arXiv subjects

James Henderson

Publications and source records attributed to James Henderson.

At least 19 recordsLinked to original sources

arXiv2026

Nonparametric Variational Differential Privacy via Embedding Parameter Clipping

The nonparametric variational information bottleneck (NVIB) provides the foundation for nonparametric variational differential privacy (NVDP), a framework for building privacy-preserving language models. However, the learned latent representations can drift into regions with high information content, leading to poor privacy guarantees, but also low utility due to numerical instability during training. In this work, we introduce a principled parameter clipping strategy to directly address this issue. Our method is mathematically derived from the objective of minimizing the R\'enyi Divergence (RD) upper bound, yielding specific, theoretically grounded constraints on the posterior mean, variance, and mixture weight parameters. We apply our technique to an NVIB based model and empirically compare it against an unconstrained baseline. Our findings demonstrate that the clipped model consistently achieves tighter RD bounds, implying stronger privacy, while simultaneously attaining higher performance on several downstream tasks. This work presents a simple yet effective method for improving the privacy-utility trade-off in variational models, making them more robust and practical.

cs.LG↗

arXiv2026

Differential Privacy for Transformer Embeddings of Text with Nonparametric Variational Information Bottleneck

We propose a privacy-preserving method for sharing text data by sharing noisy versions of their transformer embeddings. It has been shown that hidden representations learned by deep models can encode sensitive information from the input, making it possible for adversaries to recover the input data with considerable accuracy. This problem is exacerbated in transformer embeddings because they consist of multiple vectors, one per token. To mitigate this risk, we propose Nonparametric Variational Differential Privacy (NVDP), which ensures both useful data sharing and strong privacy protection. We take a differential privacy (DP) approach, integrating a nonparametric variational information bottleneck (NVIB) layer into the transformer architecture to inject noise into its multivector embeddings and thereby hide information, and measuring privacy protection with R\'enyi Divergence (RD) and its corresponding Bayesian Differential Privacy (BDP) guarantee. Training the NVIB layer calibrates the noise level according to the utility of the downstream task. We test NVDP on the General Language Understanding Evaluation (GLUE) benchmark and show that varying the noise level gives us a useful trade-off between privacy and accuracy. With lower noise levels, our model maintains high accuracy while offering strong privacy guarantees, effectively balancing privacy and utility.

cs.LG↗

arXiv2025

Discovering Meaningful Units with Visually Grounded Semantics from Image Captions

Fine-grained knowledge is crucial for vision-language models to obtain a better understanding of the real world. While there has been work trying to acquire this kind of knowledge in the space of vision and language, it has mostly focused on aligning the image patches with the tokens on the language side. However, image patches do not have any meaning to the human eye, and individual tokens do not necessarily carry groundable information in the image. It is groups of tokens which describe different aspects of the scene. In this work, we propose a model which groups the caption tokens as part of its architecture in order to capture a fine-grained representation of the language. We expect our representations to be at the level of objects present in the image, and therefore align our representations with the output of an image encoder trained to discover objects. We show that by learning to group the tokens, the vision-language model has a better fine-grained understanding of vision and language. In addition, the token groups that our model discovers are highly similar to groundable phrases in text, both qualitatively and quantitatively.

cs.CV↗

arXiv2025

RAGferee: Building Contextual Reward Models for Retrieval-Augmented Generation

Existing Reward Models (RMs), typically trained on general preference data, struggle in Retrieval Augmented Generation (RAG) settings, which require judging responses for faithfulness to retrieved context, relevance to the user query, appropriate refusals when context is insufficient, completeness and conciseness of information. To address the lack of publicly available RAG-centric preference datasets and specialised RMs, we introduce RAGferee, a methodology that repurposes question-answering (QA) datasets into preference pairs that prioritise groundedness over stylistic features, enabling the training of contextual RMs better suited to judging RAG responses. Using RAGferee, we curate a small preference dataset of 4K samples and fine-tune RMs ranging from 7B to 24B parameters. Our RAG-centric RMs achieve state-of-the-art performance on ContextualJudgeBench, surpassing existing 70B+ RMs trained on much larger (up to 2.4M samples) general corpora, with an absolute improvement of +15.5%.

cs.CL↗

arXiv2025

Reduction of Supervision for Biomedical Knowledge Discovery

Knowledge discovery is hindered by the increasing volume of publications and the scarcity of extensive annotated data. To tackle the challenge of information overload, it is essential to employ automated methods for knowledge extraction and processing. Finding the right balance between the level of supervision and the effectiveness of models poses a significant challenge. While supervised techniques generally result in better performance, they have the major drawback of demanding labeled data. This requirement is labor-intensive and time-consuming and hinders scalability when exploring new domains. In this context, our study addresses the challenge of identifying semantic relationships between biomedical entities (e.g., diseases, proteins) in unstructured text while minimizing dependency on supervision. We introduce a suite of unsupervised algorithms based on dependency trees and attention mechanisms and employ a range of pointwise binary classification methods. Transitioning from weakly supervised to fully unsupervised settings, we assess the methods' ability to learn from data with noisy labels. The evaluation on biomedical benchmark datasets explores the effectiveness of the methods. Our approach tackles a central issue in knowledge discovery: balancing performance with minimal supervision. By gradually decreasing supervision, we assess the robustness of pointwise binary classification techniques in handling noisy labels, revealing their capability to shift from weakly supervised to entirely unsupervised scenarios. Comprehensive benchmarking offers insights into the effectiveness of these techniques, suggesting an encouraging direction toward adaptable knowledge discovery systems, representing progress in creating data-efficient methodologies for extracting useful insights when annotated data is limited.

cs.AI↗

arXiv2024

Data-driven Discovery of Biophysical T Cell Receptor Co-specificity Rules

The biophysical interactions between the T cell receptor (TCR) and its ligands determine the specificity of the cellular immune response. However, the immense diversity of receptors and ligands has made it challenging to discover generalizable rules across the distinct binding affinity landscapes created by different ligands. Here, we present an optimization framework for discovering biophysical rules that predict whether TCRs share specificity to a ligand. Applying this framework to TCRs associated with a collection of SARS-CoV-2 peptides we systematically characterize how co-specificity depends on the type and position of amino-acid differences between receptors. We also demonstrate that the inferred rules generalize to ligands highly dissimilar to any seen during training. Our analysis reveals that matching of steric properties between substituted amino acids is more important for receptor co-specificity than the hydrophobic properties that prominently determine evolutionary substitutability. Our analysis also quantifies the substantial importance of positions not in direct contact with the peptide for specificity. These findings highlight the potential for data-driven approaches to uncover the molecular mechanisms underpinning the specificity of adaptive immune responses.

q-bio.BM↗

arXiv2024

Fast-and-Frugal Text-Graph Transformers are Effective Link Predictors

We propose Fast-and-Frugal Text-Graph (FnF-TG) Transformers, a Transformer-based framework that unifies textual and structural information for inductive link prediction in text-attributed knowledge graphs. We demonstrate that, by effectively encoding ego-graphs (1-hop neighbourhoods), we can reduce the reliance on resource-intensive textual encoders. This makes the model both fast at training and inference time, as well as frugal in terms of cost. We perform a comprehensive evaluation on three popular datasets and show that FnF-TG can achieve superior performance compared to previous state-of-the-art methods. We also extend inductive learning to a fully inductive setting, where relations don't rely on transductive (fixed) representations, as in previous work, but are a function of their textual description. Additionally, we introduce new variants of existing datasets, specifically designed to test the performance of models on unseen relations at inference time, thus offering a new test-bench for fully inductive link prediction.

cs.CL↗

arXiv2024

Enhancing Biomedical Knowledge Discovery for Diseases: An Open-Source Framework Applied on Rett Syndrome and Alzheimer's Disease

The ever-growing volume of biomedical publications creates a critical need for efficient knowledge discovery. In this context, we introduce an open-source end-to-end framework designed to construct knowledge around specific diseases directly from raw text. To facilitate research in disease-related knowledge discovery, we create two annotated datasets focused on Rett syndrome and Alzheimer's disease, enabling the identification of semantic relations between biomedical entities. Extensive benchmarking explores various ways to represent relations and entity representations, offering insights into optimal modeling strategies for semantic relation detection and highlighting language models' competence in knowledge discovery. We also conduct probing experiments using different layer representations and attention scores to explore transformers' ability to capture semantic relations.

cs.CL↗

arXiv2024

Contrastive learning of T cell receptor representations

Computational prediction of the interaction of T cell receptors (TCRs) and their ligands is a grand challenge in immunology. Despite advances in high-throughput assays, specificity-labelled TCR data remains sparse. In other domains, the pre-training of language models on unlabelled data has been successfully used to address data bottlenecks. However, it is unclear how to best pre-train protein language models for TCR specificity prediction. Here we introduce a TCR language model called SCEPTR (Simple Contrastive Embedding of the Primary sequence of T cell Receptors), capable of data-efficient transfer learning. Through our model, we introduce a novel pre-training strategy combining autocontrastive learning and masked-language modelling, which enables SCEPTR to achieve its state-of-the-art performance. In contrast, existing protein language models and a variant of SCEPTR pre-trained without autocontrastive learning are outperformed by sequence alignment-based methods. We anticipate that contrastive learning will be a useful paradigm to decode the rules of TCR specificity.

q-bio.BM↗

arXiv2024

Limits on Inferring T-cell Specificity from Partial Information

A key challenge in molecular biology is to decipher the mapping of protein sequence to function. To perform this mapping requires the identification of sequence features most informative about function. Here, we quantify the amount of information (in bits) that T-cell receptor (TCR) sequence features provide about antigen specificity. We identify informative features by their degree of conservation among antigen-specific receptors relative to null expectations. We find that TCR specificity synergistically depends on the hypervariable regions of both receptor chains, with a degree of synergy that strongly depends on the ligand. Using a coincidence-based approach to measuring information enables us to directly bound the accuracy with which TCR specificity can be predicted from partial matches to reference sequences. We anticipate that our statistical framework will be of use for developing machine learning models for TCR specificity prediction and for optimizing TCRs for cell therapies. The proposed coincidence-based information measures might find further applications in bounding the performance of pairwise classifiers in other fields.

q-bio.BM↗

arXiv2023

Nonparametric Variational Regularisation of Pretrained Transformers

The current paradigm of large-scale pre-training and fine-tuning Transformer large language models has lead to significant improvements across the board in natural language processing. However, such large models are susceptible to overfitting to their training data, and as a result the models perform poorly when the domain changes. Also, due to the model's scale, the cost of fine-tuning the model to the new domain is large. Nonparametric Variational Information Bottleneck (NVIB) has been proposed as a regulariser for training cross-attention in Transformers, potentially addressing the overfitting problem. We extend the NVIB framework to replace all types of attention functions in Transformers, and show that existing pretrained Transformers can be reinterpreted as Nonparametric Variational (NV) models using a proposed identity initialisation. We then show that changing the initialisation introduces a novel, information-theoretic post-training regularisation in the attention mechanism, which improves out-of-domain generalisation without any training. This success supports the hypothesis that pretrained Transformers are implicitly NV Bayesian models.

cs.LG↗

arXiv2023

HyperMixer: An MLP-based Low Cost Alternative to Transformers

Transformer-based architectures are the model of choice for natural language understanding, but they come at a significant cost, as they have quadratic complexity in the input length, require a lot of training data, and can be difficult to tune. In the pursuit of lower costs, we investigate simple MLP-based architectures. We find that existing architectures such as MLPMixer, which achieves token mixing through a static MLP applied to each feature independently, are too detached from the inductive biases required for natural language understanding. In this paper, we propose a simple variant, HyperMixer, which forms the token mixing MLP dynamically using hypernetworks. Empirically, we demonstrate that our model performs better than alternative MLP-based models, and on par with Transformers. In contrast to Transformers, HyperMixer achieves these results at substantially lower costs in terms of processing time, training data, and hyperparameter tuning.

cs.CL↗

arXiv2023

Progress Metrics in DAG-based Consensus

Lachesis protocol~\cite{lachesis2021} leverages a DAG of events to allow nodes to reach fast consensus of events. This work introduces DAG progress metrics to drive the nodes to emit new events more effectively. With these metrics, nodes can select event timing and can choose previous events as parents for their own new events. Our results show that our event timing and parent selection methods can help reaching consensus quicker and thus can reduce lower time to finality significantly.

cs.DC↗

arXiv2023

Transformers as Graph-to-Graph Models

We argue that Transformers are essentially graph-to-graph models, with sequences just being a special case. Attention weights are functionally equivalent to graph edges. Our Graph-to-Graph Transformer architecture makes this ability explicit, by inputting graph edges into the attention weight computations and predicting graph edges with attention-like functions, thereby integrating explicit graphs into the latent graphs learned by pretrained Transformers. Adding iterative graph refinement provides a joint embedding of input, output, and latent graphs, allowing non-autoregressive graph prediction to optimise the complete graph without any bespoke pipeline or decoding strategy. Empirical results show that this architecture achieves state-of-the-art accuracies for modelling a variety of linguistic structures, integrating very effectively with the latent linguistic representations learned by pretraining.

cs.CL↗

arXiv2023

Learning to Abstract with Nonparametric Variational Information Bottleneck

Learned representations at the level of characters, sub-words, words and sentences, have each contributed to advances in understanding different NLP tasks and linguistic phenomena. However, learning textual embeddings is costly as they are tokenization specific and require different models to be trained for each level of abstraction. We introduce a novel language representation model which can learn to compress to different levels of abstraction at different layers of the same model. We apply Nonparametric Variational Information Bottleneck (NVIB) to stacked Transformer self-attention layers in the encoder, which encourages an information-theoretic compression of the representations through the model. We find that the layers within the model correspond to increasing levels of abstraction and that their representations are more linguistically informed. Finally, we show that NVIB compression results in a model which is more robust to adversarial perturbations.

cs.CL↗

arXiv2023

GADePo: Graph-Assisted Declarative Pooling Transformers for Document-Level Relation Extraction

Document-level relation extraction typically relies on text-based encoders and hand-coded pooling heuristics to aggregate information learned by the encoder. In this paper, we leverage the intrinsic graph processing capabilities of the Transformer model and propose replacing hand-coded pooling methods with new tokens in the input, which are designed to aggregate information via explicit graph relations in the computation of attention weights. We introduce a joint text-graph Transformer model and a graph-assisted declarative pooling (GADePo) specification of the input, which provides explicit and high-level instructions for information aggregation. GADePo allows the pooling process to be guided by domain-specific knowledge or desired outcomes but still learned by the Transformer, leading to more flexible and customisable pooling strategies. We evaluate our method across diverse datasets and models and show that our approach yields promising results that are consistently better than those achieved by the hand-coded pooling functions.

cs.CL↗

arXiv2023

What Do Compressed Multilingual Machine Translation Models Forget?

Recently, very large pre-trained models achieve state-of-the-art results in various natural language processing (NLP) tasks, but their size makes it more challenging to apply them in resource-constrained environments. Compression techniques allow to drastically reduce the size of the models and therefore their inference time with negligible impact on top-tier metrics. However, the general performance averaged across multiple tasks and/or languages may hide a drastic performance drop on under-represented features, which could result in the amplification of biases encoded by the models. In this work, we assess the impact of compression methods on Multilingual Neural Machine Translation models (MNMT) for various language groups, gender, and semantic biases by extensive analysis of compressed models on different machine translation benchmarks, i.e. FLORES-101, MT-Gender, and DiBiMT. We show that the performance of under-represented languages drops significantly, while the average BLEU metric only slightly decreases. Interestingly, the removal of noisy memorization with compression leads to a significant improvement for some medium-resource languages. Finally, we demonstrate that compression amplifies intrinsic gender and semantic biases, even in high-resource languages. Code: https://github.com/alirezamshi/bias-compressedMT

cs.CL↗

arXiv2023

Syntax-Aware Graph-to-Graph Transformer for Semantic Role Labelling

Recent models have shown that incorporating syntactic knowledge into the semantic role labelling (SRL) task leads to a significant improvement. In this paper, we propose Syntax-aware Graph-to-Graph Transformer (SynG2G-Tr) model, which encodes the syntactic structure using a novel way to input graph relations as embeddings, directly into the self-attention mechanism of Transformer. This approach adds a soft bias towards attention patterns that follow the syntactic structure but also allows the model to use this information to learn alternative patterns. We evaluate our model on both span-based and dependency-based SRL datasets, and outperform previous alternative methods in both in-domain and out-of-domain settings, on CoNLL 2005 and CoNLL 2009 datasets.

cs.CL↗