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Jun 22

Freeing the Law with LOCUS: A Local Ordinance Corpus for the United States

Progress in legal AI increasingly depends on access to authoritative legal text at scale. Yet one of the most consequential layers of American law remains largely absent from existing machine-readable corpora: local ordinances. Local codes govern zoning, housing, business licensing, public health, noise, animal control, and many other domains of everyday regulation, but they are fragmented across vendor platforms designed for human browsing rather than bulk research access. We introduce LOCUS - the Local Ordinance Corpus for the United States - a comprehensive corpus and county-harmonized access layer for U.S. municipal and county ordinance codes. The raw corpus, available for release to researchers, represents nearly all publicly available municipal and county ordinance codes. The resulting raw corpus contains codes from 9,239 cities and counties. A smaller county-harmonized LOCUS access layer provides coverage for the largest 2,309 of 3,144 U.S. counties, accounting for a majority of the population. We use OCR to handle the myriad of document formats that have kept the law from being a public resource. We release the corpus with coverage metadata to support reproducibility, downstream legal AI research, and the incremental expansion of machine-readable access to local law. We train a collection of ModernBERT-based classifiers and scorers to facilitate analyzing U.S. local law among several dimensions, such as opacity and paternalism, that have not previously been studied at this scale. LOCUS-v1 and its derivative models are available at: https://huggingface.co/datasets/LocalLaws/LOCUS-v1

LocalLaws LOCUS
·
Jun 16 2

It's All in The [MASK]: Simple Instruction-Tuning Enables BERT-like Masked Language Models As Generative Classifiers

While encoder-only models such as BERT and ModernBERT are ubiquitous in real-world NLP applications, their conventional reliance on task-specific classification heads can limit their applicability compared to decoder-based large language models (LLMs). In this work, we introduce ModernBERT-Large-Instruct, a 0.4B-parameter encoder model that leverages its masked language modelling (MLM) head for generative classification. Our approach employs an intentionally simple training loop and inference mechanism that requires no heavy pre-processing, heavily engineered prompting, or architectural modifications. ModernBERT-Large-Instruct exhibits strong zero-shot performance on both classification and knowledge-based tasks, outperforming similarly sized LLMs on MMLU and achieving 93% of Llama3-1B's MMLU performance with 60% less parameters. We also demonstrate that, when fine-tuned, the generative approach using the MLM head matches or even surpasses traditional classification-head methods across diverse NLU tasks.This capability emerges specifically in models trained on contemporary, diverse data mixes, with models trained on lower volume, less-diverse data yielding considerably weaker performance. Although preliminary, these results demonstrate the potential of using the original generative masked language modelling head over traditional task-specific heads for downstream tasks. Our work suggests that further exploration into this area is warranted, highlighting many avenues for future improvements.

  • 3 authors
·
Feb 6, 2025

Large Language Models and Synthetic Data for Monitoring Dataset Mentions in Research Papers

Tracking how data is mentioned and used in research papers provides critical insights for improving data discoverability, quality, and production. However, manually identifying and classifying dataset mentions across vast academic literature is resource-intensive and not scalable. This paper presents a machine learning framework that automates dataset mention detection across research domains by leveraging large language models (LLMs), synthetic data, and a two-stage fine-tuning process. We employ zero-shot extraction from research papers, an LLM-as-a-Judge for quality assessment, and a reasoning agent for refinement to generate a weakly supervised synthetic dataset. The Phi-3.5-mini instruct model is pre-fine-tuned on this dataset, followed by fine-tuning on a manually annotated subset. At inference, a ModernBERT-based classifier efficiently filters dataset mentions, reducing computational overhead while maintaining high recall. Evaluated on a held-out manually annotated sample, our fine-tuned model outperforms NuExtract-v1.5 and GLiNER-large-v2.1 in dataset extraction accuracy. Our results highlight how LLM-generated synthetic data can effectively address training data scarcity, improving generalization in low-resource settings. This framework offers a pathway toward scalable monitoring of dataset usage, enhancing transparency, and supporting researchers, funders, and policymakers in identifying data gaps and strengthening data accessibility for informed decision-making.

  • 3 authors
·
Feb 14, 2025

ModernBERT is More Efficient than Conventional BERT for Chest CT Findings Classification in Japanese Radiology Reports

Objective: This study aims to evaluate and compare the performance of two Japanese language models-conventional Bidirectional Encoder Representations from Transformers (BERT) and the newer ModernBERT-in classifying findings from chest CT reports, with a focus on tokenization efficiency, processing time, and classification performance. Methods: We conducted a retrospective study using the CT-RATE-JPN dataset containing 22,778 training reports and 150 test reports. Both models were fine-tuned for multi-label classification of 18 common chest CT conditions. The training data was split in 18,222:4,556 for training and validation. Performance was evaluated using F1 scores for each condition and exact match accuracy across all 18 labels. Results: ModernBERT demonstrated superior tokenization efficiency, requiring 24.0% fewer tokens per document (258.1 vs. 339.6) compared to BERT Base. This translated to significant performance improvements, with ModernBERT completing training in 1877.67 seconds versus BERT's 3090.54 seconds (39% reduction). ModernBERT processed 38.82 samples per second during training (1.65x faster) and 139.90 samples per second during inference (1.66x faster). Despite these efficiency gains, classification performance remained comparable, with ModernBERT achieving superior F1 scores in 8 conditions, while BERT performed better in 4 conditions. Overall exact match accuracy was slightly higher for ModernBERT (74.67% vs. 72.67%), though this difference was not statistically significant (p=0.6291). Conclusion: ModernBERT offers substantial improvements in tokenization efficiency and training speed without sacrificing classification performance. These results suggest that ModernBERT is a promising candidate for clinical applications in Japanese radiology reports analysis.

  • 5 authors
·
Mar 6, 2025

TabiBERT: A Large-Scale ModernBERT Foundation Model and Unified Benchmarking Framework for Turkish

Since the inception of BERT, encoder-only Transformers have evolved significantly in computational efficiency, training stability, and long-context modeling. ModernBERT consolidates these advances by integrating Rotary Positional Embeddings (RoPE), FlashAttention, and refined normalization. Despite these developments, Turkish NLP lacks a monolingual encoder trained from scratch incorporating such modern architectural paradigms. This work introduces TabiBERT, a monolingual Turkish encoder based on ModernBERT architecture trained from scratch on a large, curated corpus. TabiBERT is pre-trained on one trillion tokens sampled from an 84.88B token multi-domain corpus: web text (73%), scientific publications (20%), source code (6%), and mathematical content (0.3%). The model supports 8,192-token context length (16x original BERT), achieves up to 2.65x inference speedup, and reduces GPU memory consumption, enabling larger batch sizes. We introduce TabiBench with 28 datasets across eight task categories with standardized splits and protocols, evaluated using GLUE-style macro-averaging. TabiBERT attains 77.58 on TabiBench, outperforming BERTurk by 1.62 points and establishing state-of-the-art on five of eight categories: question answering (+9.55), code retrieval (+2.41), and document retrieval (+0.60). Compared with task-specific prior best results, including specialized models like TurkishBERTweet, TabiBERT achieves +1.47 average improvement, indicating robust cross-domain generalization. We release model weights, training configurations, and evaluation code for transparent, reproducible Turkish encoder research.

boun-tabilab BOUN TabiLab
·
Dec 28, 2025

Chinese ModernBERT with Whole-Word Masking

Encoder-only Transformers have advanced along three axes -- architecture, data, and systems -- yielding Pareto gains in accuracy, speed, and memory efficiency. Yet these improvements have not fully transferred to Chinese, where tokenization and morphology differ markedly from English. We introduce Chinese ModernBERT, a from-scratch Chinese encoder that couples: (i) a hardware-aware 32k BPE vocabulary tailored to frequent Chinese affixes/compounds, lowering the embedding budget; (ii) whole-word masking (WWM) with a dynamic masking curriculum (30% -> 15%) to align task difficulty with training progress; (iii) a two-stage pre-training pipeline that extends the native context from 1,024 to 8,192 tokens using RoPE and alternating local/global attention; and (iv) a damped-cosine learning-rate schedule for stable long-horizon optimization. We pre-train on ~1.2T Chinese tokens from CCI3-HQ, CCI4 (Chinese), and Cosmopedia-Chinese. On CLUE, Chinese ModernBERT is competitive with strong Chinese encoders under a unified fine-tuning protocol. Under bf16 it achieves high long-sequence throughput while maintaining strong short-sequence speed, reflecting benefits from budget allocation and attention design. To probe retrieval-oriented quality, we add a small amount of open contrastive data: fine-tuning on SimCLUE (~3M pairs) improves further when adding T2Ranking (~2M), reaching 0.505 (Pearson) / 0.537 (Spearman) on the SimCLUE test set. Under this open-data setting, Chinese ModernBERT surpasses Qwen-0.6B-embedding on SimCLUE, suggesting a clear scaling path for STS with additional curated pairs. We will release tokenizer and weights to facilitate reproducible research.

  • 4 authors
·
Oct 14, 2025

Turk-LettuceDetect: A Hallucination Detection Models for Turkish RAG Applications

The widespread adoption of Large Language Models (LLMs) has been hindered by their tendency to hallucinate, generating plausible but factually incorrect information. While Retrieval-Augmented Generation (RAG) systems attempt to address this issue by grounding responses in external knowledge, hallucination remains a persistent challenge, particularly for morphologically complex, low-resource languages like Turkish. This paper introduces Turk-LettuceDetect, the first suite of hallucination detection models specifically designed for Turkish RAG applications. Building on the LettuceDetect framework, we formulate hallucination detection as a token-level classification task and fine-tune three distinct encoder architectures: a Turkish-specific ModernBERT, TurkEmbed4STS, and multilingual EuroBERT. These models were trained on a machine-translated version of the RAGTruth benchmark dataset containing 17,790 instances across question answering, data-to-text generation, and summarization tasks. Our experimental results show that the ModernBERT-based model achieves an F1-score of 0.7266 on the complete test set, with particularly strong performance on structured tasks. The models maintain computational efficiency while supporting long contexts up to 8,192 tokens, making them suitable for real-time deployment. Comparative analysis reveals that while state-of-the-art LLMs demonstrate high recall, they suffer from low precision due to over-generation of hallucinated content, underscoring the necessity of specialized detection mechanisms. By releasing our models and translated dataset, this work addresses a critical gap in multilingual NLP and establishes a foundation for developing more reliable and trustworthy AI applications for Turkish and other languages.

  • 5 authors
·
Sep 22, 2025 2

RexBERT: Context Specialized Bidirectional Encoders for E-commerce

Encoder-only transformers remain indispensable in retrieval, classification, and ranking systems where latency, stability, and cost are paramount. Most general purpose encoders, however, are trained on generic corpora with limited coverage of specialized domains. We introduce RexBERT, a family of BERT-style encoders designed specifically for e-commerce semantics. We make three contributions. First, we release Ecom-niverse, a 350 billion token corpus curated from diverse retail and shopping sources. We describe a modular pipeline that isolates and extracts e-commerce content from FineFineWeb and other open web resources, and characterize the resulting domain distribution. Second, we present a reproducible pretraining recipe building on ModernBERT's architectural advances. The recipe consists of three phases: general pre-training, context extension, and annealed domain specialization. Third, we train RexBERT models ranging from 17M to 400M parameters and evaluate them on token classification, semantic similarity, and general natural language understanding tasks using e-commerce datasets. Despite having 2-3x fewer parameters, RexBERT outperforms larger general-purpose encoders and matches or surpasses modern long-context models on domain-specific benchmarks. Our results demonstrate that high quality in-domain data combined with a principled training approach provides a stronger foundation for e-commerce applications than indiscriminate scaling alone.

owlgebra-ai Owlgebra AI
·
Feb 4 3

Few-Shot Class-Incremental Learning via Training-Free Prototype Calibration

Real-world scenarios are usually accompanied by continuously appearing classes with scare labeled samples, which require the machine learning model to incrementally learn new classes and maintain the knowledge of base classes. In this Few-Shot Class-Incremental Learning (FSCIL) scenario, existing methods either introduce extra learnable components or rely on a frozen feature extractor to mitigate catastrophic forgetting and overfitting problems. However, we find a tendency for existing methods to misclassify the samples of new classes into base classes, which leads to the poor performance of new classes. In other words, the strong discriminability of base classes distracts the classification of new classes. To figure out this intriguing phenomenon, we observe that although the feature extractor is only trained on base classes, it can surprisingly represent the semantic similarity between the base and unseen new classes. Building upon these analyses, we propose a simple yet effective Training-frEE calibratioN (TEEN) strategy to enhance the discriminability of new classes by fusing the new prototypes (i.e., mean features of a class) with weighted base prototypes. In addition to standard benchmarks in FSCIL, TEEN demonstrates remarkable performance and consistent improvements over baseline methods in the few-shot learning scenario. Code is available at: https://github.com/wangkiw/TEEN

  • 5 authors
·
Dec 8, 2023

NorBERTo: A ModernBERT Model Trained for Portuguese with 331 Billion Tokens Corpus

High-quality corpora are essential for advancing Natural Language Processing (NLP) in Portuguese. Building on previous encoder-only models such as BERTimbau and Albertina PT-BR, we introduce NorBERTo, a modern encoder based on the ModernBERT architecture, featuring long-context support and efficient attention mechanisms. NorBERTo is trained on Aurora-PT, a newly curated Brazilian Portuguese corpus comprising 331 billion GPT-2 tokens collected from diverse web sources and existing multilingual datasets. We systematically benchmark NorBERTo against Strong baselines on semantic similarity, textual entailment and classification tasks using standardized datasets such as ASSIN 2 and PLUE. On PLUE, NorBERTo-large achieves the best results among the encoder models we evaluated, notably reaching 0.9191 F1 on MRPC and 0.7689 accuracy on RTE. On ASSIN 2, NorBERTo-large attains the highest entailment F1 (~0.904) among all encoders considered, although Albertina-900M and BERTimbau-large still hold an advantage. To the best of our knowledge, Aurora-PT is currently the largest openly available monolingual Portuguese corpus, surpassing previous resources. NorBERTo provides a modern, mid-sized encoder designed for realistic deployment scenarios: it is straight-forward to fine-tune, efficient to serve, and well suited as a backbone for retrieval-augmented generation and other downstream Portuguese NLP systems.

  • 11 authors
·
Apr 29

FireBERT: Hardening BERT-based classifiers against adversarial attack

We present FireBERT, a set of three proof-of-concept NLP classifiers hardened against TextFooler-style word-perturbation by producing diverse alternatives to original samples. In one approach, we co-tune BERT against the training data and synthetic adversarial samples. In a second approach, we generate the synthetic samples at evaluation time through substitution of words and perturbation of embedding vectors. The diversified evaluation results are then combined by voting. A third approach replaces evaluation-time word substitution with perturbation of embedding vectors. We evaluate FireBERT for MNLI and IMDB Movie Review datasets, in the original and on adversarial examples generated by TextFooler. We also test whether TextFooler is less successful in creating new adversarial samples when manipulating FireBERT, compared to working on unhardened classifiers. We show that it is possible to improve the accuracy of BERT-based models in the face of adversarial attacks without significantly reducing the accuracy for regular benchmark samples. We present co-tuning with a synthetic data generator as a highly effective method to protect against 95% of pre-manufactured adversarial samples while maintaining 98% of original benchmark performance. We also demonstrate evaluation-time perturbation as a promising direction for further research, restoring accuracy up to 75% of benchmark performance for pre-made adversarials, and up to 65% (from a baseline of 75% orig. / 12% attack) under active attack by TextFooler.

  • 3 authors
·
Aug 10, 2020

SecureBERT 2.0: Advanced Language Model for Cybersecurity Intelligence

Effective analysis of cybersecurity and threat intelligence data demands language models that can interpret specialized terminology, complex document structures, and the interdependence of natural language and source code. Encoder-only transformer architectures provide efficient and robust representations that support critical tasks such as semantic search, technical entity extraction, and semantic analysis, which are key to automated threat detection, incident triage, and vulnerability assessment. However, general-purpose language models often lack the domain-specific adaptation required for high precision. We present SecureBERT 2.0, an enhanced encoder-only language model purpose-built for cybersecurity applications. Leveraging the ModernBERT architecture, SecureBERT 2.0 introduces improved long-context modeling and hierarchical encoding, enabling effective processing of extended and heterogeneous documents, including threat reports and source code artifacts. Pretrained on a domain-specific corpus more than thirteen times larger than its predecessor, comprising over 13 billion text tokens and 53 million code tokens from diverse real-world sources, SecureBERT 2.0 achieves state-of-the-art performance on multiple cybersecurity benchmarks. Experimental results demonstrate substantial improvements in semantic search for threat intelligence, semantic analysis, cybersecurity-specific named entity recognition, and automated vulnerability detection in code within the cybersecurity domain.

  • 4 authors
·
Sep 30, 2025

Self-Training: A Survey

Semi-supervised algorithms aim to learn prediction functions from a small set of labeled observations and a large set of unlabeled observations. Because this framework is relevant in many applications, they have received a lot of interest in both academia and industry. Among the existing techniques, self-training methods have undoubtedly attracted greater attention in recent years. These models are designed to find the decision boundary on low density regions without making additional assumptions about the data distribution, and use the unsigned output score of a learned classifier, or its margin, as an indicator of confidence. The working principle of self-training algorithms is to learn a classifier iteratively by assigning pseudo-labels to the set of unlabeled training samples with a margin greater than a certain threshold. The pseudo-labeled examples are then used to enrich the labeled training data and to train a new classifier in conjunction with the labeled training set. In this paper, we present self-training methods for binary and multi-class classification; as well as their variants and two related approaches, namely consistency-based approaches and transductive learning. We examine the impact of significant self-training features on various methods, using different general and image classification benchmarks, and we discuss our ideas for future research in self-training. To the best of our knowledge, this is the first thorough and complete survey on this subject.

  • 6 authors
·
Feb 24, 2022

FashionBERT: Text and Image Matching with Adaptive Loss for Cross-modal Retrieval

In this paper, we address the text and image matching in cross-modal retrieval of the fashion industry. Different from the matching in the general domain, the fashion matching is required to pay much more attention to the fine-grained information in the fashion images and texts. Pioneer approaches detect the region of interests (i.e., RoIs) from images and use the RoI embeddings as image representations. In general, RoIs tend to represent the "object-level" information in the fashion images, while fashion texts are prone to describe more detailed information, e.g. styles, attributes. RoIs are thus not fine-grained enough for fashion text and image matching. To this end, we propose FashionBERT, which leverages patches as image features. With the pre-trained BERT model as the backbone network, FashionBERT learns high level representations of texts and images. Meanwhile, we propose an adaptive loss to trade off multitask learning in the FashionBERT modeling. Two tasks (i.e., text and image matching and cross-modal retrieval) are incorporated to evaluate FashionBERT. On the public dataset, experiments demonstrate FashionBERT achieves significant improvements in performances than the baseline and state-of-the-art approaches. In practice, FashionBERT is applied in a concrete cross-modal retrieval application. We provide the detailed matching performance and inference efficiency analysis.

  • 8 authors
·
May 19, 2020

Mecellem Models: Turkish Models Trained from Scratch and Continually Pre-trained for the Legal Domain

This paper presents Mecellem models, a framework for developing specialized language models for the Turkish legal domain through domain adaptation strategies. We make two contributions: (1)Encoder Model Pre-trained from Scratch: ModernBERT-based bidirectional encoders pre-trained on a Turkish-dominant corpus of 112.7 billion tokens. We implement a checkpoint selection strategy that evaluates downstream retrieval performance throughout training, revealing that optimal checkpoints achieve best retrieval scores before pre-training loss reaches its minimum. Our encoder models achieve top-3 rankings on the Turkish retrieval leaderboard, with smaller models (155M parameters) achieving comparable performance to larger reference models (307M-567M parameters). Our approach achieves 92.36% production efficiency compared to state-of-the-art models (embeddinggemma-300m: 100.00%, BAAI/bge-m3: 99.54%, newmindai/bge-m3-stsb: 94.38%), ranking fourth overall despite requiring less computational resources. SOTA models rely on multi-stage, computationally intensive training pipelines, making our single-stage pre-training followed by efficient post-training approach a cost-effective alternative; (2)Decoder Model with Continual Pre-training (CPT): Qwen3-1.7B and Qwen3-4B models adapted to Turkish legal domain through controlled curriculum learning. Four-phase CPT with optimal sample ratios enables gradual transition from general language knowledge to specialized legal terminology and long-context reasoning. This approach achieves 36.2% perplexity reduction on Turkish legal text, demonstrating domain adaptation gains.

newmindai NewMind AI
·
Jan 22 5

Stationary Representations: Optimally Approximating Compatibility and Implications for Improved Model Replacements

Learning compatible representations enables the interchangeable use of semantic features as models are updated over time. This is particularly relevant in search and retrieval systems where it is crucial to avoid reprocessing of the gallery images with the updated model. While recent research has shown promising empirical evidence, there is still a lack of comprehensive theoretical understanding about learning compatible representations. In this paper, we demonstrate that the stationary representations learned by the d-Simplex fixed classifier optimally approximate compatibility representation according to the two inequality constraints of its formal definition. This not only establishes a solid foundation for future works in this line of research but also presents implications that can be exploited in practical learning scenarios. An exemplary application is the now-standard practice of downloading and fine-tuning new pre-trained models. Specifically, we show the strengths and critical issues of stationary representations in the case in which a model undergoing sequential fine-tuning is asynchronously replaced by downloading a better-performing model pre-trained elsewhere. Such a representation enables seamless delivery of retrieval service (i.e., no reprocessing of gallery images) and offers improved performance without operational disruptions during model replacement. Code available at: https://github.com/miccunifi/iamcl2r.

  • 4 authors
·
May 4, 2024

Modeling Collaborator: Enabling Subjective Vision Classification With Minimal Human Effort via LLM Tool-Use

From content moderation to wildlife conservation, the number of applications that require models to recognize nuanced or subjective visual concepts is growing. Traditionally, developing classifiers for such concepts requires substantial manual effort measured in hours, days, or even months to identify and annotate data needed for training. Even with recently proposed Agile Modeling techniques, which enable rapid bootstrapping of image classifiers, users are still required to spend 30 minutes or more of monotonous, repetitive data labeling just to train a single classifier. Drawing on Fiske's Cognitive Miser theory, we propose a new framework that alleviates manual effort by replacing human labeling with natural language interactions, reducing the total effort required to define a concept by an order of magnitude: from labeling 2,000 images to only 100 plus some natural language interactions. Our framework leverages recent advances in foundation models, both large language models and vision-language models, to carve out the concept space through conversation and by automatically labeling training data points. Most importantly, our framework eliminates the need for crowd-sourced annotations. Moreover, our framework ultimately produces lightweight classification models that are deployable in cost-sensitive scenarios. Across 15 subjective concepts and across 2 public image classification datasets, our trained models outperform traditional Agile Modeling as well as state-of-the-art zero-shot classification models like ALIGN, CLIP, CuPL, and large visual question-answering models like PaLI-X.

  • 13 authors
·
Mar 4, 2024 1

INGENIOUS: Using Informative Data Subsets for Efficient Pre-Training of Language Models

A salient characteristic of pre-trained language models (PTLMs) is a remarkable improvement in their generalization capability and emergence of new capabilities with increasing model capacity and pre-training dataset size. Consequently, we are witnessing the development of enormous models pushing the state-of-the-art. It is, however, imperative to realize that this inevitably leads to prohibitively long training times, extortionate computing costs, and a detrimental environmental impact. Significant efforts are underway to make PTLM training more efficient through innovations in model architectures, training pipelines, and loss function design, with scant attention being paid to optimizing the utility of training data. The key question that we ask is whether it is possible to train PTLMs by employing only highly informative subsets of the training data while maintaining downstream performance? Building upon the recent progress in informative data subset selection, we show how we can employ submodular optimization to select highly representative subsets of the training corpora and demonstrate that the proposed framework can be applied to efficiently train multiple PTLMs (BERT, BioBERT, GPT-2) using only a fraction of data. Further, we perform a rigorous empirical evaluation to show that the resulting models achieve up to sim99% of the performance of the fully-trained models. We made our framework publicly available at https://github.com/Efficient-AI/ingenious.

  • 7 authors
·
May 11, 2023

A Robust Prototype-Based Network with Interpretable RBF Classifier Foundations

Prototype-based classification learning methods are known to be inherently interpretable. However, this paradigm suffers from major limitations compared to deep models, such as lower performance. This led to the development of the so-called deep Prototype-Based Networks (PBNs), also known as prototypical parts models. In this work, we analyze these models with respect to different properties, including interpretability. In particular, we focus on the Classification-by-Components (CBC) approach, which uses a probabilistic model to ensure interpretability and can be used as a shallow or deep architecture. We show that this model has several shortcomings, like creating contradicting explanations. Based on these findings, we propose an extension of CBC that solves these issues. Moreover, we prove that this extension has robustness guarantees and derive a loss that optimizes robustness. Additionally, our analysis shows that most (deep) PBNs are related to (deep) RBF classifiers, which implies that our robustness guarantees generalize to shallow RBF classifiers. The empirical evaluation demonstrates that our deep PBN yields state-of-the-art classification accuracy on different benchmarks while resolving the interpretability shortcomings of other approaches. Further, our shallow PBN variant outperforms other shallow PBNs while being inherently interpretable and exhibiting provable robustness guarantees.

  • 4 authors
·
Dec 19, 2024

BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic

ibm-research IBM Research
·
Jun 26, 2025

A Stationary (and Therefore Compatible) Representation is All You Need

Learning compatible representations aims to learn feature representations that can be used interchangeably over time whenever a model undergoes updates. In this paper, we demonstrate that stationary representations learned by d-Simplex fixed classifiers imply compatibility as in its formal definition. This result establishes a foundation for future works and can be directly exploited in practical learning scenarios. We address the challenge of learning compatibility using d-Simplex fixed classifiers when the model is sequentially fine-tuned. Learning according to a d-Simplex fixed classifier with the cross-entropy loss aligns feature distributions at the first-order statistics. Consequently, it may not fully capture higher-order dependencies in the representation between model updates. To address this issue, we demonstrate that training the model using a d-Simplex fixed classifier through a convex combination of the cross-entropy loss and a contrastive loss not only captures higher-order dependencies, but is also equivalent to learning with the cross-entropy under the compatibility constraints. We confirm our findings with extensive experiments also considering a new scenario where a pre-trained model is sequentially fine-tuned and occasionally replaced with an improved model. We show that stationary representations enable uninterrupted retrieval services (without reprocessing gallery images) while improving performance during model updates and replacements, achieving state-of-the-art. Code at https://github.com/miccunifi/iamcl2r.

A Simple Unified Framework for Detecting Out-of-Distribution Samples and Adversarial Attacks

Detecting test samples drawn sufficiently far away from the training distribution statistically or adversarially is a fundamental requirement for deploying a good classifier in many real-world machine learning applications. However, deep neural networks with the softmax classifier are known to produce highly overconfident posterior distributions even for such abnormal samples. In this paper, we propose a simple yet effective method for detecting any abnormal samples, which is applicable to any pre-trained softmax neural classifier. We obtain the class conditional Gaussian distributions with respect to (low- and upper-level) features of the deep models under Gaussian discriminant analysis, which result in a confidence score based on the Mahalanobis distance. While most prior methods have been evaluated for detecting either out-of-distribution or adversarial samples, but not both, the proposed method achieves the state-of-the-art performances for both cases in our experiments. Moreover, we found that our proposed method is more robust in harsh cases, e.g., when the training dataset has noisy labels or small number of samples. Finally, we show that the proposed method enjoys broader usage by applying it to class-incremental learning: whenever out-of-distribution samples are detected, our classification rule can incorporate new classes well without further training deep models.

  • 4 authors
·
Jul 10, 2018

Learning Support and Trivial Prototypes for Interpretable Image Classification

Prototypical part network (ProtoPNet) methods have been designed to achieve interpretable classification by associating predictions with a set of training prototypes, which we refer to as trivial prototypes because they are trained to lie far from the classification boundary in the feature space. Note that it is possible to make an analogy between ProtoPNet and support vector machine (SVM) given that the classification from both methods relies on computing similarity with a set of training points (i.e., trivial prototypes in ProtoPNet, and support vectors in SVM). However, while trivial prototypes are located far from the classification boundary, support vectors are located close to this boundary, and we argue that this discrepancy with the well-established SVM theory can result in ProtoPNet models with inferior classification accuracy. In this paper, we aim to improve the classification of ProtoPNet with a new method to learn support prototypes that lie near the classification boundary in the feature space, as suggested by the SVM theory. In addition, we target the improvement of classification results with a new model, named ST-ProtoPNet, which exploits our support prototypes and the trivial prototypes to provide more effective classification. Experimental results on CUB-200-2011, Stanford Cars, and Stanford Dogs datasets demonstrate that ST-ProtoPNet achieves state-of-the-art classification accuracy and interpretability results. We also show that the proposed support prototypes tend to be better localised in the object of interest rather than in the background region.

  • 8 authors
·
Jan 8, 2023

Empirical study of Machine Learning Classifier Evaluation Metrics behavior in Massively Imbalanced and Noisy data

With growing credit card transaction volumes, the fraud percentages are also rising, including overhead costs for institutions to combat and compensate victims. The use of machine learning into the financial sector permits more effective protection against fraud and other economic crime. Suitably trained machine learning classifiers help proactive fraud detection, improving stakeholder trust and robustness against illicit transactions. However, the design of machine learning based fraud detection algorithms has been challenging and slow due the massively unbalanced nature of fraud data and the challenges of identifying the frauds accurately and completely to create a gold standard ground truth. Furthermore, there are no benchmarks or standard classifier evaluation metrics to measure and identify better performing classifiers, thus keeping researchers in the dark. In this work, we develop a theoretical foundation to model human annotation errors and extreme imbalance typical in real world fraud detection data sets. By conducting empirical experiments on a hypothetical classifier, with a synthetic data distribution approximated to a popular real world credit card fraud data set, we simulate human annotation errors and extreme imbalance to observe the behavior of popular machine learning classifier evaluation matrices. We demonstrate that a combined F1 score and g-mean, in that specific order, is the best evaluation metric for typical imbalanced fraud detection model classification.

  • 2 authors
·
Aug 25, 2022

ArchBERT: Bi-Modal Understanding of Neural Architectures and Natural Languages

Building multi-modal language models has been a trend in the recent years, where additional modalities such as image, video, speech, etc. are jointly learned along with natural languages (i.e., textual information). Despite the success of these multi-modal language models with different modalities, there is no existing solution for neural network architectures and natural languages. Providing neural architectural information as a new modality allows us to provide fast architecture-2-text and text-2-architecture retrieval/generation services on the cloud with a single inference. Such solution is valuable in terms of helping beginner and intermediate ML users to come up with better neural architectures or AutoML approaches with a simple text query. In this paper, we propose ArchBERT, a bi-modal model for joint learning and understanding of neural architectures and natural languages, which opens up new avenues for research in this area. We also introduce a pre-training strategy named Masked Architecture Modeling (MAM) for a more generalized joint learning. Moreover, we introduce and publicly release two new bi-modal datasets for training and validating our methods. The ArchBERT's performance is verified through a set of numerical experiments on different downstream tasks such as architecture-oriented reasoning, question answering, and captioning (summarization). Datasets, codes, and demos are available supplementary materials.

When Noisy Labels Meet Long Tail Dilemmas: A Representation Calibration Method

Real-world large-scale datasets are both noisily labeled and class-imbalanced. The issues seriously hurt the generalization of trained models. It is hence significant to address the simultaneous incorrect labeling and class-imbalance, i.e., the problem of learning with noisy labels on long-tailed data. Previous works develop several methods for the problem. However, they always rely on strong assumptions that are invalid or hard to be checked in practice. In this paper, to handle the problem and address the limitations of prior works, we propose a representation calibration method RCAL. Specifically, RCAL works with the representations extracted by unsupervised contrastive learning. We assume that without incorrect labeling and class imbalance, the representations of instances in each class conform to a multivariate Gaussian distribution, which is much milder and easier to be checked. Based on the assumption, we recover underlying representation distributions from polluted ones resulting from mislabeled and class-imbalanced data. Additional data points are then sampled from the recovered distributions to help generalization. Moreover, during classifier training, representation learning takes advantage of representation robustness brought by contrastive learning, which further improves the classifier performance. We derive theoretical results to discuss the effectiveness of our representation calibration. Experiments on multiple benchmarks justify our claims and confirm the superiority of the proposed method.

  • 5 authors
·
Nov 20, 2022

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts. We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.

  • 7 authors
·
Jan 25, 2019

A Survey on Cost Types, Interaction Schemes, and Annotator Performance Models in Selection Algorithms for Active Learning in Classification

Pool-based active learning (AL) aims to optimize the annotation process (i.e., labeling) as the acquisition of annotations is often time-consuming and therefore expensive. For this purpose, an AL strategy queries annotations intelligently from annotators to train a high-performance classification model at a low annotation cost. Traditional AL strategies operate in an idealized framework. They assume a single, omniscient annotator who never gets tired and charges uniformly regardless of query difficulty. However, in real-world applications, we often face human annotators, e.g., crowd or in-house workers, who make annotation mistakes and can be reluctant to respond if tired or faced with complex queries. Recently, a wide range of novel AL strategies has been proposed to address these issues. They differ in at least one of the following three central aspects from traditional AL: (1) They explicitly consider (multiple) human annotators whose performances can be affected by various factors, such as missing expertise. (2) They generalize the interaction with human annotators by considering different query and annotation types, such as asking an annotator for feedback on an inferred classification rule. (3) They take more complex cost schemes regarding annotations and misclassifications into account. This survey provides an overview of these AL strategies and refers to them as real-world AL. Therefore, we introduce a general real-world AL strategy as part of a learning cycle and use its elements, e.g., the query and annotator selection algorithm, to categorize about 60 real-world AL strategies. Finally, we outline possible directions for future research in the field of AL.

  • 4 authors
·
Sep 23, 2021

An Analysis of Active Learning Algorithms using Real-World Crowd-sourced Text Annotations

Active learning algorithms automatically identify the most informative samples from large amounts of unlabeled data and tremendously reduce human annotation effort in inducing a machine learning model. In a conventional active learning setup, the labeling oracles are assumed to be infallible, that is, they always provide correct answers (in terms of class labels) to the queried unlabeled instances, which cannot be guaranteed in real-world applications. To this end, a body of research has focused on the development of active learning algorithms in the presence of imperfect / noisy oracles. Existing research on active learning with noisy oracles typically simulate the oracles using machine learning models; however, real-world situations are much more challenging, and using ML models to simulate the annotation patterns may not appropriately capture the nuances of real-world annotation challenges. In this research, we first collect annotations of text samples (from 3 benchmark text classification datasets) from crowd-sourced workers through a crowd-sourcing platform. We then conduct extensive empirical studies of 8 commonly used active learning techniques (in conjunction with deep neural networks) using the obtained annotations. Our analyses sheds light on the performance of these techniques under real-world challenges, where annotators can provide incorrect labels, and can also refuse to provide labels. We hope this research will provide valuable insights that will be useful for the deployment of deep active learning systems in real-world applications. The obtained annotations can be accessed at https://github.com/varuntotakura/al_rcta/.

  • 4 authors
·
Apr 24 1

Active Self-Paced Learning for Cost-Effective and Progressive Face Identification

This paper aims to develop a novel cost-effective framework for face identification, which progressively maintains a batch of classifiers with the increasing face images of different individuals. By naturally combining two recently rising techniques: active learning (AL) and self-paced learning (SPL), our framework is capable of automatically annotating new instances and incorporating them into training under weak expert re-certification. We first initialize the classifier using a few annotated samples for each individual, and extract image features using the convolutional neural nets. Then, a number of candidates are selected from the unannotated samples for classifier updating, in which we apply the current classifiers ranking the samples by the prediction confidence. In particular, our approach utilizes the high-confidence and low-confidence samples in the self-paced and the active user-query way, respectively. The neural nets are later fine-tuned based on the updated classifiers. Such heuristic implementation is formulated as solving a concise active SPL optimization problem, which also advances the SPL development by supplementing a rational dynamic curriculum constraint. The new model finely accords with the "instructor-student-collaborative" learning mode in human education. The advantages of this proposed framework are two-folds: i) The required number of annotated samples is significantly decreased while the comparable performance is guaranteed. A dramatic reduction of user effort is also achieved over other state-of-the-art active learning techniques. ii) The mixture of SPL and AL effectively improves not only the classifier accuracy compared to existing AL/SPL methods but also the robustness against noisy data. We evaluate our framework on two challenging datasets, and demonstrate very promising results. (http://hcp.sysu.edu.cn/projects/aspl/)

  • 5 authors
·
Jan 12, 2017

Subclass-balancing Contrastive Learning for Long-tailed Recognition

Long-tailed recognition with imbalanced class distribution naturally emerges in practical machine learning applications. Existing methods such as data reweighing, resampling, and supervised contrastive learning enforce the class balance with a price of introducing imbalance between instances of head class and tail class, which may ignore the underlying rich semantic substructures of the former and exaggerate the biases in the latter. We overcome these drawbacks by a novel ``subclass-balancing contrastive learning (SBCL)'' approach that clusters each head class into multiple subclasses of similar sizes as the tail classes and enforce representations to capture the two-layer class hierarchy between the original classes and their subclasses. Since the clustering is conducted in the representation space and updated during the course of training, the subclass labels preserve the semantic substructures of head classes. Meanwhile, it does not overemphasize tail class samples, so each individual instance contribute to the representation learning equally. Hence, our method achieves both the instance- and subclass-balance, while the original class labels are also learned through contrastive learning among subclasses from different classes. We evaluate SBCL over a list of long-tailed benchmark datasets and it achieves the state-of-the-art performance. In addition, we present extensive analyses and ablation studies of SBCL to verify its advantages.

  • 4 authors
·
Jun 28, 2023