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Dec 31

Text-ADBench: Text Anomaly Detection Benchmark based on LLMs Embedding

Text anomaly detection is a critical task in natural language processing (NLP), with applications spanning fraud detection, misinformation identification, spam detection and content moderation, etc. Despite significant advances in large language models (LLMs) and anomaly detection algorithms, the absence of standardized and comprehensive benchmarks for evaluating the existing anomaly detection methods on text data limits rigorous comparison and development of innovative approaches. This work performs a comprehensive empirical study and introduces a benchmark for text anomaly detection, leveraging embeddings from diverse pre-trained language models across a wide array of text datasets. Our work systematically evaluates the effectiveness of embedding-based text anomaly detection by incorporating (1) early language models (GloVe, BERT); (2) multiple LLMs (LLaMa-2, LLama-3, Mistral, OpenAI (small, ada, large)); (3) multi-domain text datasets (news, social media, scientific publications); (4) comprehensive evaluation metrics (AUROC, AUPRC). Our experiments reveal a critical empirical insight: embedding quality significantly governs anomaly detection efficacy, and deep learning-based approaches demonstrate no performance advantage over conventional shallow algorithms (e.g., KNN, Isolation Forest) when leveraging LLM-derived embeddings.In addition, we observe strongly low-rank characteristics in cross-model performance matrices, which enables an efficient strategy for rapid model evaluation (or embedding evaluation) and selection in practical applications. Furthermore, by open-sourcing our benchmark toolkit that includes all embeddings from different models and code at https://github.com/jicongfan/Text-Anomaly-Detection-Benchmark, this work provides a foundation for future research in robust and scalable text anomaly detection systems.

  • 2 authors
·
Jul 16

Reliable and Efficient Concept Erasure of Text-to-Image Diffusion Models

Text-to-image models encounter safety issues, including concerns related to copyright and Not-Safe-For-Work (NSFW) content. Despite several methods have been proposed for erasing inappropriate concepts from diffusion models, they often exhibit incomplete erasure, consume a lot of computing resources, and inadvertently damage generation ability. In this work, we introduce Reliable and Efficient Concept Erasure (RECE), a novel approach that modifies the model in 3 seconds without necessitating additional fine-tuning. Specifically, RECE efficiently leverages a closed-form solution to derive new target embeddings, which are capable of regenerating erased concepts within the unlearned model. To mitigate inappropriate content potentially represented by derived embeddings, RECE further aligns them with harmless concepts in cross-attention layers. The derivation and erasure of new representation embeddings are conducted iteratively to achieve a thorough erasure of inappropriate concepts. Besides, to preserve the model's generation ability, RECE introduces an additional regularization term during the derivation process, resulting in minimizing the impact on unrelated concepts during the erasure process. All the processes above are in closed-form, guaranteeing extremely efficient erasure in only 3 seconds. Benchmarking against previous approaches, our method achieves more efficient and thorough erasure with minor damage to original generation ability and demonstrates enhanced robustness against red-teaming tools. Code is available at https://github.com/CharlesGong12/RECE.

  • 5 authors
·
Jul 17, 2024

Large Language Models Enhanced Collaborative Filtering

Recent advancements in Large Language Models (LLMs) have attracted considerable interest among researchers to leverage these models to enhance Recommender Systems (RSs). Existing work predominantly utilizes LLMs to generate knowledge-rich texts or utilizes LLM-derived embeddings as features to improve RSs. Although the extensive world knowledge embedded in LLMs generally benefits RSs, the application can only take limited number of users and items as inputs, without adequately exploiting collaborative filtering information. Considering its crucial role in RSs, one key challenge in enhancing RSs with LLMs lies in providing better collaborative filtering information through LLMs. In this paper, drawing inspiration from the in-context learning and chain of thought reasoning in LLMs, we propose the Large Language Models enhanced Collaborative Filtering (LLM-CF) framework, which distils the world knowledge and reasoning capabilities of LLMs into collaborative filtering. We also explored a concise and efficient instruction-tuning method, which improves the recommendation capabilities of LLMs while preserving their general functionalities (e.g., not decreasing on the LLM benchmark). Comprehensive experiments on three real-world datasets demonstrate that LLM-CF significantly enhances several backbone recommendation models and consistently outperforms competitive baselines, showcasing its effectiveness in distilling the world knowledge and reasoning capabilities of LLM into collaborative filtering.

  • 7 authors
·
Mar 26, 2024

A Comparative Analysis of Static Word Embeddings for Hungarian

This paper presents a comprehensive analysis of various static word embeddings for Hungarian, including traditional models such as Word2Vec, FastText, as well as static embeddings derived from BERT-based models using different extraction methods. We evaluate these embeddings on both intrinsic and extrinsic tasks to provide a holistic view of their performance. For intrinsic evaluation, we employ a word analogy task, which assesses the embeddings ability to capture semantic and syntactic relationships. Our results indicate that traditional static embeddings, particularly FastText, excel in this task, achieving high accuracy and mean reciprocal rank (MRR) scores. Among the BERT-based models, the X2Static method for extracting static embeddings demonstrates superior performance compared to decontextualized and aggregate methods, approaching the effectiveness of traditional static embeddings. For extrinsic evaluation, we utilize a bidirectional LSTM model to perform Named Entity Recognition (NER) and Part-of-Speech (POS) tagging tasks. The results reveal that embeddings derived from dynamic models, especially those extracted using the X2Static method, outperform purely static embeddings. Notably, ELMo embeddings achieve the highest accuracy in both NER and POS tagging tasks, underscoring the benefits of contextualized representations even when used in a static form. Our findings highlight the continued relevance of static word embeddings in NLP applications and the potential of advanced extraction methods to enhance the utility of BERT-based models. This piece of research contributes to the understanding of embedding performance in the Hungarian language and provides valuable insights for future developments in the field. The training scripts, evaluation codes, restricted vocabulary, and extracted embeddings will be made publicly available to support further research and reproducibility.

  • 1 authors
·
May 12

Tandem spoofing-robust automatic speaker verification based on time-domain embeddings

Spoofing-robust automatic speaker verification (SASV) systems are a crucial technology for the protection against spoofed speech. In this study, we focus on logical access attacks and introduce a novel approach to SASV tasks. A novel representation of genuine and spoofed speech is employed, based on the probability mass function (PMF) of waveform amplitudes in the time domain. This methodology generates novel time embeddings derived from the PMF of selected groups within the training set. This paper highlights the role of gender segregation and its positive impact on performance. We propose a countermeasure (CM) system that employs time-domain embeddings derived from the PMF of spoofed and genuine speech, as well as gender recognition based on male and female time-based embeddings. The method exhibits notable gender recognition capabilities, with mismatch rates of 0.94% and 1.79% for males and females, respectively. The male and female CM systems achieve an equal error rate (EER) of 8.67% and 10.12%, respectively. By integrating this approach with traditional speaker verification systems, we demonstrate improved generalization ability and tandem detection cost function evaluation using the ASVspoof2019 challenge database. Furthermore, we investigate the impact of fusing the time embedding approach with traditional CM and illustrate how this fusion enhances generalization in SASV architectures.

  • 3 authors
·
Dec 22, 2024

Beginning with You: Perceptual-Initialization Improves Vision-Language Representation and Alignment

We introduce Perceptual-Initialization (PI), a paradigm shift in visual representation learning that incorporates human perceptual structure during the initialization phase rather than as a downstream fine-tuning step. By integrating human-derived triplet embeddings from the NIGHTS dataset to initialize a CLIP vision encoder, followed by self-supervised learning on YFCC15M, our approach demonstrates significant zero-shot performance improvements, without any task-specific fine-tuning, across 29 zero shot classification and 2 retrieval benchmarks. On ImageNet-1K, zero-shot gains emerge after approximately 15 epochs of pretraining. Benefits are observed across datasets of various scales, with improvements manifesting at different stages of the pretraining process depending on dataset characteristics. Our approach consistently enhances zero-shot top-1 accuracy, top-5 accuracy, and retrieval recall (e.g., R@1, R@5) across these diverse evaluation tasks, without requiring any adaptation to target domains. These findings challenge the conventional wisdom of using human-perceptual data primarily for fine-tuning and demonstrate that embedding human perceptual structure during early representation learning yields more capable and vision-language aligned systems that generalize immediately to unseen tasks. Our work shows that "beginning with you", starting with human perception, provides a stronger foundation for general-purpose vision-language intelligence.

  • 7 authors
·
May 20

Sensing Cardiac Health Across Scenarios and Devices: A Multi-Modal Foundation Model Pretrained on Heterogeneous Data from 1.7 Million Individuals

Cardiac biosignals, such as electrocardiograms (ECG) and photoplethysmograms (PPG), are of paramount importance for the diagnosis, prevention, and management of cardiovascular diseases, and have been extensively used in a variety of clinical tasks. Conventional deep learning approaches for analyzing these signals typically rely on homogeneous datasets and static bespoke models, limiting their robustness and generalizability across diverse clinical settings and acquisition protocols. In this study, we present a cardiac sensing foundation model (CSFM) that leverages advanced transformer architectures and a generative, masked pretraining strategy to learn unified representations from vast, heterogeneous health records. Our model is pretrained on an innovative multi-modal integration of data from multiple large-scale datasets (including MIMIC-III-WDB, MIMIC-IV-ECG, and CODE), comprising cardiac signals and the corresponding clinical or machine-generated text reports from approximately 1.7 million individuals. We demonstrate that the embeddings derived from our CSFM not only serve as effective feature extractors across diverse cardiac sensing scenarios, but also enable seamless transfer learning across varying input configurations and sensor modalities. Extensive evaluations across diagnostic tasks, demographic information recognition, vital sign measurement, clinical outcome prediction, and ECG question answering reveal that CSFM consistently outperforms traditional one-modal-one-task approaches. Notably, CSFM exhibits robust performance across multiple ECG lead configurations from standard 12-lead systems to single-lead setups, and in scenarios where only ECG, only PPG, or a combination thereof is available. These findings highlight the potential of CSFM as a versatile and scalable solution, for comprehensive cardiac monitoring.

  • 13 authors
·
Jun 23

Pseudo-Relevance Feedback for Multiple Representation Dense Retrieval

Pseudo-relevance feedback mechanisms, from Rocchio to the relevance models, have shown the usefulness of expanding and reweighting the users' initial queries using information occurring in an initial set of retrieved documents, known as the pseudo-relevant set. Recently, dense retrieval -- through the use of neural contextual language models such as BERT for analysing the documents' and queries' contents and computing their relevance scores -- has shown a promising performance on several information retrieval tasks still relying on the traditional inverted index for identifying documents relevant to a query. Two different dense retrieval families have emerged: the use of single embedded representations for each passage and query (e.g. using BERT's [CLS] token), or via multiple representations (e.g. using an embedding for each token of the query and document). In this work, we conduct the first study into the potential for multiple representation dense retrieval to be enhanced using pseudo-relevance feedback. In particular, based on the pseudo-relevant set of documents identified using a first-pass dense retrieval, we extract representative feedback embeddings (using KMeans clustering) -- while ensuring that these embeddings discriminate among passages (based on IDF) -- which are then added to the query representation. These additional feedback embeddings are shown to both enhance the effectiveness of a reranking as well as an additional dense retrieval operation. Indeed, experiments on the MSMARCO passage ranking dataset show that MAP can be improved by upto 26% on the TREC 2019 query set and 10% on the TREC 2020 query set by the application of our proposed ColBERT-PRF method on a ColBERT dense retrieval approach.

  • 4 authors
·
Jun 21, 2021

SQUARE: Semantic Query-Augmented Fusion and Efficient Batch Reranking for Training-free Zero-Shot Composed Image Retrieval

Composed Image Retrieval (CIR) aims to retrieve target images that preserve the visual content of a reference image while incorporating user-specified textual modifications. Training-free zero-shot CIR (ZS-CIR) approaches, which require no task-specific training or labeled data, are highly desirable, yet accurately capturing user intent remains challenging. In this paper, we present SQUARE, a novel two-stage training-free framework that leverages Multimodal Large Language Models (MLLMs) to enhance ZS-CIR. In the Semantic Query-Augmented Fusion (SQAF) stage, we enrich the query embedding derived from a vision-language model (VLM) such as CLIP with MLLM-generated captions of the target image. These captions provide high-level semantic guidance, enabling the query to better capture the user's intent and improve global retrieval quality. In the Efficient Batch Reranking (EBR) stage, top-ranked candidates are presented as an image grid with visual marks to the MLLM, which performs joint visual-semantic reasoning across all candidates. Our reranking strategy operates in a single pass and yields more accurate rankings. Experiments show that SQUARE, with its simplicity and effectiveness, delivers strong performance on four standard CIR benchmarks. Notably, it maintains high performance even with lightweight pre-trained, demonstrating its potential applicability.

  • 3 authors
·
Sep 30 3

Growing Transformers: Modular Composition and Layer-wise Expansion on a Frozen Substrate

The prevailing paradigm for scaling large language models (LLMs) involves monolithic, end-to-end training, a resource-intensive process that lacks flexibility. This paper explores an alternative, constructive approach to model development, built upon the foundation of non-trainable, deterministic input embeddings. In prior [1], we established that high-level semantic reasoning can emerge in Transformers using frozen embeddings derived from the visual structure of Unicode glyphs. Here, we demonstrate that this fixed representational substrate acts as a universal "docking port," enabling two powerful and efficient scaling paradigms: seamless modular composition and progressive layer-wise growth. First, we show that specialist models trained on disparate datasets (e.g., Russian and Chinese text) can be merged into a single, more capable Mixture-of-Experts (MoE) model, post-training, with zero architectural modification. This is achieved by simply averaging their output logits. The resulting MoE model exhibits immediate performance improvements on reasoning benchmarks like MMLU, surpassing its constituent experts without catastrophic forgetting. Second, we introduce a layer-wise constructive training methodology, where a deep Transformer is "grown" by progressively stacking and training one layer at a time. This method demonstrates stable convergence and a clear correlation between model depth and the emergence of complex reasoning abilities, such as those required for SQuAD. Our findings suggest a paradigm shift from monolithic optimization towards a more biological or constructive model of AI development, where complexity is built incrementally and modules can be composed freely. This opens new avenues for resource-efficient scaling, continual learning, and a more democratized ecosystem for building powerful AI systems. We release all code and models to facilitate further research.

  • 1 authors
·
Jul 8 2

Reasoning to Attend: Try to Understand How <SEG> Token Works

Current Large Multimodal Models (LMMs) empowered visual grounding typically rely on <SEG> tokens as a text prompt to jointly optimize the vision-language model (e.g., LLaVA) and the downstream task-specific model (e.g., SAM). However, we observe that little research has looked into how it works.In this work, we first visualize the similarity maps, which are obtained by computing the semantic similarity between the <SEG> token and the image token embeddings derived from the last hidden layer in both the LLaVA encoder and SAM decoder. Intriguingly, we have found that a striking consistency holds in terms of activation responses in the similarity map, which reveals that what the <SEG> token contributes to is semantic similarity within image-text pairs. Specifically, the <SEG> token, a placeholder expanded in text vocabulary, extensively queries among individual tokenized image patches to match the semantics of an object from text to the paired image, while the Large Language Models (LLMs) are being fine-tuned. Upon the above findings, we present READ, which facilitates LMMs' resilient REAsoning capability of where to attenD under the guidance of highly activated points borrowed from similarity maps. Remarkably, READ features an intuitive design, Similarity as Points module (SasP), which can be seamlessly applied to <SEG>-like paradigms in a plug-and-play fashion. Also, extensive experiments have been conducted on ReasonSeg and RefCOCO(+/g) datasets. To validate whether READ suffers from catastrophic forgetting of previous skills after fine-tuning, we further assess its generation ability on an augmented FP-RefCOCO(+/g) dataset. All codes and models are publicly available at https://github.com/rui-qian/READ.

  • 3 authors
·
Dec 23, 2024

GaussianGrasper: 3D Language Gaussian Splatting for Open-vocabulary Robotic Grasping

Constructing a 3D scene capable of accommodating open-ended language queries, is a pivotal pursuit, particularly within the domain of robotics. Such technology facilitates robots in executing object manipulations based on human language directives. To tackle this challenge, some research efforts have been dedicated to the development of language-embedded implicit fields. However, implicit fields (e.g. NeRF) encounter limitations due to the necessity of processing a large number of input views for reconstruction, coupled with their inherent inefficiencies in inference. Thus, we present the GaussianGrasper, which utilizes 3D Gaussian Splatting to explicitly represent the scene as a collection of Gaussian primitives. Our approach takes a limited set of RGB-D views and employs a tile-based splatting technique to create a feature field. In particular, we propose an Efficient Feature Distillation (EFD) module that employs contrastive learning to efficiently and accurately distill language embeddings derived from foundational models. With the reconstructed geometry of the Gaussian field, our method enables the pre-trained grasping model to generate collision-free grasp pose candidates. Furthermore, we propose a normal-guided grasp module to select the best grasp pose. Through comprehensive real-world experiments, we demonstrate that GaussianGrasper enables robots to accurately query and grasp objects with language instructions, providing a new solution for language-guided manipulation tasks. Data and codes can be available at https://github.com/MrSecant/GaussianGrasper.

  • 15 authors
·
Mar 14, 2024

RAVE: Residual Vector Embedding for CLIP-Guided Backlit Image Enhancement

In this paper we propose a novel modification of Contrastive Language-Image Pre-Training (CLIP) guidance for the task of unsupervised backlit image enhancement. Our work builds on the state-of-the-art CLIP-LIT approach, which learns a prompt pair by constraining the text-image similarity between a prompt (negative/positive sample) and a corresponding image (backlit image/well-lit image) in the CLIP embedding space. Learned prompts then guide an image enhancement network. Based on the CLIP-LIT framework, we propose two novel methods for CLIP guidance. First, we show that instead of tuning prompts in the space of text embeddings, it is possible to directly tune their embeddings in the latent space without any loss in quality. This accelerates training and potentially enables the use of additional encoders that do not have a text encoder. Second, we propose a novel approach that does not require any prompt tuning. Instead, based on CLIP embeddings of backlit and well-lit images from training data, we compute the residual vector in the embedding space as a simple difference between the mean embeddings of the well-lit and backlit images. This vector then guides the enhancement network during training, pushing a backlit image towards the space of well-lit images. This approach further dramatically reduces training time, stabilizes training and produces high quality enhanced images without artifacts, both in supervised and unsupervised training regimes. Additionally, we show that residual vectors can be interpreted, revealing biases in training data, and thereby enabling potential bias correction.

  • 3 authors
·
Apr 2, 2024

Benchmarking pre-trained text embedding models in aligning built asset information

Accurate mapping of the built asset information to established data classification systems and taxonomies is crucial for effective asset management, whether for compliance at project handover or ad-hoc data integration scenarios. Due to the complex nature of built asset data, which predominantly comprises technical text elements, this process remains largely manual and reliant on domain expert input. Recent breakthroughs in contextual text representation learning (text embedding), particularly through pre-trained large language models, offer promising approaches that can facilitate the automation of cross-mapping of the built asset data. However, no comprehensive evaluation has yet been conducted to assess these models' ability to effectively represent the complex semantics specific to built asset technical terminology. This study presents a comparative benchmark of state-of-the-art text embedding models to evaluate their effectiveness in aligning built asset information with domain-specific technical concepts. Our proposed datasets are derived from two renowned built asset data classification dictionaries. The results of our benchmarking across six proposed datasets, covering three tasks of clustering, retrieval, and reranking, highlight the need for future research on domain adaptation techniques. The benchmarking resources are published as an open-source library, which will be maintained and extended to support future evaluations in this field.

  • 2 authors
·
Nov 18, 2024

Unified Work Embeddings: Contrastive Learning of a Bidirectional Multi-task Ranker

Workforce transformation across diverse industries has driven an increased demand for specialized natural language processing capabilities. Nevertheless, tasks derived from work-related contexts inherently reflect real-world complexities, characterized by long-tailed distributions, extreme multi-label target spaces, and scarce data availability. The rise of generalist embedding models prompts the question of their performance in the work domain, especially as progress in the field has focused mainly on individual tasks. To this end, we introduce WorkBench, the first unified evaluation suite spanning six work-related tasks formulated explicitly as ranking problems, establishing a common ground for multi-task progress. Based on this benchmark, we find significant positive cross-task transfer, and use this insight to compose task-specific bipartite graphs from real-world data, synthetically enriched through grounding. This leads to Unified Work Embeddings (UWE), a task-agnostic bi-encoder that exploits our training-data structure with a many-to-many InfoNCE objective, and leverages token-level embeddings with task-agnostic soft late interaction. UWE demonstrates zero-shot ranking performance on unseen target spaces in the work domain, enables low-latency inference by caching the task target space embeddings, and shows significant gains in macro-averaged MAP and RP@10 over generalist embedding models.

  • 3 authors
·
Nov 11

Deep Clustering via Joint Convolutional Autoencoder Embedding and Relative Entropy Minimization

Image clustering is one of the most important computer vision applications, which has been extensively studied in literature. However, current clustering methods mostly suffer from lack of efficiency and scalability when dealing with large-scale and high-dimensional data. In this paper, we propose a new clustering model, called DEeP Embedded RegularIzed ClusTering (DEPICT), which efficiently maps data into a discriminative embedding subspace and precisely predicts cluster assignments. DEPICT generally consists of a multinomial logistic regression function stacked on top of a multi-layer convolutional autoencoder. We define a clustering objective function using relative entropy (KL divergence) minimization, regularized by a prior for the frequency of cluster assignments. An alternating strategy is then derived to optimize the objective by updating parameters and estimating cluster assignments. Furthermore, we employ the reconstruction loss functions in our autoencoder, as a data-dependent regularization term, to prevent the deep embedding function from overfitting. In order to benefit from end-to-end optimization and eliminate the necessity for layer-wise pretraining, we introduce a joint learning framework to minimize the unified clustering and reconstruction loss functions together and train all network layers simultaneously. Experimental results indicate the superiority and faster running time of DEPICT in real-world clustering tasks, where no labeled data is available for hyper-parameter tuning.

  • 5 authors
·
Apr 20, 2017

Semantics derived automatically from language corpora contain human-like biases

Artificial intelligence and machine learning are in a period of astounding growth. However, there are concerns that these technologies may be used, either with or without intention, to perpetuate the prejudice and unfairness that unfortunately characterizes many human institutions. Here we show for the first time that human-like semantic biases result from the application of standard machine learning to ordinary language---the same sort of language humans are exposed to every day. We replicate a spectrum of standard human biases as exposed by the Implicit Association Test and other well-known psychological studies. We replicate these using a widely used, purely statistical machine-learning model---namely, the GloVe word embedding---trained on a corpus of text from the Web. Our results indicate that language itself contains recoverable and accurate imprints of our historic biases, whether these are morally neutral as towards insects or flowers, problematic as towards race or gender, or even simply veridical, reflecting the {\em status quo} for the distribution of gender with respect to careers or first names. These regularities are captured by machine learning along with the rest of semantics. In addition to our empirical findings concerning language, we also contribute new methods for evaluating bias in text, the Word Embedding Association Test (WEAT) and the Word Embedding Factual Association Test (WEFAT). Our results have implications not only for AI and machine learning, but also for the fields of psychology, sociology, and human ethics, since they raise the possibility that mere exposure to everyday language can account for the biases we replicate here.

  • 3 authors
·
Aug 25, 2016

Emergent Semantics Beyond Token Embeddings: Transformer LMs with Frozen Visual Unicode Representations

Understanding the locus of semantic representation in large language models (LLMs) is crucial for interpretability and architectural innovation. The dominant paradigm posits that trainable input embeddings serve as foundational "meaning vectors." This paper challenges that view. We construct Transformer models where the embedding layer is entirely frozen, with vectors derived not from data, but from the visual structure of Unicode glyphs. These non-semantic, precomputed visual embeddings are fixed throughout training. Our method is compatible with any tokenizer, including a novel Unicode-centric tokenizer we introduce to ensure universal text coverage. Despite the absence of trainable, semantically initialized embeddings, our models converge, generate coherent text, and, critically, outperform architecturally identical models with trainable embeddings on the MMLU reasoning benchmark. We attribute this to "representational interference" in conventional models, where the embedding layer is burdened with learning both structural and semantic features. Our results indicate that high-level semantics are not inherent to input embeddings but are an emergent property of the Transformer's compositional architecture and data scale. This reframes the role of embeddings from meaning containers to structural primitives. We release all code and models to foster further research.

  • 1 authors
·
Jul 7 1

DSeq-JEPA: Discriminative Sequential Joint-Embedding Predictive Architecture

Image-based Joint-Embedding Predictive Architecture (I-JEPA) learns visual representations by predicting latent embeddings of masked regions from visible context. However, it treats all regions uniformly and independently, lacking an explicit notion of where or in what order predictions should be made. Inspired by human visual perception, which deploys attention selectively and sequentially from the most informative to secondary regions, we propose DSeq-JEPA, a Discriminative Sequential Joint-Embedding Predictive Architecture that bridges predictive and autoregressive self-supervised learning, integrating JEPA-style latent prediction with GPT-style sequential reasoning. Specifically, DSeq-JEPA (i) first identifies primary discriminative regions based on a transformer-derived saliency map, emphasizing the distribution of visual importance, and then (ii) predicts subsequent regions in this discriminative order, progressively forming a curriculum-like semantic progression from primary to secondary cues -- a form of GPT-style pre-training. Extensive experiments across diverse tasks, including image classification (ImageNet), fine-grained visual categorization (iNaturalist21, CUB-200-2011, Stanford-Cars), detection and segmentation (MS-COCO, ADE20K), and low-level reasoning tasks (Clevr/Count, Clevr/Dist), demonstrate that DSeq-JEPA consistently focuses on more discriminative and generalizable representations than I-JEPA variants. Project page: https://github.com/SkyShunsuke/DSeq-JEPA.

  • 6 authors
·
Nov 21

NMIXX: Domain-Adapted Neural Embeddings for Cross-Lingual eXploration of Finance

General-purpose sentence embedding models often struggle to capture specialized financial semantics, especially in low-resource languages like Korean, due to domain-specific jargon, temporal meaning shifts, and misaligned bilingual vocabularies. To address these gaps, we introduce NMIXX (Neural eMbeddings for Cross-lingual eXploration of Finance), a suite of cross-lingual embedding models fine-tuned with 18.8K high-confidence triplets that pair in-domain paraphrases, hard negatives derived from a semantic-shift typology, and exact Korean-English translations. Concurrently, we release KorFinSTS, a 1,921-pair Korean financial STS benchmark spanning news, disclosures, research reports, and regulations, designed to expose nuances that general benchmarks miss. When evaluated against seven open-license baselines, NMIXX's multilingual bge-m3 variant achieves Spearman's rho gains of +0.10 on English FinSTS and +0.22 on KorFinSTS, outperforming its pre-adaptation checkpoint and surpassing other models by the largest margin, while revealing a modest trade-off in general STS performance. Our analysis further shows that models with richer Korean token coverage adapt more effectively, underscoring the importance of tokenizer design in low-resource, cross-lingual settings. By making both models and the benchmark publicly available, we provide the community with robust tools for domain-adapted, multilingual representation learning in finance.

  • 7 authors
·
Jul 13

DNABERT-S: Learning Species-Aware DNA Embedding with Genome Foundation Models

Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C^2LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at https://github.com/Zhihan1996/DNABERT_S.

  • 8 authors
·
Feb 13, 2024

Benchmarking Filtered Approximate Nearest Neighbor Search Algorithms on Transformer-based Embedding Vectors

Advances in embedding models for text, image, audio, and video drive progress across multiple domains, including retrieval-augmented generation, recommendation systems, vehicle/person reidentification, and face recognition. Many applications in these domains require an efficient method to retrieve items that are close to a given query in the embedding space while satisfying a filter condition based on the item's attributes, a problem known as Filtered Approximate Nearest Neighbor Search (FANNS). In this work, we present a comprehensive survey and taxonomy of FANNS methods and analyze how they are benchmarked in the literature. By doing so, we identify a key challenge in the current FANNS landscape: the lack of diverse and realistic datasets, particularly ones derived from the latest transformer-based text embedding models. To address this, we introduce a novel dataset consisting of embedding vectors for the abstracts of over 2.7 million research articles from the arXiv repository, accompanied by 11 real-world attributes such as authors and categories. We benchmark a wide range of FANNS methods on our novel dataset and find that each method has distinct strengths and limitations; no single approach performs best across all scenarios. ACORN, for example, supports various filter types and performs reliably across dataset scales but is often outperformed by more specialized methods. SeRF shows excellent performance for range filtering on ordered attributes but cannot handle categorical attributes. Filtered-DiskANN and UNG excel on the medium-scale dataset but fail on the large-scale dataset, highlighting the challenge posed by transformer-based embeddings, which are often more than an order of magnitude larger than earlier embeddings. We conclude that no universally best method exists.

  • 5 authors
·
Jul 29

SynchroRaMa : Lip-Synchronized and Emotion-Aware Talking Face Generation via Multi-Modal Emotion Embedding

Audio-driven talking face generation has received growing interest, particularly for applications requiring expressive and natural human-avatar interaction. However, most existing emotion-aware methods rely on a single modality (either audio or image) for emotion embedding, limiting their ability to capture nuanced affective cues. Additionally, most methods condition on a single reference image, restricting the model's ability to represent dynamic changes in actions or attributes across time. To address these issues, we introduce SynchroRaMa, a novel framework that integrates a multi-modal emotion embedding by combining emotional signals from text (via sentiment analysis) and audio (via speech-based emotion recognition and audio-derived valence-arousal features), enabling the generation of talking face videos with richer and more authentic emotional expressiveness and fidelity. To ensure natural head motion and accurate lip synchronization, SynchroRaMa includes an audio-to-motion (A2M) module that generates motion frames aligned with the input audio. Finally, SynchroRaMa incorporates scene descriptions generated by Large Language Model (LLM) as additional textual input, enabling it to capture dynamic actions and high-level semantic attributes. Conditioning the model on both visual and textual cues enhances temporal consistency and visual realism. Quantitative and qualitative experiments on benchmark datasets demonstrate that SynchroRaMa outperforms the state-of-the-art, achieving improvements in image quality, expression preservation, and motion realism. A user study further confirms that SynchroRaMa achieves higher subjective ratings than competing methods in overall naturalness, motion diversity, and video smoothness. Our project page is available at <https://novicemm.github.io/synchrorama>.

  • 4 authors
·
Sep 24

VideoScan: Enabling Efficient Streaming Video Understanding via Frame-level Semantic Carriers

This paper introduces VideoScan, an efficient vision-language model (VLM) inference framework designed for real-time video interaction that effectively comprehends and retains streamed video inputs while delivering rapid and accurate responses. A longstanding challenge in video understanding--particularly for long-term or real-time applications--stems from the substantial computational overhead caused by the extensive length of visual tokens. To address this, VideoScan employs a single semantic carrier token to represent each frame, progressively reducing computational and memory overhead during its two-phase inference process: prefilling and decoding. The embedding of the semantic carrier token is derived from an optimized aggregation of frame-level visual features, ensuring compact yet semantically rich representations. Critically, the corresponding key-value pairs are trained to retain contextual semantics from prior frames, enabling efficient memory management without sacrificing temporal coherence. During inference, the visual tokens of each frame are processed only once during the prefilling phase and subsequently discarded in the decoding stage, eliminating redundant computations. This design ensures efficient VLM inference even under stringent real-time constraints. Comprehensive experiments on diverse offline and online benchmarks demonstrate that LLaVA-Video, supported by our method, achieves up to sim 5times and 1.29times speedups compared to its original version and previous efficient streaming video understanding approaches, respectively. Crucially, these improvements are attained while maintaining competitive performance and ensuring stable GPU memory consumption (consistently sim 18GB, independent of video duration).

  • 4 authors
·
Mar 12

CLOOB: Modern Hopfield Networks with InfoLOOB Outperform CLIP

CLIP yielded impressive results on zero-shot transfer learning tasks and is considered as a foundation model like BERT or GPT3. CLIP vision models that have a rich representation are pre-trained using the InfoNCE objective and natural language supervision before they are fine-tuned on particular tasks. Though CLIP excels at zero-shot transfer learning, it suffers from an explaining away problem, that is, it focuses on one or few features, while neglecting other relevant features. This problem is caused by insufficiently extracting the covariance structure in the original multi-modal data. We suggest to use modern Hopfield networks to tackle the problem of explaining away. Their retrieved embeddings have an enriched covariance structure derived from co-occurrences of features in the stored embeddings. However, modern Hopfield networks increase the saturation effect of the InfoNCE objective which hampers learning. We propose to use the InfoLOOB objective to mitigate this saturation effect. We introduce the novel "Contrastive Leave One Out Boost" (CLOOB), which uses modern Hopfield networks for covariance enrichment together with the InfoLOOB objective. In experiments we compare CLOOB to CLIP after pre-training on the Conceptual Captions and the YFCC dataset with respect to their zero-shot transfer learning performance on other datasets. CLOOB consistently outperforms CLIP at zero-shot transfer learning across all considered architectures and datasets.

  • 11 authors
·
Oct 21, 2021

Sharper Bounds for $\ell_p$ Sensitivity Sampling

In large scale machine learning, random sampling is a popular way to approximate datasets by a small representative subset of examples. In particular, sensitivity sampling is an intensely studied technique which provides provable guarantees on the quality of approximation, while reducing the number of examples to the product of the VC dimension d and the total sensitivity mathfrak S in remarkably general settings. However, guarantees going beyond this general bound of mathfrak S d are known in perhaps only one setting, for ell_2 subspace embeddings, despite intense study of sensitivity sampling in prior work. In this work, we show the first bounds for sensitivity sampling for ell_p subspace embeddings for pneq 2 that improve over the general mathfrak S d bound, achieving a bound of roughly mathfrak S^{2/p} for 1leq p<2 and mathfrak S^{2-2/p} for 2<p<infty. For 1leq p<2, we show that this bound is tight, in the sense that there exist matrices for which mathfrak S^{2/p} samples is necessary. Furthermore, our techniques yield further new results in the study of sampling algorithms, showing that the root leverage score sampling algorithm achieves a bound of roughly d for 1leq p<2, and that a combination of leverage score and sensitivity sampling achieves an improved bound of roughly d^{2/p}mathfrak S^{2-4/p} for 2<p<infty. Our sensitivity sampling results yield the best known sample complexity for a wide class of structured matrices that have small ell_p sensitivity.

  • 2 authors
·
Jun 1, 2023

CausaLM: Causal Model Explanation Through Counterfactual Language Models

Understanding predictions made by deep neural networks is notoriously difficult, but also crucial to their dissemination. As all machine learning based methods, they are as good as their training data, and can also capture unwanted biases. While there are tools that can help understand whether such biases exist, they do not distinguish between correlation and causation, and might be ill-suited for text-based models and for reasoning about high level language concepts. A key problem of estimating the causal effect of a concept of interest on a given model is that this estimation requires the generation of counterfactual examples, which is challenging with existing generation technology. To bridge that gap, we propose CausaLM, a framework for producing causal model explanations using counterfactual language representation models. Our approach is based on fine-tuning of deep contextualized embedding models with auxiliary adversarial tasks derived from the causal graph of the problem. Concretely, we show that by carefully choosing auxiliary adversarial pre-training tasks, language representation models such as BERT can effectively learn a counterfactual representation for a given concept of interest, and be used to estimate its true causal effect on model performance. A byproduct of our method is a language representation model that is unaffected by the tested concept, which can be useful in mitigating unwanted bias ingrained in the data.

  • 4 authors
·
May 27, 2020

Geometry-Editable and Appearance-Preserving Object Compositon

General object composition (GOC) aims to seamlessly integrate a target object into a background scene with desired geometric properties, while simultaneously preserving its fine-grained appearance details. Recent approaches derive semantic embeddings and integrate them into advanced diffusion models to enable geometry-editable generation. However, these highly compact embeddings encode only high-level semantic cues and inevitably discard fine-grained appearance details. We introduce a Disentangled Geometry-editable and Appearance-preserving Diffusion (DGAD) model that first leverages semantic embeddings to implicitly capture the desired geometric transformations and then employs a cross-attention retrieval mechanism to align fine-grained appearance features with the geometry-edited representation, facilitating both precise geometry editing and faithful appearance preservation in object composition. Specifically, DGAD builds on CLIP/DINO-derived and reference networks to extract semantic embeddings and appearance-preserving representations, which are then seamlessly integrated into the encoding and decoding pipelines in a disentangled manner. We first integrate the semantic embeddings into pre-trained diffusion models that exhibit strong spatial reasoning capabilities to implicitly capture object geometry, thereby facilitating flexible object manipulation and ensuring effective editability. Then, we design a dense cross-attention mechanism that leverages the implicitly learned object geometry to retrieve and spatially align appearance features with their corresponding regions, ensuring faithful appearance consistency. Extensive experiments on public benchmarks demonstrate the effectiveness of the proposed DGAD framework.

  • 6 authors
·
May 27 2

Dissecting CLIP: Decomposition with a Schur Complement-based Approach

The use of CLIP embeddings to assess the alignment of samples produced by text-to-image generative models has been extensively explored in the literature. While the widely adopted CLIPScore, derived from the cosine similarity of text and image embeddings, effectively measures the relevance of a generated image, it does not quantify the diversity of images generated by a text-to-image model. In this work, we extend the application of CLIP embeddings to quantify and interpret the intrinsic diversity of text-to-image models, which is responsible for generating diverse images from similar text prompts. To achieve this, we propose a decomposition of the CLIP-based kernel covariance matrix of image data into text-based and non-text-based components. Using the Schur complement of the joint image-text kernel covariance matrix, we perform this decomposition and define the matrix-based entropy of the decomposed component as the Schur Complement Entropy (SCE) score, a measure of the intrinsic diversity of a text-to-image model based on data collected with varying text prompts. Additionally, we demonstrate the use of the Schur complement-based decomposition to nullify the influence of a given prompt in the CLIP embedding of an image, enabling focus or defocus of embeddings on specific objects or properties for downstream tasks. We present several numerical results that apply our Schur complement-based approach to evaluate text-to-image models and modify CLIP image embeddings. The codebase is available at https://github.com/aziksh-ospanov/CLIP-DISSECTION

  • 3 authors
·
Dec 24, 2024

Classification of BCI-EEG based on augmented covariance matrix

Objective: Electroencephalography signals are recorded as a multidimensional dataset. We propose a new framework based on the augmented covariance extracted from an autoregressive model to improve motor imagery classification. Methods: From the autoregressive model can be derived the Yule-Walker equations, which show the emergence of a symmetric positive definite matrix: the augmented covariance matrix. The state-of the art for classifying covariance matrices is based on Riemannian Geometry. A fairly natural idea is therefore to extend the standard approach using these augmented covariance matrices. The methodology for creating the augmented covariance matrix shows a natural connection with the delay embedding theorem proposed by Takens for dynamical systems. Such an embedding method is based on the knowledge of two parameters: the delay and the embedding dimension, respectively related to the lag and the order of the autoregressive model. This approach provides new methods to compute the hyper-parameters in addition to standard grid search. Results: The augmented covariance matrix performed noticeably better than any state-of-the-art methods. We will test our approach on several datasets and several subjects using the MOABB framework, using both within-session and cross-session evaluation. Conclusion: The improvement in results is due to the fact that the augmented covariance matrix incorporates not only spatial but also temporal information, incorporating nonlinear components of the signal through an embedding procedure, which allows the leveraging of dynamical systems algorithms. Significance: These results extend the concepts and the results of the Riemannian distance based classification algorithm.

  • 2 authors
·
Feb 9, 2023

Geometry-Aware Adaptation for Pretrained Models

Machine learning models -- including prominent zero-shot models -- are often trained on datasets whose labels are only a small proportion of a larger label space. Such spaces are commonly equipped with a metric that relates the labels via distances between them. We propose a simple approach to exploit this information to adapt the trained model to reliably predict new classes -- or, in the case of zero-shot prediction, to improve its performance -- without any additional training. Our technique is a drop-in replacement of the standard prediction rule, swapping argmax with the Fr\'echet mean. We provide a comprehensive theoretical analysis for this approach, studying (i) learning-theoretic results trading off label space diameter, sample complexity, and model dimension, (ii) characterizations of the full range of scenarios in which it is possible to predict any unobserved class, and (iii) an optimal active learning-like next class selection procedure to obtain optimal training classes for when it is not possible to predict the entire range of unobserved classes. Empirically, using easily-available external metrics, our proposed approach, Loki, gains up to 29.7% relative improvement over SimCLR on ImageNet and scales to hundreds of thousands of classes. When no such metric is available, Loki can use self-derived metrics from class embeddings and obtains a 10.5% improvement on pretrained zero-shot models such as CLIP.

  • 7 authors
·
Jul 23, 2023

Predicting and generating antibiotics against future pathogens with ApexOracle

Antimicrobial resistance (AMR) is escalating and outpacing current antibiotic development. Thus, discovering antibiotics effective against emerging pathogens is becoming increasingly critical. However, existing approaches cannot rapidly identify effective molecules against novel pathogens or emerging drug-resistant strains. Here, we introduce ApexOracle, an artificial intelligence (AI) model that both predicts the antibacterial potency of existing compounds and designs de novo molecules active against strains it has never encountered. Departing from models that rely solely on molecular features, ApexOracle incorporates pathogen-specific context through the integration of molecular features captured via a foundational discrete diffusion language model and a dual-embedding framework that combines genomic- and literature-derived strain representations. Across diverse bacterial species and chemical modalities, ApexOracle consistently outperformed state-of-the-art approaches in activity prediction and demonstrated reliable transferability to novel pathogens with little or no antimicrobial data. Its unified representation-generation architecture further enables the in silico creation of "new-to-nature" molecules with high predicted efficacy against priority threats. By pairing rapid activity prediction with targeted molecular generation, ApexOracle offers a scalable strategy for countering AMR and preparing for future infectious-disease outbreaks.

  • 4 authors
·
Jul 10

$\textit{Labor Space}$: A Unifying Representation of the Labor Market via Large Language Models

The labor market is a complex ecosystem comprising diverse, interconnected entities, such as industries, occupations, skills, and firms. Due to the lack of a systematic method to map these heterogeneous entities together, each entity has been analyzed in isolation or only through pairwise relationships, inhibiting comprehensive understanding of the whole ecosystem. Here, we introduce Labor Space, a vector-space embedding of heterogeneous labor market entities, derived through applying a large language model with fine-tuning. Labor Space exposes the complex relational fabric of various labor market constituents, facilitating coherent integrative analysis of industries, occupations, skills, and firms, while retaining type-specific clustering. We demonstrate its unprecedented analytical capacities, including positioning heterogeneous entities on an economic axes, such as `Manufacturing--Healthcare'. Furthermore, by allowing vector arithmetic of these entities, Labor Space enables the exploration of complex inter-unit relations, and subsequently the estimation of the ramifications of economic shocks on individual units and their ripple effect across the labor market. We posit that Labor Space provides policymakers and business leaders with a comprehensive unifying framework for labor market analysis and simulation, fostering more nuanced and effective strategic decision-making.

  • 3 authors
·
Nov 9, 2023

BIOSCAN-5M: A Multimodal Dataset for Insect Biodiversity

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, and geographical information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at {https://github.com/zahrag/BIOSCAN-5M}

  • 13 authors
·
Jun 18, 2024

The Newspaper Navigator Dataset: Extracting And Analyzing Visual Content from 16 Million Historic Newspaper Pages in Chronicling America

Chronicling America is a product of the National Digital Newspaper Program, a partnership between the Library of Congress and the National Endowment for the Humanities to digitize historic newspapers. Over 16 million pages of historic American newspapers have been digitized for Chronicling America to date, complete with high-resolution images and machine-readable METS/ALTO OCR. Of considerable interest to Chronicling America users is a semantified corpus, complete with extracted visual content and headlines. To accomplish this, we introduce a visual content recognition model trained on bounding box annotations of photographs, illustrations, maps, comics, and editorial cartoons collected as part of the Library of Congress's Beyond Words crowdsourcing initiative and augmented with additional annotations including those of headlines and advertisements. We describe our pipeline that utilizes this deep learning model to extract 7 classes of visual content: headlines, photographs, illustrations, maps, comics, editorial cartoons, and advertisements, complete with textual content such as captions derived from the METS/ALTO OCR, as well as image embeddings for fast image similarity querying. We report the results of running the pipeline on 16.3 million pages from the Chronicling America corpus and describe the resulting Newspaper Navigator dataset, the largest dataset of extracted visual content from historic newspapers ever produced. The Newspaper Navigator dataset, finetuned visual content recognition model, and all source code are placed in the public domain for unrestricted re-use.

  • 9 authors
·
May 4, 2020

LLMs are Also Effective Embedding Models: An In-depth Overview

Large language models (LLMs) have revolutionized natural language processing by achieving state-of-the-art performance across various tasks. Recently, their effectiveness as embedding models has gained attention, marking a paradigm shift from traditional encoder-only models like ELMo and BERT to decoder-only, large-scale LLMs such as GPT, LLaMA, and Mistral. This survey provides an in-depth overview of this transition, beginning with foundational techniques before the LLM era, followed by LLM-based embedding models through two main strategies to derive embeddings from LLMs. 1) Direct prompting: We mainly discuss the prompt designs and the underlying rationale for deriving competitive embeddings. 2) Data-centric tuning: We cover extensive aspects that affect tuning an embedding model, including model architecture, training objectives, data constructions, etc. Upon the above, we also cover advanced methods, such as handling longer texts, and multilingual and cross-modal data. Furthermore, we discuss factors affecting choices of embedding models, such as performance/efficiency comparisons, dense vs sparse embeddings, pooling strategies, and scaling law. Lastly, the survey highlights the limitations and challenges in adapting LLMs for embeddings, including cross-task embedding quality, trade-offs between efficiency and accuracy, low-resource, long-context, data bias, robustness, etc. This survey serves as a valuable resource for researchers and practitioners by synthesizing current advancements, highlighting key challenges, and offering a comprehensive framework for future work aimed at enhancing the effectiveness and efficiency of LLMs as embedding models.

  • 7 authors
·
Dec 17, 2024

COKE: Causal Discovery with Chronological Order and Expert Knowledge in High Proportion of Missing Manufacturing Data

Understanding causal relationships between machines is crucial for fault diagnosis and optimization in manufacturing processes. Real-world datasets frequently exhibit up to 90% missing data and high dimensionality from hundreds of sensors. These datasets also include domain-specific expert knowledge and chronological order information, reflecting the recording order across different machines, which is pivotal for discerning causal relationships within the manufacturing data. However, previous methods for handling missing data in scenarios akin to real-world conditions have not been able to effectively utilize expert knowledge. Conversely, prior methods that can incorporate expert knowledge struggle with datasets that exhibit missing values. Therefore, we propose COKE to construct causal graphs in manufacturing datasets by leveraging expert knowledge and chronological order among sensors without imputing missing data. Utilizing the characteristics of the recipe, we maximize the use of samples with missing values, derive embeddings from intersections with an initial graph that incorporates expert knowledge and chronological order, and create a sensor ordering graph. The graph-generating process has been optimized by an actor-critic architecture to obtain a final graph that has a maximum reward. Experimental evaluations in diverse settings of sensor quantities and missing proportions demonstrate that our approach compared with the benchmark methods shows an average improvement of 39.9% in the F1-score. Moreover, the F1-score improvement can reach 62.6% when considering the configuration similar to real-world datasets, and 85.0% in real-world semiconductor datasets. The source code is available at https://github.com/OuTingYun/COKE.

  • 3 authors
·
Jul 16, 2024

Unsupervised Matching of Data and Text

Entity resolution is a widely studied problem with several proposals to match records across relations. Matching textual content is a widespread task in many applications, such as question answering and search. While recent methods achieve promising results for these two tasks, there is no clear solution for the more general problem of matching textual content and structured data. We introduce a framework that supports this new task in an unsupervised setting for any pair of corpora, being relational tables or text documents. Our method builds a fine-grained graph over the content of the corpora and derives word embeddings to represent the objects to match in a low dimensional space. The learned representation enables effective and efficient matching at different granularity, from relational tuples to text sentences and paragraphs. Our flexible framework can exploit pre-trained resources, but it does not depends on their existence and achieves better quality performance in matching content when the vocabulary is domain specific. We also introduce optimizations in the graph creation process with an "expand and compress" approach that first identifies new valid relationships across elements, to improve matching, and then prunes nodes and edges, to reduce the graph size. Experiments on real use cases and public datasets show that our framework produces embeddings that outperform word embeddings and fine-tuned language models both in results' quality and in execution times.

  • 3 authors
·
Dec 16, 2021

Generating Drug Repurposing Hypotheses through the Combination of Disease-Specific Hypergraphs

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

  • 5 authors
·
Nov 16, 2023