new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Feb 20

SlimFit: Memory-Efficient Fine-Tuning of Transformer-based Models Using Training Dynamics

Transformer-based models, such as BERT and ViT, have achieved state-of-the-art results across different natural language processing (NLP) and computer vision (CV) tasks. However, these models are extremely memory intensive during their fine-tuning process, making them difficult to deploy on GPUs with limited memory resources. To address this issue, we introduce a new tool called SlimFit that reduces the memory requirements of these models by dynamically analyzing their training dynamics and freezing less-contributory layers during fine-tuning. The layers to freeze are chosen using a runtime inter-layer scheduling algorithm. SlimFit adopts quantization and pruning for particular layers to balance the load of dynamic activations and to minimize the memory footprint of static activations, where static activations refer to those that cannot be discarded regardless of freezing. This allows SlimFit to freeze up to 95% of layers and reduce the overall on-device GPU memory usage of transformer-based models such as ViT and BERT by an average of 2.2x, across different NLP and CV benchmarks/datasets such as GLUE, SQuAD 2.0, CIFAR-10, CIFAR-100 and ImageNet with an average degradation of 0.2% in accuracy. For such NLP and CV tasks, SlimFit can reduce up to 3.1x the total on-device memory usage with an accuracy degradation of only up to 0.4%. As a result, while fine-tuning of ViT on ImageNet and BERT on SQuAD 2.0 with a batch size of 128 requires 3 and 2 32GB GPUs respectively, SlimFit enables their fine-tuning on a single 32GB GPU without any significant accuracy degradation.

  • 7 authors
·
May 29, 2023

Q-BERT: Hessian Based Ultra Low Precision Quantization of BERT

Transformer based architectures have become de-facto models used for a range of Natural Language Processing tasks. In particular, the BERT based models achieved significant accuracy gain for GLUE tasks, CoNLL-03 and SQuAD. However, BERT based models have a prohibitive memory footprint and latency. As a result, deploying BERT based models in resource constrained environments has become a challenging task. In this work, we perform an extensive analysis of fine-tuned BERT models using second order Hessian information, and we use our results to propose a novel method for quantizing BERT models to ultra low precision. In particular, we propose a new group-wise quantization scheme, and we use a Hessian based mix-precision method to compress the model further. We extensively test our proposed method on BERT downstream tasks of SST-2, MNLI, CoNLL-03, and SQuAD. We can achieve comparable performance to baseline with at most 2.3% performance degradation, even with ultra-low precision quantization down to 2 bits, corresponding up to 13times compression of the model parameters, and up to 4times compression of the embedding table as well as activations. Among all tasks, we observed the highest performance loss for BERT fine-tuned on SQuAD. By probing into the Hessian based analysis as well as visualization, we show that this is related to the fact that current training/fine-tuning strategy of BERT does not converge for SQuAD.

  • 8 authors
·
Sep 12, 2019

Fine-tuning Transformer-based Encoder for Turkish Language Understanding Tasks

Deep learning-based and lately Transformer-based language models have been dominating the studies of natural language processing in the last years. Thanks to their accurate and fast fine-tuning characteristics, they have outperformed traditional machine learning-based approaches and achieved state-of-the-art results for many challenging natural language understanding (NLU) problems. Recent studies showed that the Transformer-based models such as BERT, which is Bidirectional Encoder Representations from Transformers, have reached impressive achievements on many tasks. Moreover, thanks to their transfer learning capacity, these architectures allow us to transfer pre-built models and fine-tune them to specific NLU tasks such as question answering. In this study, we provide a Transformer-based model and a baseline benchmark for the Turkish Language. We successfully fine-tuned a Turkish BERT model, namely BERTurk that is trained with base settings, to many downstream tasks and evaluated with a the Turkish Benchmark dataset. We showed that our studies significantly outperformed other existing baseline approaches for Named-Entity Recognition, Sentiment Analysis, Question Answering and Text Classification in Turkish Language. We publicly released these four fine-tuned models and resources in reproducibility and with the view of supporting other Turkish researchers and applications.

  • 1 authors
·
Jan 30, 2024

Benchmarking and Building Long-Context Retrieval Models with LoCo and M2-BERT

Retrieval pipelines-an integral component of many machine learning systems-perform poorly in domains where documents are long (e.g., 10K tokens or more) and where identifying the relevant document requires synthesizing information across the entire text. Developing long-context retrieval encoders suitable for these domains raises three challenges: (1) how to evaluate long-context retrieval performance, (2) how to pretrain a base language model to represent both short contexts (corresponding to queries) and long contexts (corresponding to documents), and (3) how to fine-tune this model for retrieval under the batch size limitations imposed by GPU memory constraints. To address these challenges, we first introduce LoCoV1, a novel 12 task benchmark constructed to measure long-context retrieval where chunking is not possible or not effective. We next present the M2-BERT retrieval encoder, an 80M parameter state-space encoder model built from the Monarch Mixer architecture, capable of scaling to documents up to 32K tokens long. We describe a pretraining data mixture which allows this encoder to process both short and long context sequences, and a finetuning approach that adapts this base model to retrieval with only single-sample batches. Finally, we validate the M2-BERT retrieval encoder on LoCoV1, finding that it outperforms competitive Transformer-based models by at least 23.3 points, despite containing upwards of 90x fewer parameters.

  • 5 authors
·
Feb 12, 2024

Evaluating Large Language Models for Phishing Detection, Self-Consistency, Faithfulness, and Explainability

Phishing attacks remain one of the most prevalent and persistent cybersecurity threat with attackers continuously evolving and intensifying tactics to evade the general detection system. Despite significant advances in artificial intelligence and machine learning, faithfully reproducing the interpretable reasoning with classification and explainability that underpin phishing judgments remains challenging. Due to recent advancement in Natural Language Processing, Large Language Models (LLMs) show a promising direction and potential for improving domain specific phishing classification tasks. However, enhancing the reliability and robustness of classification models requires not only accurate predictions from LLMs but also consistent and trustworthy explanations aligning with those predictions. Therefore, a key question remains: can LLMs not only classify phishing emails accurately but also generate explanations that are reliably aligned with their predictions and internally self-consistent? To answer these questions, we have fine-tuned transformer based models, including BERT, Llama models, and Wizard, to improve domain relevance and make them more tailored to phishing specific distinctions, using Binary Sequence Classification, Contrastive Learning (CL) and Direct Preference Optimization (DPO). To that end, we examined their performance in phishing classification and explainability by applying the ConsistenCy measure based on SHAPley values (CC SHAP), which measures prediction explanation token alignment to test the model's internal faithfulness and consistency and uncover the rationale behind its predictions and reasoning. Overall, our findings show that Llama models exhibit stronger prediction explanation token alignment with higher CC SHAP scores despite lacking reliable decision making accuracy, whereas Wizard achieves better prediction accuracy but lower CC SHAP scores.

  • 3 authors
·
Jun 16, 2025

FlexiBERT: Are Current Transformer Architectures too Homogeneous and Rigid?

The existence of a plethora of language models makes the problem of selecting the best one for a custom task challenging. Most state-of-the-art methods leverage transformer-based models (e.g., BERT) or their variants. Training such models and exploring their hyperparameter space, however, is computationally expensive. Prior work proposes several neural architecture search (NAS) methods that employ performance predictors (e.g., surrogate models) to address this issue; however, analysis has been limited to homogeneous models that use fixed dimensionality throughout the network. This leads to sub-optimal architectures. To address this limitation, we propose a suite of heterogeneous and flexible models, namely FlexiBERT, that have varied encoder layers with a diverse set of possible operations and different hidden dimensions. For better-posed surrogate modeling in this expanded design space, we propose a new graph-similarity-based embedding scheme. We also propose a novel NAS policy, called BOSHNAS, that leverages this new scheme, Bayesian modeling, and second-order optimization, to quickly train and use a neural surrogate model to converge to the optimal architecture. A comprehensive set of experiments shows that the proposed policy, when applied to the FlexiBERT design space, pushes the performance frontier upwards compared to traditional models. FlexiBERT-Mini, one of our proposed models, has 3% fewer parameters than BERT-Mini and achieves 8.9% higher GLUE score. A FlexiBERT model with equivalent performance as the best homogeneous model achieves 2.6x smaller size. FlexiBERT-Large, another proposed model, achieves state-of-the-art results, outperforming the baseline models by at least 5.7% on the GLUE benchmark.

  • 4 authors
·
May 23, 2022

White-Box Transformers via Sparse Rate Reduction: Compression Is All There Is?

In this paper, we contend that a natural objective of representation learning is to compress and transform the distribution of the data, say sets of tokens, towards a low-dimensional Gaussian mixture supported on incoherent subspaces. The goodness of such a representation can be evaluated by a principled measure, called sparse rate reduction, that simultaneously maximizes the intrinsic information gain and extrinsic sparsity of the learned representation. From this perspective, popular deep network architectures, including transformers, can be viewed as realizing iterative schemes to optimize this measure. Particularly, we derive a transformer block from alternating optimization on parts of this objective: the multi-head self-attention operator compresses the representation by implementing an approximate gradient descent step on the coding rate of the features, and the subsequent multi-layer perceptron sparsifies the features. This leads to a family of white-box transformer-like deep network architectures, named CRATE, which are mathematically fully interpretable. We show, by way of a novel connection between denoising and compression, that the inverse to the aforementioned compressive encoding can be realized by the same class of CRATE architectures. Thus, the so-derived white-box architectures are universal to both encoders and decoders. Experiments show that these networks, despite their simplicity, indeed learn to compress and sparsify representations of large-scale real-world image and text datasets, and achieve performance very close to highly engineered transformer-based models: ViT, MAE, DINO, BERT, and GPT2. We believe the proposed computational framework demonstrates great potential in bridging the gap between theory and practice of deep learning, from a unified perspective of data compression. Code is available at: https://ma-lab-berkeley.github.io/CRATE .

  • 10 authors
·
Nov 21, 2023

SPT: Fine-Tuning Transformer-based Language Models Efficiently with Sparsification

Transformer-based large language models (e.g., BERT and GPT) achieve great success, and fine-tuning, which tunes a pre-trained model on a task-specific dataset, is the standard practice to utilize these models for downstream tasks. However, Transformer fine-tuning has long running time and high memory consumption due to the large size of the models. We propose the SPT system to fine-tune Transformer-based models efficiently by introducing sparsity. We observe that the memory consumption of Transformer mainly comes from storing attention weights for multi-head attention (MHA), and the majority of running time is spent on feed-forward network (FFN). Thus, we design the sparse MHA module, which computes and stores only large attention weights to reduce memory consumption, and the routed FFN module, which dynamically activates a subset of model parameters for each token to reduce computation cost. We implement SPT on PyTorch and customize CUDA kernels to run sparse MHA and routed FFN efficiently. Specifically, we use product quantization to identify the large attention weights and compute attention via sparse matrix multiplication for sparse MHA. For routed FFN, we batch the tokens according to their activated model parameters for efficient computation. We conduct extensive experiments to evaluate SPT on various model configurations. The results show that SPT consistently outperforms well-optimized baselines, reducing the peak memory consumption by up to 50% and accelerating fine-tuning by up to 2.2x.

  • 5 authors
·
Dec 16, 2023 2

An Efficient Sparse Inference Software Accelerator for Transformer-based Language Models on CPUs

In recent years, Transformer-based language models have become the standard approach for natural language processing tasks. However, stringent throughput and latency requirements in industrial applications are limiting their adoption. To mitigate the gap, model compression techniques such as structured pruning are being used to improve inference efficiency. However, most existing neural network inference runtimes lack adequate support for structured sparsity. In this paper, we propose an efficient sparse deep learning inference software stack for Transformer-based language models where the weights are pruned with constant block size. Our sparse software accelerator leverages Intel Deep Learning Boost to maximize the performance of sparse matrix - dense matrix multiplication (commonly abbreviated as SpMM) on CPUs. Our SpMM kernel outperforms the existing sparse libraries (oneMKL, TVM, and LIBXSMM) by an order of magnitude on a wide range of GEMM shapes under 5 representative sparsity ratios (70%, 75%, 80%, 85%, 90%). Moreover, our SpMM kernel shows up to 5x speedup over dense GEMM kernel of oneDNN, a well-optimized dense library widely used in industry. We apply our sparse accelerator on widely-used Transformer-based language models including Bert-Mini, DistilBERT, Bert-Base, and BERT-Large. Our sparse inference software shows up to 1.5x speedup over Neural Magic's Deepsparse under same configurations on Xeon on Amazon Web Services under proxy production latency constraints. We also compare our solution with two framework-based inference solutions, ONNX Runtime and PyTorch, and demonstrate up to 37x speedup over ONNX Runtime and 345x over PyTorch on Xeon under the latency constraints. All the source code is publicly available on Github: https://github.com/intel/intel-extension-for-transformers.

  • 12 authors
·
Jun 28, 2023

The Optimal BERT Surgeon: Scalable and Accurate Second-Order Pruning for Large Language Models

Transformer-based language models have become a key building block for natural language processing. While these models are extremely accurate, they can be too large and computationally intensive to run on standard deployments. A variety of compression methods, including distillation, quantization, structured and unstructured pruning are known to decrease model size and increase inference speed, with low accuracy loss. In this context, this paper's contributions are two-fold. We perform an in-depth study of the accuracy-compression trade-off for unstructured weight pruning of BERT models. We introduce Optimal BERT Surgeon (oBERT), an efficient and accurate weight pruning method based on approximate second-order information, which we show to yield state-of-the-art results in both stages of language tasks: pre-training and fine-tuning. Specifically, oBERT extends existing work on unstructured second-order pruning by allowing for pruning blocks of weights, and by being applicable at the BERT scale. Second, we investigate the impact of this pruning method when compounding compression approaches to obtain highly compressed but accurate models for deployment on edge devices. These models significantly push boundaries of the current state-of-the-art sparse BERT models with respect to all metrics: model size, inference speed and task accuracy. For example, relative to the dense BERT-base, we obtain 10x model size compression (in MB) with < 1% accuracy drop, 10x CPU-inference speedup with < 2% accuracy drop, and 29x CPU-inference speedup with < 7.5% accuracy drop. Our code, fully integrated with Transformers and SparseML, is available at https://github.com/neuralmagic/sparseml/tree/main/research/optimal_BERT_surgeon_oBERT.

  • 8 authors
·
Mar 14, 2022

Pre-training technique to localize medical BERT and enhance biomedical BERT

Pre-training large-scale neural language models on raw texts has made a significant contribution to improving transfer learning in natural language processing (NLP). With the introduction of transformer-based language models, such as bidirectional encoder representations from transformers (BERT), the performance of information extraction from a free text by NLP has significantly improved for both the general domain and medical domain; however, it is difficult to train specific BERT models that perform well for domains in which there are few publicly available databases of high quality and large size. We hypothesized that this problem can be addressed by up-sampling a domain-specific corpus and using it for pre-training with a larger corpus in a balanced manner. Our proposed method consists of a single intervention with one option: simultaneous pre-training after up-sampling and amplified vocabulary. We conducted three experiments and evaluated the resulting products. We confirmed that our Japanese medical BERT outperformed conventional baselines and the other BERT models in terms of the medical document classification task and that our English BERT pre-trained using both the general and medical-domain corpora performed sufficiently well for practical use in terms of the biomedical language understanding evaluation (BLUE) benchmark. Moreover, our enhanced biomedical BERT model, in which clinical notes were not used during pre-training, showed that both the clinical and biomedical scores of the BLUE benchmark were 0.3 points above that of the ablation model trained without our proposed method. Well-balanced pre-training by up-sampling instances derived from a corpus appropriate for the target task allows us to construct a high-performance BERT model.

  • 6 authors
·
May 14, 2020

Large Pre-trained Language Models Contain Human-like Biases of What is Right and Wrong to Do

Artificial writing is permeating our lives due to recent advances in large-scale, transformer-based language models (LMs) such as BERT, its variants, GPT-2/3, and others. Using them as pre-trained models and fine-tuning them for specific tasks, researchers have extended state of the art for many NLP tasks and shown that they capture not only linguistic knowledge but also retain general knowledge implicitly present in the data. Unfortunately, LMs trained on unfiltered text corpora suffer from degenerated and biased behaviour. While this is well established, we show that recent LMs also contain human-like biases of what is right and wrong to do, some form of ethical and moral norms of the society -- they bring a "moral direction" to surface. That is, we show that these norms can be captured geometrically by a direction, which can be computed, e.g., by a PCA, in the embedding space, reflecting well the agreement of phrases to social norms implicitly expressed in the training texts and providing a path for attenuating or even preventing toxic degeneration in LMs. Being able to rate the (non-)normativity of arbitrary phrases without explicitly training the LM for this task, we demonstrate the capabilities of the "moral direction" for guiding (even other) LMs towards producing normative text and showcase it on RealToxicityPrompts testbed, preventing the neural toxic degeneration in GPT-2.

  • 5 authors
·
Mar 8, 2021

L3Cube-HingCorpus and HingBERT: A Code Mixed Hindi-English Dataset and BERT Language Models

Code-switching occurs when more than one language is mixed in a given sentence or a conversation. This phenomenon is more prominent on social media platforms and its adoption is increasing over time. Therefore code-mixed NLP has been extensively studied in the literature. As pre-trained transformer-based architectures are gaining popularity, we observe that real code-mixing data are scarce to pre-train large language models. We present L3Cube-HingCorpus, the first large-scale real Hindi-English code mixed data in a Roman script. It consists of 52.93M sentences and 1.04B tokens, scraped from Twitter. We further present HingBERT, HingMBERT, HingRoBERTa, and HingGPT. The BERT models have been pre-trained on codemixed HingCorpus using masked language modelling objectives. We show the effectiveness of these BERT models on the subsequent downstream tasks like code-mixed sentiment analysis, POS tagging, NER, and LID from the GLUECoS benchmark. The HingGPT is a GPT2 based generative transformer model capable of generating full tweets. We also release L3Cube-HingLID Corpus, the largest code-mixed Hindi-English language identification(LID) dataset and HingBERT-LID, a production-quality LID model to facilitate capturing of more code-mixed data using the process outlined in this work. The dataset and models are available at https://github.com/l3cube-pune/code-mixed-nlp .

  • 2 authors
·
Apr 18, 2022

Beyond 512 Tokens: Siamese Multi-depth Transformer-based Hierarchical Encoder for Long-Form Document Matching

Many natural language processing and information retrieval problems can be formalized as the task of semantic matching. Existing work in this area has been largely focused on matching between short texts (e.g., question answering), or between a short and a long text (e.g., ad-hoc retrieval). Semantic matching between long-form documents, which has many important applications like news recommendation, related article recommendation and document clustering, is relatively less explored and needs more research effort. In recent years, self-attention based models like Transformers and BERT have achieved state-of-the-art performance in the task of text matching. These models, however, are still limited to short text like a few sentences or one paragraph due to the quadratic computational complexity of self-attention with respect to input text length. In this paper, we address the issue by proposing the Siamese Multi-depth Transformer-based Hierarchical (SMITH) Encoder for long-form document matching. Our model contains several innovations to adapt self-attention models for longer text input. In order to better capture sentence level semantic relations within a document, we pre-train the model with a novel masked sentence block language modeling task in addition to the masked word language modeling task used by BERT. Our experimental results on several benchmark datasets for long-form document matching show that our proposed SMITH model outperforms the previous state-of-the-art models including hierarchical attention, multi-depth attention-based hierarchical recurrent neural network, and BERT. Comparing to BERT based baselines, our model is able to increase maximum input text length from 512 to 2048. We will open source a Wikipedia based benchmark dataset, code and a pre-trained checkpoint to accelerate future research on long-form document matching.

  • 5 authors
·
Apr 26, 2020

CrisisTransformers: Pre-trained language models and sentence encoders for crisis-related social media texts

Social media platforms play an essential role in crisis communication, but analyzing crisis-related social media texts is challenging due to their informal nature. Transformer-based pre-trained models like BERT and RoBERTa have shown success in various NLP tasks, but they are not tailored for crisis-related texts. Furthermore, general-purpose sentence encoders are used to generate sentence embeddings, regardless of the textual complexities in crisis-related texts. Advances in applications like text classification, semantic search, and clustering contribute to effective processing of crisis-related texts, which is essential for emergency responders to gain a comprehensive view of a crisis event, whether historical or real-time. To address these gaps in crisis informatics literature, this study introduces CrisisTransformers, an ensemble of pre-trained language models and sentence encoders trained on an extensive corpus of over 15 billion word tokens from tweets associated with more than 30 crisis events, including disease outbreaks, natural disasters, conflicts, and other critical incidents. We evaluate existing models and CrisisTransformers on 18 crisis-specific public datasets. Our pre-trained models outperform strong baselines across all datasets in classification tasks, and our best-performing sentence encoder improves the state-of-the-art by 17.43% in sentence encoding tasks. Additionally, we investigate the impact of model initialization on convergence and evaluate the significance of domain-specific models in generating semantically meaningful sentence embeddings. All models are publicly released (https://huggingface.co/crisistransformers), with the anticipation that they will serve as a robust baseline for tasks involving the analysis of crisis-related social media texts.

  • 3 authors
·
Sep 11, 2023

Cross-lingual transfer of multilingual models on low resource African Languages

Large multilingual models have significantly advanced natural language processing (NLP) research. However, their high resource demands and potential biases from diverse data sources have raised concerns about their effectiveness across low-resource languages. In contrast, monolingual models, trained on a single language, may better capture the nuances of the target language, potentially providing more accurate results. This study benchmarks the cross-lingual transfer capabilities from a high-resource language to a low-resource language for both, monolingual and multilingual models, focusing on Kinyarwanda and Kirundi, two Bantu languages. We evaluate the performance of transformer based architectures like Multilingual BERT (mBERT), AfriBERT, and BantuBERTa against neural-based architectures such as BiGRU, CNN, and char-CNN. The models were trained on Kinyarwanda and tested on Kirundi, with fine-tuning applied to assess the extent of performance improvement and catastrophic forgetting. AfriBERT achieved the highest cross-lingual accuracy of 88.3% after fine-tuning, while BiGRU emerged as the best-performing neural model with 83.3% accuracy. We also analyze the degree of forgetting in the original language post-fine-tuning. While monolingual models remain competitive, this study highlights that multilingual models offer strong cross-lingual transfer capabilities in resource limited settings.

  • 4 authors
·
Sep 17, 2024

Designing BERT for Convolutional Networks: Sparse and Hierarchical Masked Modeling

We identify and overcome two key obstacles in extending the success of BERT-style pre-training, or the masked image modeling, to convolutional networks (convnets): (i) convolution operation cannot handle irregular, random-masked input images; (ii) the single-scale nature of BERT pre-training is inconsistent with convnet's hierarchical structure. For (i), we treat unmasked pixels as sparse voxels of 3D point clouds and use sparse convolution to encode. This is the first use of sparse convolution for 2D masked modeling. For (ii), we develop a hierarchical decoder to reconstruct images from multi-scale encoded features. Our method called Sparse masKed modeling (SparK) is general: it can be used directly on any convolutional model without backbone modifications. We validate it on both classical (ResNet) and modern (ConvNeXt) models: on three downstream tasks, it surpasses both state-of-the-art contrastive learning and transformer-based masked modeling by similarly large margins (around +1.0%). Improvements on object detection and instance segmentation are more substantial (up to +3.5%), verifying the strong transferability of features learned. We also find its favorable scaling behavior by observing more gains on larger models. All this evidence reveals a promising future of generative pre-training on convnets. Codes and models are released at https://github.com/keyu-tian/SparK.

  • 6 authors
·
Jan 9, 2023

A Review of Multi-Modal Large Language and Vision Models

Large Language Models (LLMs) have recently emerged as a focal point of research and application, driven by their unprecedented ability to understand and generate text with human-like quality. Even more recently, LLMs have been extended into multi-modal large language models (MM-LLMs) which extends their capabilities to deal with image, video and audio information, in addition to text. This opens up applications like text-to-video generation, image captioning, text-to-speech, and more and is achieved either by retro-fitting an LLM with multi-modal capabilities, or building a MM-LLM from scratch. This paper provides an extensive review of the current state of those LLMs with multi-modal capabilities as well as the very recent MM-LLMs. It covers the historical development of LLMs especially the advances enabled by transformer-based architectures like OpenAI's GPT series and Google's BERT, as well as the role of attention mechanisms in enhancing model performance. The paper includes coverage of the major and most important of the LLMs and MM-LLMs and also covers the techniques of model tuning, including fine-tuning and prompt engineering, which tailor pre-trained models to specific tasks or domains. Ethical considerations and challenges, such as data bias and model misuse, are also analysed to underscore the importance of responsible AI development and deployment. Finally, we discuss the implications of open-source versus proprietary models in AI research. Through this review, we provide insights into the transformative potential of MM-LLMs in various applications.

  • 3 authors
·
Mar 28, 2024

HELM-BERT: A Transformer for Medium-sized Peptide Property Prediction

Therapeutic peptides have emerged as a pivotal modality in modern drug discovery, occupying a chemically and topologically rich space. While accurate prediction of their physicochemical properties is essential for accelerating peptide development, existing molecular language models rely on representations that fail to capture this complexity. Atom-level SMILES notation generates long token sequences and obscures cyclic topology, whereas amino-acid-level representations cannot encode the diverse chemical modifications central to modern peptide design. To bridge this representational gap, the Hierarchical Editing Language for Macromolecules (HELM) offers a unified framework enabling precise description of both monomer composition and connectivity, making it a promising foundation for peptide language modeling. Here, we propose HELM-BERT, the first encoder-based peptide language model trained on HELM notation. Based on DeBERTa, HELM-BERT is specifically designed to capture hierarchical dependencies within HELM sequences. The model is pre-trained on a curated corpus of 39,079 chemically diverse peptides spanning linear and cyclic structures. HELM-BERT significantly outperforms state-of-the-art SMILES-based language models in downstream tasks, including cyclic peptide membrane permeability prediction and peptide-protein interaction prediction. These results demonstrate that HELM's explicit monomer- and topology-aware representations offer substantial data-efficiency advantages for modeling therapeutic peptides, bridging a long-standing gap between small-molecule and protein language models.

  • 5 authors
·
Dec 28, 2025

VTrans: Accelerating Transformer Compression with Variational Information Bottleneck based Pruning

In recent years, there has been a growing emphasis on compressing large pre-trained transformer models for resource-constrained devices. However, traditional pruning methods often leave the embedding layer untouched, leading to model over-parameterization. Additionally, they require extensive compression time with large datasets to maintain performance in pruned models. To address these challenges, we propose VTrans, an iterative pruning framework guided by the Variational Information Bottleneck (VIB) principle. Our method compresses all structural components, including embeddings, attention heads, and layers using VIB-trained masks. This approach retains only essential weights in each layer, ensuring compliance with specified model size or computational constraints. Notably, our method achieves upto 70% more compression than prior state-of-the-art approaches, both task-agnostic and task-specific. We further propose faster variants of our method: Fast-VTrans utilizing only 3% of the data and Faster-VTrans, a time efficient alternative that involves exclusive finetuning of VIB masks, accelerating compression by upto 25 times with minimal performance loss compared to previous methods. Extensive experiments on BERT, ROBERTa, and GPT-2 models substantiate the efficacy of our method. Moreover, our method demonstrates scalability in compressing large models such as LLaMA-2-7B, achieving superior performance compared to previous pruning methods. Additionally, we use attention-based probing to qualitatively assess model redundancy and interpret the efficiency of our approach. Notably, our method considers heads with high attention to special and current tokens in un-pruned model as foremost candidates for pruning while retained heads are observed to attend more to task-critical keywords.

  • 3 authors
·
Jun 7, 2024 2

BERTuit: Understanding Spanish language in Twitter through a native transformer

The appearance of complex attention-based language models such as BERT, Roberta or GPT-3 has allowed to address highly complex tasks in a plethora of scenarios. However, when applied to specific domains, these models encounter considerable difficulties. This is the case of Social Networks such as Twitter, an ever-changing stream of information written with informal and complex language, where each message requires careful evaluation to be understood even by humans given the important role that context plays. Addressing tasks in this domain through Natural Language Processing involves severe challenges. When powerful state-of-the-art multilingual language models are applied to this scenario, language specific nuances use to get lost in translation. To face these challenges we present BERTuit, the larger transformer proposed so far for Spanish language, pre-trained on a massive dataset of 230M Spanish tweets using RoBERTa optimization. Our motivation is to provide a powerful resource to better understand Spanish Twitter and to be used on applications focused on this social network, with special emphasis on solutions devoted to tackle the spreading of misinformation in this platform. BERTuit is evaluated on several tasks and compared against M-BERT, XLM-RoBERTa and XLM-T, very competitive multilingual transformers. The utility of our approach is shown with applications, in this case: a zero-shot methodology to visualize groups of hoaxes and profiling authors spreading disinformation. Misinformation spreads wildly on platforms such as Twitter in languages other than English, meaning performance of transformers may suffer when transferred outside English speaking communities.

  • 3 authors
·
Apr 7, 2022

Can bidirectional encoder become the ultimate winner for downstream applications of foundation models?

Over the past few decades, Artificial Intelligence(AI) has progressed from the initial machine learning stage to the deep learning stage, and now to the stage of foundational models. Foundational models have the characteristics of pre-training, transfer learning, and self-supervised learning, and pre-trained models can be fine-tuned and applied to various downstream tasks. Under the framework of foundational models, models such as Bidirectional Encoder Representations from Transformers(BERT) and Generative Pre-trained Transformer(GPT) have greatly advanced the development of natural language processing(NLP), especially the emergence of many models based on BERT. BERT broke through the limitation of only using one-way methods for language modeling in pre-training by using a masked language model. It can capture bidirectional context information to predict the masked words in the sequence, this can improve the feature extraction ability of the model. This makes the model very useful for downstream tasks, especially for specialized applications. The model using the bidirectional encoder can better understand the domain knowledge and be better applied to these downstream tasks. So we hope to help understand how this technology has evolved and improved model performance in various natural language processing tasks under the background of foundational models and reveal its importance in capturing context information and improving the model's performance on downstream tasks. This article analyzes one-way and bidirectional models based on GPT and BERT and compares their differences based on the purpose of the model. It also briefly analyzes BERT and the improvements of some models based on BERT. The model's performance on the Stanford Question Answering Dataset(SQuAD) and General Language Understanding Evaluation(GLUE) was compared.

  • 5 authors
·
Nov 26, 2024

Pushing on Personality Detection from Verbal Behavior: A Transformer Meets Text Contours of Psycholinguistic Features

Research at the intersection of personality psychology, computer science, and linguistics has recently focused increasingly on modeling and predicting personality from language use. We report two major improvements in predicting personality traits from text data: (1) to our knowledge, the most comprehensive set of theory-based psycholinguistic features and (2) hybrid models that integrate a pre-trained Transformer Language Model BERT and Bidirectional Long Short-Term Memory (BLSTM) networks trained on within-text distributions ('text contours') of psycholinguistic features. We experiment with BLSTM models (with and without Attention) and with two techniques for applying pre-trained language representations from the transformer model - 'feature-based' and 'fine-tuning'. We evaluate the performance of the models we built on two benchmark datasets that target the two dominant theoretical models of personality: the Big Five Essay dataset and the MBTI Kaggle dataset. Our results are encouraging as our models outperform existing work on the same datasets. More specifically, our models achieve improvement in classification accuracy by 2.9% on the Essay dataset and 8.28% on the Kaggle MBTI dataset. In addition, we perform ablation experiments to quantify the impact of different categories of psycholinguistic features in the respective personality prediction models.

  • 4 authors
·
Apr 10, 2022

Motamot: A Dataset for Revealing the Supremacy of Large Language Models over Transformer Models in Bengali Political Sentiment Analysis

Sentiment analysis is the process of identifying and categorizing people's emotions or opinions regarding various topics. Analyzing political sentiment is critical for understanding the complexities of public opinion processes, especially during election seasons. It gives significant information on voter preferences, attitudes, and current trends. In this study, we investigate political sentiment analysis during Bangladeshi elections, specifically examining how effectively Pre-trained Language Models (PLMs) and Large Language Models (LLMs) capture complex sentiment characteristics. Our study centers on the creation of the "Motamot" dataset, comprising 7,058 instances annotated with positive and negative sentiments, sourced from diverse online newspaper portals, forming a comprehensive resource for political sentiment analysis. We meticulously evaluate the performance of various PLMs including BanglaBERT, Bangla BERT Base, XLM-RoBERTa, mBERT, and sahajBERT, alongside LLMs such as Gemini 1.5 Pro and GPT 3.5 Turbo. Moreover, we explore zero-shot and few-shot learning strategies to enhance our understanding of political sentiment analysis methodologies. Our findings underscore BanglaBERT's commendable accuracy of 88.10% among PLMs. However, the exploration into LLMs reveals even more promising results. Through the adept application of Few-Shot learning techniques, Gemini 1.5 Pro achieves an impressive accuracy of 96.33%, surpassing the remarkable performance of GPT 3.5 Turbo, which stands at 94%. This underscores Gemini 1.5 Pro's status as the superior performer in this comparison.

  • 6 authors
·
Jul 28, 2024

Greenformers: Improving Computation and Memory Efficiency in Transformer Models via Low-Rank Approximation

In this thesis, we introduce Greenformers, a collection of model efficiency methods to improve the model efficiency of the recently renowned transformer models with a low-rank approximation approach. The development trend of deep learning models tends to results in a more complex and larger model. Although it leads to a better and more accurate prediction, the resulting model becomes even more costly, as it requires weeks of training with a huge amount of GPU resources. Particularly, the size and computational cost of transformer-based models have increased tremendously since its first debut in 2017 from ~100 million parameters up to ~1.6 trillion parameters in early 2021. This computationally hungry model also incurs a substantial cost to the environment and even reaches an alarming level of carbon footprint. Some of these models are so massive that it is even impossible to run the model without a GPU cluster. Greenformers improve the model efficiency of transformer models by applying low-rank approximation approaches. Specifically, we propose a low-rank factorization approach to improve the efficiency of the transformer model called Low-Rank Transformer. We further compare our model with an existing low-rank factorization approach called Linformer. Based on our analysis, the Low-Rank Transformer model is suitable for improving both the time and memory efficiency in processing short-sequence (<= 512) input data, while the Linformer model is suitable for improving the efficiency in processing long-sequence input data (>= 512). We also show that Low-Rank Transformer is more suitable for on-device deployment, as it significantly reduces the model size. Additionally, we estimate that applying LRT to the existing BERT-base model can significantly reduce the computational, economical, and environmental costs for developing such models by more than 30% of its original costs.

  • 1 authors
·
Aug 24, 2021

Training-free Neural Architecture Search for RNNs and Transformers

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.

  • 2 authors
·
May 31, 2023

FinAI-BERT: A Transformer-Based Model for Sentence-Level Detection of AI Disclosures in Financial Reports

The proliferation of artificial intelligence (AI) in financial services has prompted growing demand for tools that can systematically detect AI-related disclosures in corporate filings. While prior approaches often rely on keyword expansion or document-level classification, they fall short in granularity, interpretability, and robustness. This study introduces FinAI-BERT, a domain-adapted transformer-based language model designed to classify AI-related content at the sentence level within financial texts. The model was fine-tuned on a manually curated and balanced dataset of 1,586 sentences drawn from 669 annual reports of U.S. banks (2015 to 2023). FinAI-BERT achieved near-perfect classification performance (accuracy of 99.37 percent, F1 score of 0.993), outperforming traditional baselines such as Logistic Regression, Naive Bayes, Random Forest, and XGBoost. Interpretability was ensured through SHAP-based token attribution, while bias analysis and robustness checks confirmed the model's stability across sentence lengths, adversarial inputs, and temporal samples. Theoretically, the study advances financial NLP by operationalizing fine-grained, theme-specific classification using transformer architectures. Practically, it offers a scalable, transparent solution for analysts, regulators, and scholars seeking to monitor the diffusion and framing of AI across financial institutions.

  • 1 authors
·
Jun 29, 2025

A Multi-Level Framework for Accelerating Training Transformer Models

The fast growing capabilities of large-scale deep learning models, such as Bert, GPT and ViT, are revolutionizing the landscape of NLP, CV and many other domains. Training such models, however, poses an unprecedented demand for computing power, which incurs exponentially increasing energy cost and carbon dioxide emissions. It is thus critical to develop efficient training solutions to reduce the training costs. Motivated by a set of key observations of inter- and intra-layer similarities among feature maps and attentions that can be identified from typical training processes, we propose a multi-level framework for training acceleration. Specifically, the framework is based on three basic operators, Coalescing, De-coalescing and Interpolation, which can be orchestrated to build a multi-level training framework. The framework consists of a V-cycle training process, which progressively down- and up-scales the model size and projects the parameters between adjacent levels of models via coalescing and de-coalescing. The key idea is that a smaller model that can be trained for fast convergence and the trained parameters provides high-qualities intermediate solutions for the next level larger network. The interpolation operator is designed to break the symmetry of neurons incurred by de-coalescing for better convergence performance. Our experiments on transformer-based language models (e.g. Bert, GPT) as well as a vision model (e.g. DeiT) prove that the proposed framework reduces the computational cost by about 20% on training BERT/GPT-Base models and up to 51.6% on training the BERT-Large model while preserving the performance.

  • 3 authors
·
Apr 6, 2024

Point-BERT: Pre-training 3D Point Cloud Transformers with Masked Point Modeling

We present Point-BERT, a new paradigm for learning Transformers to generalize the concept of BERT to 3D point cloud. Inspired by BERT, we devise a Masked Point Modeling (MPM) task to pre-train point cloud Transformers. Specifically, we first divide a point cloud into several local point patches, and a point cloud Tokenizer with a discrete Variational AutoEncoder (dVAE) is designed to generate discrete point tokens containing meaningful local information. Then, we randomly mask out some patches of input point clouds and feed them into the backbone Transformers. The pre-training objective is to recover the original point tokens at the masked locations under the supervision of point tokens obtained by the Tokenizer. Extensive experiments demonstrate that the proposed BERT-style pre-training strategy significantly improves the performance of standard point cloud Transformers. Equipped with our pre-training strategy, we show that a pure Transformer architecture attains 93.8% accuracy on ModelNet40 and 83.1% accuracy on the hardest setting of ScanObjectNN, surpassing carefully designed point cloud models with much fewer hand-made designs. We also demonstrate that the representations learned by Point-BERT transfer well to new tasks and domains, where our models largely advance the state-of-the-art of few-shot point cloud classification task. The code and pre-trained models are available at https://github.com/lulutang0608/Point-BERT

  • 6 authors
·
Nov 29, 2021

Clinical-Longformer and Clinical-BigBird: Transformers for long clinical sequences

Transformers-based models, such as BERT, have dramatically improved the performance for various natural language processing tasks. The clinical knowledge enriched model, namely ClinicalBERT, also achieved state-of-the-art results when performed on clinical named entity recognition and natural language inference tasks. One of the core limitations of these transformers is the substantial memory consumption due to their full self-attention mechanism. To overcome this, long sequence transformer models, e.g. Longformer and BigBird, were proposed with the idea of sparse attention mechanism to reduce the memory usage from quadratic to the sequence length to a linear scale. These models extended the maximum input sequence length from 512 to 4096, which enhanced the ability of modeling long-term dependency and consequently achieved optimal results in a variety of tasks. Inspired by the success of these long sequence transformer models, we introduce two domain enriched language models, namely Clinical-Longformer and Clinical-BigBird, which are pre-trained from large-scale clinical corpora. We evaluate both pre-trained models using 10 baseline tasks including named entity recognition, question answering, and document classification tasks. The results demonstrate that Clinical-Longformer and Clinical-BigBird consistently and significantly outperform ClinicalBERT as well as other short-sequence transformers in all downstream tasks. We have made our source code available at [https://github.com/luoyuanlab/Clinical-Longformer] the pre-trained models available for public download at: [https://huggingface.co/yikuan8/Clinical-Longformer].

  • 5 authors
·
Jan 27, 2022

Benchmarking for Public Health Surveillance tasks on Social Media with a Domain-Specific Pretrained Language Model

A user-generated text on social media enables health workers to keep track of information, identify possible outbreaks, forecast disease trends, monitor emergency cases, and ascertain disease awareness and response to official health correspondence. This exchange of health information on social media has been regarded as an attempt to enhance public health surveillance (PHS). Despite its potential, the technology is still in its early stages and is not ready for widespread application. Advancements in pretrained language models (PLMs) have facilitated the development of several domain-specific PLMs and a variety of downstream applications. However, there are no PLMs for social media tasks involving PHS. We present and release PHS-BERT, a transformer-based PLM, to identify tasks related to public health surveillance on social media. We compared and benchmarked the performance of PHS-BERT on 25 datasets from different social medial platforms related to 7 different PHS tasks. Compared with existing PLMs that are mainly evaluated on limited tasks, PHS-BERT achieved state-of-the-art performance on all 25 tested datasets, showing that our PLM is robust and generalizable in the common PHS tasks. By making PHS-BERT available, we aim to facilitate the community to reduce the computational cost and introduce new baselines for future works across various PHS-related tasks.

  • 5 authors
·
Apr 9, 2022