger model sizes, and keeps its appeal when training for multiple epochs. Gains are especially pronounced on generative benchmarks like coding, where our models consistently outperform strong baselines by several percentage points. Our 13B parameter models solves 12 % more problems on HumanEval and 17 % more on MBPP than comparable next-token models. Experiments on small algorithmic tasks demonstrate that multi-token prediction is favorable for the development of induction heads and algorithmic reasoning capabilities. As an additional benefit, models trained with 4-token prediction are up to 3 times faster at inference, even with large batch sizes.

International Classification of Disease (ICD) coding procedure which refers to tagging medical notes with diagnosis codes has been shown to be effective and crucial to the billing system in medical sector. Currently, ICD codes are assigned to a clinical note manually which is likely to cause many errors. Moreover, training skilled coders also requires time and human resources. Therefore, automating the ICD code determination process is an important task. With the advancement of artificial intelligence theory and computational hardware, machine learning approach has emerged as a suitable solution to automate this process. In this project, we apply a transformer-based architecture to capture the interdependence among the tokens of a document and then use a code-wise attention mechanism to learn code-specific representations of the entire document. Finally, they are fed to separate dense layers for corresponding code prediction. Furthermore, to handle the imbalance in the code frequency of clinical datasets, we employ a label distribution aware margin (LDAM) loss function. The experimental results on the MIMIC-III dataset show that our proposed model outperforms other baselines by a significant margin. In particular, our best setting achieves a micro-AUC score of 0.923 compared to 0.868 of bidirectional recurrent neural networks. We also show that by using the code-wise attention mechanism, the model can provide more insights about its prediction, and thus it can support clinicians to make reliable decisions. Our code is available online (https://github.com/biplob1ly/TransICD)

Causal decoder-only transformer models used for generative language modelling, such as Generative Pre-trained Transformers (GPT), are trained to predict the next token in a sequence based only on its previous tokens. Despite this simple training objective, they have proved to be powerful AI tools. However, only predicting the next token results in top layer embedding vectors that are highly token-focused. There may be benefits in generating embedding vectors at each token position that better capture the overall meaning of longer sequences of future text. Recent studies matching brain scans with deep language models suggest that humans also predict upcoming words when listening or reading but consider multiple future tokens rather than just one. This research investigates a new pretraining method called Future Token Prediction (FTP). In FTP, a large transformer encoder generates top layer embedding vectors for each token position, which, instead of being passed to a language head, are linearly and expansively projected to a pseudo-sequence, which is cross attended to by a small transformer decoder to predict the next N tokens forward from that position in the sequence. The top layer embedding vectors from FTP models exhibit distinct properties compared to those from standard GPT models, varying smoothly along a text sequence as measured by cosine similarity between adjacent tokens. Text generated by FTP models show improved topic coherence compared to standard GPT-like models trained with the same prediction perplexity for the next single token. The vectors are shown to better represent the topic of text based on the results of text classification examples. On a toy, but complex, coding problem, FTP networks produce significantly better results than GPT networks.

Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel fine-tuning approach to improve the performance of PLMs with experimental maps of variant effects from Deep Mutational Scanning (DMS) assays using a Normalised Log-odds Ratio (NLR) head. We find consistent improvements in a held-out protein test set, and on independent DMS and clinical variant annotation benchmarks from ProteinGym and ClinVar. These findings demonstrate that DMS is a promising source of sequence diversity and supervised training data for improving the performance of PLMs for variant effect prediction.

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.

Recently, large language models (LLMs) have demonstrated outstanding reasoning capabilities on mathematical and coding tasks. However, their application to financial tasks-especially the most fundamental task of stock movement prediction-remains underexplored. We study a three-class classification problem (up, hold, down) and, by analyzing existing reasoning responses, observe that: (1) LLMs follow analysts' opinions rather than exhibit a systematic, independent analytical logic (CoTs). (2) LLMs list summaries from different sources without weighing adversarial evidence, yet such counterevidence is crucial for reliable prediction. It shows that the model does not make good use of its reasoning ability to complete the task. To address this, we propose Reflective Evidence Tuning (RETuning), a cold-start method prior to reinforcement learning, to enhance prediction ability. While generating CoT, RETuning encourages dynamically constructing an analytical framework from diverse information sources, organizing and scoring evidence for price up or down based on that framework-rather than on contextual viewpoints-and finally reflecting to derive the prediction. This approach maximally aligns the model with its learned analytical framework, ensuring independent logical reasoning and reducing undue influence from context. We also build a large-scale dataset spanning all of 2024 for 5,123 A-share stocks, with long contexts (32K tokens) and over 200K samples. In addition to price and news, it incorporates analysts' opinions, quantitative reports, fundamental data, macroeconomic indicators, and similar stocks. Experiments show that RETuning successfully unlocks the model's reasoning ability in the financial domain. Inference-time scaling still works even after 6 months or on out-of-distribution stocks, since the models gain valuable insights about stock movement prediction.

Large language models (LLMs) have manifested strong ability to generate codes for productive activities. However, current benchmarks for code synthesis, such as HumanEval, MBPP, and DS-1000, are predominantly oriented towards introductory tasks on algorithm and data science, insufficiently satisfying challenging requirements prevalent in real-world coding. To fill this gap, we propose NaturalCodeBench (NCB), a challenging code benchmark designed to mirror the complexity and variety of scenarios in real coding tasks. NCB comprises 402 high-quality problems in Python and Java, meticulously selected from natural user queries from online coding services, covering 6 different domains. Noting the extraordinary difficulty in creating testing cases for real-world queries, we also introduce a semi-automated pipeline to enhance the efficiency of test case construction. Comparing with manual solutions, it achieves an efficiency increase of more than 4 times. Our systematic experiments on 39 LLMs find that performance gaps on NCB between models with close HumanEval scores could still be significant, indicating a lack of focus on practical code synthesis scenarios or over-specified optimization on HumanEval. On the other hand, even the best-performing GPT-4 is still far from satisfying on NCB. The evaluation toolkit and development set are available at https://github.com/THUDM/NaturalCodeBench.

The rapid advancement of large language models (LLMs) has led to the widespread adoption of AI-powered coding assistants integrated into a development environment. On one hand, low-latency code completion offers completion suggestions but is fundamentally constrained to the cursor's current position. On the other hand, chat-based editing can perform complex modifications, yet forces developers to stop their work, describe the intent in natural language, which causes a context-switch away from the code. This creates a suboptimal user experience, as neither paradigm proactively predicts the developer's next edit in a sequence of related edits. To bridge this gap and provide the seamless code edit suggestion, we introduce the task of Next Edit Prediction, a novel task designed to infer developer intent from recent interaction history to predict both the location and content of the subsequent edit. Specifically, we curate a high-quality supervised fine-tuning dataset and an evaluation benchmark for the Next Edit Prediction task. Then, we conduct supervised fine-tuning on a series of models and performed a comprehensive evaluation of both the fine-tuned models and other baseline models, yielding several novel findings. This work lays the foundation for a new interaction paradigm that proactively collaborate with developers by anticipating their following action, rather than merely reacting to explicit instructions.

This study aims to explore the implementation of Natural Language Processing (NLP) and machine learning (ML) techniques to automate the coding of medical letters with visualised explainability and light-weighted local computer settings. Currently in clinical settings, coding is a manual process that involves assigning codes to each condition, procedure, and medication in a patient's paperwork (e.g., 56265001 heart disease using SNOMED CT code). There are preliminary research on automatic coding in this field using state-of-the-art ML models; however, due to the complexity and size of the models, the real-world deployment is not achieved. To further facilitate the possibility of automatic coding practice, we explore some solutions in a local computer setting; in addition, we explore the function of explainability for transparency of AI models. We used the publicly available MIMIC-III database and the HAN/HLAN network models for ICD code prediction purposes. We also experimented with the mapping between ICD and SNOMED CT knowledge bases. In our experiments, the models provided useful information for 97.98\% of codes. The result of this investigation can shed some light on implementing automatic clinical coding in practice, such as in hospital settings, on the local computers used by clinicians , project page https://github.com/Glenj01/Medical-Coding.

Hospitals and healthcare systems rely on operational decisions that determine patient flow, cost, and quality of care. Despite strong performance on medical knowledge and conversational benchmarks, foundation models trained on general text may lack the specialized knowledge required for these operational decisions. We introduce Lang1, a family of models (100M-7B parameters) pretrained on a specialized corpus blending 80B clinical tokens from NYU Langone Health's EHRs and 627B tokens from the internet. To rigorously evaluate Lang1 in real-world settings, we developed the REalistic Medical Evaluation (ReMedE), a benchmark derived from 668,331 EHR notes that evaluates five critical tasks: 30-day readmission prediction, 30-day mortality prediction, length of stay, comorbidity coding, and predicting insurance claims denial. In zero-shot settings, both general-purpose and specialized models underperform on four of five tasks (36.6%-71.7% AUROC), with mortality prediction being an exception. After finetuning, Lang1-1B outperforms finetuned generalist models up to 70x larger and zero-shot models up to 671x larger, improving AUROC by 3.64%-6.75% and 1.66%-23.66% respectively. We also observed cross-task scaling with joint finetuning on multiple tasks leading to improvement on other tasks. Lang1-1B effectively transfers to out-of-distribution settings, including other clinical tasks and an external health system. Our findings suggest that predictive capabilities for hospital operations require explicit supervised finetuning, and that this finetuning process is made more efficient by in-domain pretraining on EHR. Our findings support the emerging view that specialized LLMs can compete with generalist models in specialized tasks, and show that effective healthcare systems AI requires the combination of in-domain pretraining, supervised finetuning, and real-world evaluation beyond proxy benchmarks.

Large pre-trained code generation models, such as OpenAI Codex, can generate syntax- and function-correct code, making the coding of programmers more productive and our pursuit of artificial general intelligence closer. In this paper, we introduce CodeGeeX, a multilingual model with 13 billion parameters for code generation. CodeGeeX is pre-trained on 850 billion tokens of 23 programming languages as of June 2022. Our extensive experiments suggest that CodeGeeX outperforms multilingual code models of similar scale for both the tasks of code generation and translation on HumanEval-X. Building upon HumanEval (Python only), we develop the HumanEval-X benchmark for evaluating multilingual models by hand-writing the solutions in C++, Java, JavaScript, and Go. In addition, we build CodeGeeX-based extensions on Visual Studio Code, JetBrains, and Cloud Studio, generating 4.7 billion tokens for tens of thousands of active users per week. Our user study demonstrates that CodeGeeX can help to increase coding efficiency for 83.4% of its users. Finally, CodeGeeX is publicly accessible and in Sep. 2022, we open-sourced its code, model weights (the version of 850B tokens), API, extensions, and HumanEval-X at https://github.com/THUDM/CodeGeeX.

Code completion aims at speeding up code writing by recommending to developers the next tokens they are likely to type. Deep Learning (DL) models pushed the boundaries of code completion by redefining what these coding assistants can do: We moved from predicting few code tokens to automatically generating entire functions. One important factor impacting the performance of DL-based code completion techniques is the context provided as input. With "context" we refer to what the model knows about the code to complete. In a simple scenario, the DL model might be fed with a partially implemented function to complete. In this case, the context is represented by the incomplete function and, based on it, the model must generate a prediction. It is however possible to expand such a context to include additional information, like the whole source code file containing the function to complete, which could be useful to boost the prediction performance. In this work, we present an empirical study investigating how the performance of a DL-based code completion technique is affected by different contexts. We experiment with 8 types of contexts and their combinations. These contexts include: (i) coding contexts, featuring information extracted from the code base in which the code completion is invoked (e.g., code components structurally related to the one to "complete"); (ii) process context, with information aimed at depicting the current status of the project in which a code completion task is triggered (e.g., a textual representation of open issues relevant for the code to complete); and (iii) developer contexts, capturing information about the developer invoking the code completion (e.g., the APIs frequently used). Our results show that additional contextual information can benefit the performance of DL-based code completion, with relative improvements up to +22% in terms of correct predictions.

The goal of machine learning is generalization. While the No Free Lunch Theorem states that we cannot obtain theoretical guarantees for generalization without further assumptions, in practice we observe that simple models which explain the training data generalize best: a principle called Occam's razor. Despite the need for simple models, most current approaches in machine learning only minimize the training error, and at best indirectly promote simplicity through regularization or architecture design. Here, we draw a connection between Occam's razor and in-context learning: an emergent ability of certain sequence models like Transformers to learn at inference time from past observations in a sequence. In particular, we show that the next-token prediction loss used to train in-context learners is directly equivalent to a data compression technique called prequential coding, and that minimizing this loss amounts to jointly minimizing both the training error and the complexity of the model that was implicitly learned from context. Our theory and the empirical experiments we use to support it not only provide a normative account of in-context learning, but also elucidate the shortcomings of current in-context learning methods, suggesting ways in which they can be improved. We make our code available at https://github.com/3rdCore/PrequentialCode.

Despite Flow Matching and diffusion models having emerged as powerful generative paradigms for continuous variables such as images and videos, their application to high-dimensional discrete data, such as language, is still limited. In this work, we present Discrete Flow Matching, a novel discrete flow paradigm designed specifically for generating discrete data. Discrete Flow Matching offers several key contributions: (i) it works with a general family of probability paths interpolating between source and target distributions; (ii) it allows for a generic formula for sampling from these probability paths using learned posteriors such as the probability denoiser (x-prediction) and noise-prediction (epsilon-prediction); (iii) practically, focusing on specific probability paths defined with different schedulers considerably improves generative perplexity compared to previous discrete diffusion and flow models; and (iv) by scaling Discrete Flow Matching models up to 1.7B parameters, we reach 6.7% Pass@1 and 13.4% Pass@10 on HumanEval and 6.7% Pass@1 and 20.6% Pass@10 on 1-shot MBPP coding benchmarks. Our approach is capable of generating high-quality discrete data in a non-autoregressive fashion, significantly closing the gap between autoregressive models and discrete flow models.