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Jun 23

Encode-Store-Retrieve: Augmenting Human Memory through Language-Encoded Egocentric Perception

We depend on our own memory to encode, store, and retrieve our experiences. However, memory lapses can occur. One promising avenue for achieving memory augmentation is through the use of augmented reality head-mounted displays to capture and preserve egocentric videos, a practice commonly referred to as lifelogging. However, a significant challenge arises from the sheer volume of video data generated through lifelogging, as the current technology lacks the capability to encode and store such large amounts of data efficiently. Further, retrieving specific information from extensive video archives requires substantial computational power, further complicating the task of quickly accessing desired content. To address these challenges, we propose a memory augmentation agent that involves leveraging natural language encoding for video data and storing them in a vector database. This approach harnesses the power of large vision language models to perform the language encoding process. Additionally, we propose using large language models to facilitate natural language querying. Our agent underwent extensive evaluation using the QA-Ego4D dataset and achieved state-of-the-art results with a BLEU score of 8.3, outperforming conventional machine learning models that scored between 3.4 and 5.8. Additionally, we conducted a user study in which participants interacted with the human memory augmentation agent through episodic memory and open-ended questions. The results of this study show that the agent results in significantly better recall performance on episodic memory tasks compared to human participants. The results also highlight the agent's practical applicability and user acceptance.

  • 3 authors
·
Oct 17, 2024

BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

  • 7 authors
·
Aug 18, 2023

StructTransform: A Scalable Attack Surface for Safety-Aligned Large Language Models

In this work, we present a series of structure transformation attacks on LLM alignment, where we encode natural language intent using diverse syntax spaces, ranging from simple structure formats and basic query languages (e.g., SQL) to new novel spaces and syntaxes created entirely by LLMs. Our extensive evaluation shows that our simplest attacks can achieve close to a 90% success rate, even on strict LLMs (such as Claude 3.5 Sonnet) using SOTA alignment mechanisms. We improve the attack performance further by using an adaptive scheme that combines structure transformations along with existing content transformations, resulting in over 96% ASR with 0% refusals. To generalize our attacks, we explore numerous structure formats, including syntaxes purely generated by LLMs. Our results indicate that such novel syntaxes are easy to generate and result in a high ASR, suggesting that defending against our attacks is not a straightforward process. Finally, we develop a benchmark and evaluate existing safety-alignment defenses against it, showing that most of them fail with 100% ASR. Our results show that existing safety alignment mostly relies on token-level patterns without recognizing harmful concepts, highlighting and motivating the need for serious research efforts in this direction. As a case study, we demonstrate how attackers can use our attack to easily generate a sample malware and a corpus of fraudulent SMS messages, which perform well in bypassing detection.

  • 5 authors
·
Jul 2, 2025

CodeAttack: Revealing Safety Generalization Challenges of Large Language Models via Code Completion

The rapid advancement of Large Language Models (LLMs) has brought about remarkable generative capabilities but also raised concerns about their potential misuse. While strategies like supervised fine-tuning and reinforcement learning from human feedback have enhanced their safety, these methods primarily focus on natural languages, which may not generalize to other domains. This paper introduces CodeAttack, a framework that transforms natural language inputs into code inputs, presenting a novel environment for testing the safety generalization of LLMs. Our comprehensive studies on state-of-the-art LLMs including GPT-4, Claude-2, and Llama-2 series reveal a new and universal safety vulnerability of these models against code input: CodeAttack bypasses the safety guardrails of all models more than 80\% of the time. We find that a larger distribution gap between CodeAttack and natural language leads to weaker safety generalization, such as encoding natural language input with data structures. Furthermore, we give our hypotheses about the success of CodeAttack: the misaligned bias acquired by LLMs during code training, prioritizing code completion over avoiding the potential safety risk. Finally, we analyze potential mitigation measures. These findings highlight new safety risks in the code domain and the need for more robust safety alignment algorithms to match the code capabilities of LLMs.

  • 7 authors
·
Mar 12, 2024

E2S2: Encoding-Enhanced Sequence-to-Sequence Pretraining for Language Understanding and Generation

Sequence-to-sequence (seq2seq) learning is a popular fashion for large-scale pretraining language models. However, the prior seq2seq pretraining models generally focus on reconstructive objectives on the decoder side and neglect the effect of encoder-side supervision, which we argue may lead to sub-optimal performance. To verify our hypothesis, we first empirically study the functionalities of the encoder and decoder in seq2seq pretrained language models, and find that the encoder takes an important but under-exploitation role than the decoder regarding the downstream performance and neuron activation. Therefore, we propose an encoding-enhanced seq2seq pretraining strategy, namely E2S2, which improves the seq2seq models via integrating more efficient self-supervised information into the encoders. Specifically, E2S2 adopts two self-supervised objectives on the encoder side from two aspects: 1) locally denoising the corrupted sentence (denoising objective); and 2) globally learning better sentence representations (contrastive objective). With the help of both objectives, the encoder can effectively distinguish the noise tokens and capture high-level (i.e. syntactic and semantic) knowledge, thus strengthening the ability of seq2seq model to accurately achieve the conditional generation. On a large diversity of downstream natural language understanding and generation tasks, E2S2 dominantly improves the performance of its powerful backbone models, e.g. BART and T5. For example, upon BART backbone, we achieve +1.1% averaged gain on the general language understanding evaluation (GLUE) benchmark and +1.75% F_0.5 score improvement on CoNLL2014 dataset. We also provide in-depth analyses to show the improvement stems from better linguistic representation. We hope that our work will foster future self-supervision research on seq2seq language model pretraining.

  • 5 authors
·
May 30, 2022

Foundations for Near-Term Quantum Natural Language Processing

We provide conceptual and mathematical foundations for near-term quantum natural language processing (QNLP), and do so in quantum computer scientist friendly terms. We opted for an expository presentation style, and provide references for supporting empirical evidence and formal statements concerning mathematical generality. We recall how the quantum model for natural language that we employ canonically combines linguistic meanings with rich linguistic structure, most notably grammar. In particular, the fact that it takes a quantum-like model to combine meaning and structure, establishes QNLP as quantum-native, on par with simulation of quantum systems. Moreover, the now leading Noisy Intermediate-Scale Quantum (NISQ) paradigm for encoding classical data on quantum hardware, variational quantum circuits, makes NISQ exceptionally QNLP-friendly: linguistic structure can be encoded as a free lunch, in contrast to the apparently exponentially expensive classical encoding of grammar. Quantum speed-up for QNLP tasks has already been established in previous work with Will Zeng. Here we provide a broader range of tasks which all enjoy the same advantage. Diagrammatic reasoning is at the heart of QNLP. Firstly, the quantum model interprets language as quantum processes via the diagrammatic formalism of categorical quantum mechanics. Secondly, these diagrams are via ZX-calculus translated into quantum circuits. Parameterisations of meanings then become the circuit variables to be learned. Our encoding of linguistic structure within quantum circuits also embodies a novel approach for establishing word-meanings that goes beyond the current standards in mainstream AI, by placing linguistic structure at the heart of Wittgenstein's meaning-is-context.

  • 4 authors
·
Dec 7, 2020

RCMHA: Relative Convolutional Multi-Head Attention for Natural Language Modelling

The Attention module finds common usage in language modeling, presenting distinct challenges within the broader scope of Natural Language Processing. Multi-Head Attention (MHA) employs an absolute positional encoding, which imposes limitations on token length and entails substantial memory consumption during the processing of embedded inputs. The current remedy proposed by researchers involves the utilization of relative positional encoding, similar to the approach adopted in Transformer-XL or Relative Multi-Head Attention (RMHA), albeit the employed architecture consumes considerable memory resources. To address these challenges, this study endeavors to refine MHA, leveraging relative positional encoding in conjunction with the Depth-Wise Convolutional Layer architecture, which promises heightened accuracy coupled with minimized memory usage. The proposed RCMHA framework entails the modification of two integral components: firstly, the application of the Depth-Wise Convolutional Layer to the input embedding, encompassing Query, Key, and Value parameters; secondly, the incorporation of Relative Positional Encoding into the attention scoring phase, harmoniously integrated with Scaled Dot-Product Attention. Empirical experiments underscore the advantages of RCMHA, wherein it exhibits superior accuracy, boasting a score of 0.572 in comparison to alternative attention modules such as MHA, Multi-DConv-Head Attention (MDHA), and RMHA. Concerning memory utilization, RMHA emerges as the most frugal, demonstrating an average consumption of 2.98 GB, surpassing RMHA which necessitates 3.5 GB.

  • 3 authors
·
Aug 7, 2023

DKPLM: Decomposable Knowledge-enhanced Pre-trained Language Model for Natural Language Understanding

Knowledge-Enhanced Pre-trained Language Models (KEPLMs) are pre-trained models with relation triples injecting from knowledge graphs to improve language understanding abilities. To guarantee effective knowledge injection, previous studies integrate models with knowledge encoders for representing knowledge retrieved from knowledge graphs. The operations for knowledge retrieval and encoding bring significant computational burdens, restricting the usage of such models in real-world applications that require high inference speed. In this paper, we propose a novel KEPLM named DKPLM that Decomposes Knowledge injection process of the Pre-trained Language Models in pre-training, fine-tuning and inference stages, which facilitates the applications of KEPLMs in real-world scenarios. Specifically, we first detect knowledge-aware long-tail entities as the target for knowledge injection, enhancing the KEPLMs' semantic understanding abilities and avoiding injecting redundant information. The embeddings of long-tail entities are replaced by "pseudo token representations" formed by relevant knowledge triples. We further design the relational knowledge decoding task for pre-training to force the models to truly understand the injected knowledge by relation triple reconstruction. Experiments show that our model outperforms other KEPLMs significantly over zero-shot knowledge probing tasks and multiple knowledge-aware language understanding tasks. We further show that DKPLM has a higher inference speed than other competing models due to the decomposing mechanism.

  • 7 authors
·
Dec 2, 2021

ChartGPT: Leveraging LLMs to Generate Charts from Abstract Natural Language

The use of natural language interfaces (NLIs) for the creation of charts is becoming increasingly popular due to the intuitiveness of natural language interactions. One key challenge in this approach is to accurately capture user intents and transform them to proper chart specifications. This obstructs the wide use of NLI in chart generation, as users' natural language inputs are generally abstract (i.e., ambiguous or under-specified), without a clear specification of visual encodings. Recently, pre-trained large language models (LLMs) have exhibited superior performance in understanding and generating natural language, demonstrating great potential for downstream tasks. Inspired by this major trend, we propose ChartGPT, generating charts from abstract natural language inputs. However, LLMs are struggling to address complex logic problems. To enable the model to accurately specify the complex parameters and perform operations in chart generation, we decompose the generation process into a step-by-step reasoning pipeline, so that the model only needs to reason a single and specific sub-task during each run. Moreover, LLMs are pre-trained on general datasets, which might be biased for the task of chart generation. To provide adequate visualization knowledge, we create a dataset consisting of abstract utterances and charts and improve model performance through fine-tuning. We further design an interactive interface for ChartGPT that allows users to check and modify the intermediate outputs of each step. The effectiveness of the proposed system is evaluated through quantitative evaluations and a user study.

  • 7 authors
·
Nov 3, 2023

A Benchmark Dataset for Multimodal Prediction of Enzymatic Function Coupling DNA Sequences and Natural Language

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

  • 6 authors
·
Jul 21, 2024

DeWave: Discrete EEG Waves Encoding for Brain Dynamics to Text Translation

The translation of brain dynamics into natural language is pivotal for brain-computer interfaces (BCIs). With the swift advancement of large language models, such as ChatGPT, the need to bridge the gap between the brain and languages becomes increasingly pressing. Current methods, however, require eye-tracking fixations or event markers to segment brain dynamics into word-level features, which can restrict the practical application of these systems. To tackle these issues, we introduce a novel framework, DeWave, that integrates discrete encoding sequences into open-vocabulary EEG-to-text translation tasks. DeWave uses a quantized variational encoder to derive discrete codex encoding and align it with pre-trained language models. This discrete codex representation brings forth two advantages: 1) it realizes translation on raw waves without marker by introducing text-EEG contrastive alignment training, and 2) it alleviates the interference caused by individual differences in EEG waves through an invariant discrete codex with or without markers. Our model surpasses the previous baseline (40.1 and 31.7) by 3.06% and 6.34%, respectively, achieving 41.35 BLEU-1 and 33.71 Rouge-F on the ZuCo Dataset. This work is the first to facilitate the translation of entire EEG signal periods without word-level order markers (e.g., eye fixations), scoring 20.5 BLEU-1 and 29.5 Rouge-1 on the ZuCo Dataset.

  • 5 authors
·
Sep 25, 2023

Zonkey: A Hierarchical Diffusion Language Model with Differentiable Tokenization and Probabilistic Attention

Large language models (LLMs) have revolutionized natural language processing, yet they remain constrained by fixed, non-differentiable tokenizers like Byte Pair Encoding (BPE), which hinder end-to-end optimization and adaptability to noisy or domain-specific data. We introduce Zonkey, a hierarchical diffusion model that addresses these limitations through a fully trainable pipeline from raw characters to document-level representations. At its core is a differentiable tokenizer (Segment Splitter) that learns probabilistic beginning-of-sequence (BOS) decisions, enabling adaptive splits that emerge as linguistically meaningful (e.g., word boundaries at spaces, sentence starts at periods) without explicit supervision. This differentiability is enabled by our novel Probabilistic Attention mechanism, which incorporates position-specific existence probabilities to simulate soft masking over theoretically infinite sequences while preserving gradients. Sequences decay probabilistically rather than relying on end-of-sequence tokens, supporting variable-length outputs. Hierarchical levels compress sequences into higher abstractions (e.g., character n-grams to word-like vectors, then sentence-like), with reconstruction via our Denoising Diffusion Mixed Model (DDMM) for stable and efficient denoising in latent space. A Stitcher ensures overlap invariance across segments. Trained end-to-end on Wikipedia, Zonkey generates coherent, variable-length text from noise, demonstrating emergent hierarchies and promising qualitative alignment to data distributions compared to entropy-based learnable tokenizers. Our approach advances toward fully gradient-based LLMs, with potential for better domain adaptation and scalable generation. We release the source code for training and reproducing our experiments.

  • 1 authors
·
Jan 29

ResidualViT for Efficient Temporally Dense Video Encoding

Several video understanding tasks, such as natural language temporal video grounding, temporal activity localization, and audio description generation, require "temporally dense" reasoning over frames sampled at high temporal resolution. However, computing frame-level features for these tasks is computationally expensive given the temporal resolution requirements. In this paper, we make three contributions to reduce the cost of computing features for temporally dense tasks. First, we introduce a vision transformer (ViT) architecture, dubbed ResidualViT, that leverages the large temporal redundancy in videos to efficiently compute temporally dense frame-level features. Our architecture incorporates (i) learnable residual connections that ensure temporal consistency across consecutive frames and (ii) a token reduction module that enhances processing speed by selectively discarding temporally redundant information while reusing weights of a pretrained foundation model. Second, we propose a lightweight distillation strategy to approximate the frame-level features of the original foundation model. Finally, we evaluate our approach across four tasks and five datasets, in both zero-shot and fully supervised settings, demonstrating significant reductions in computational cost (up to 60%) and improvements in inference speed (up to 2.5x faster), all while closely approximating the accuracy of the original foundation model.

  • 5 authors
·
Sep 16, 2025

Verbalized Machine Learning: Revisiting Machine Learning with Language Models

Motivated by the large progress made by large language models (LLMs), we introduce the framework of verbalized machine learning (VML). In contrast to conventional machine learning models that are typically optimized over a continuous parameter space, VML constrains the parameter space to be human-interpretable natural language. Such a constraint leads to a new perspective of function approximation, where an LLM with a text prompt can be viewed as a function parameterized by the text prompt. Guided by this perspective, we revisit classical machine learning problems, such as regression and classification, and find that these problems can be solved by an LLM-parameterized learner and optimizer. The major advantages of VML include (1) easy encoding of inductive bias: prior knowledge about the problem and hypothesis class can be encoded in natural language and fed into the LLM-parameterized learner; (2) automatic model class selection: the optimizer can automatically select a concrete model class based on data and verbalized prior knowledge, and it can update the model class during training; and (3) interpretable learner updates: the LLM-parameterized optimizer can provide explanations for why each learner update is performed. We conduct several studies to empirically evaluate the effectiveness of VML, and hope that VML can serve as a stepping stone to stronger interpretability and trustworthiness in ML.

  • 4 authors
·
Jun 6, 2024

Large Language Models on Graphs: A Comprehensive Survey

Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data are associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data are paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graph scenarios (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-rich graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we mention the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

ERNIE 3.0: Large-scale Knowledge Enhanced Pre-training for Language Understanding and Generation

Pre-trained models have achieved state-of-the-art results in various Natural Language Processing (NLP) tasks. Recent works such as T5 and GPT-3 have shown that scaling up pre-trained language models can improve their generalization abilities. Particularly, the GPT-3 model with 175 billion parameters shows its strong task-agnostic zero-shot/few-shot learning capabilities. Despite their success, these large-scale models are trained on plain texts without introducing knowledge such as linguistic knowledge and world knowledge. In addition, most large-scale models are trained in an auto-regressive way. As a result, this kind of traditional fine-tuning approach demonstrates relatively weak performance when solving downstream language understanding tasks. In order to solve the above problems, we propose a unified framework named ERNIE 3.0 for pre-training large-scale knowledge enhanced models. It fuses auto-regressive network and auto-encoding network, so that the trained model can be easily tailored for both natural language understanding and generation tasks with zero-shot learning, few-shot learning or fine-tuning. We trained the model with 10 billion parameters on a 4TB corpus consisting of plain texts and a large-scale knowledge graph. Empirical results show that the model outperforms the state-of-the-art models on 54 Chinese NLP tasks, and its English version achieves the first place on the SuperGLUE benchmark (July 3, 2021), surpassing the human performance by +0.8% (90.6% vs. 89.8%).

  • 22 authors
·
Jul 5, 2021

Are Large Vision Language Models up to the Challenge of Chart Comprehension and Reasoning? An Extensive Investigation into the Capabilities and Limitations of LVLMs

Natural language is a powerful complementary modality of communication for data visualizations, such as bar and line charts. To facilitate chart-based reasoning using natural language, various downstream tasks have been introduced recently such as chart question answering, chart summarization, and fact-checking with charts. These tasks pose a unique challenge, demanding both vision-language reasoning and a nuanced understanding of chart data tables, visual encodings, and natural language prompts. Despite the recent success of Large Language Models (LLMs) across diverse NLP tasks, their abilities and limitations in the realm of data visualization remain under-explored, possibly due to their lack of multi-modal capabilities. To bridge the gap, this paper presents the first comprehensive evaluation of the recently developed large vision language models (LVLMs) for chart understanding and reasoning tasks. Our evaluation includes a comprehensive assessment of LVLMs, including GPT-4V and Gemini, across four major chart reasoning tasks. Furthermore, we perform a qualitative evaluation of LVLMs' performance on a diverse range of charts, aiming to provide a thorough analysis of their strengths and weaknesses. Our findings reveal that LVLMs demonstrate impressive abilities in generating fluent texts covering high-level data insights while also encountering common problems like hallucinations, factual errors, and data bias. We highlight the key strengths and limitations of chart comprehension tasks, offering insights for future research.

  • 6 authors
·
May 31, 2024

Aligned with LLM: a new multi-modal training paradigm for encoding fMRI activity in visual cortex

Recently, there has been a surge in the popularity of pre trained large language models (LLMs) (such as GPT-4), sweeping across the entire Natural Language Processing (NLP) and Computer Vision (CV) communities. These LLMs have demonstrated advanced multi-modal understanding capabilities and showcased strong performance across various benchmarks. The LLM has started to embody traits of artificial general intelligence, which holds vital guidance for enhancing brain-like characteristics within visual encoding models. Hence, This paper proposes a new multi-modal training paradigm, aligning with LLM, for encoding fMRI activity in visual cortex. Based on this paradigm, we trained an encoding model in fMRI data named the LLM-Visual Encoding Model (LLM-VEM). Specifically, we utilize LLM (miniGPT4) to generate descriptive text for all stimulus images, forming a high-quality textual description set. Moreover, we use the pre-trained text encoder (CLIP) to process these detailed descriptions, obtaining the text embedding features. Next, we use the contrast loss function to minimize the distance between the image embedding features and the text embedding features to complete the alignment operation of the stimulus image and text information. With the assistance of the pre-trained LLM, this alignment process facilitates better learning of the visual encoding model, resulting in higher precision. The final experimental results indicate that our training paradigm has significantly aided in enhancing the performance of the visual encoding model.

  • 4 authors
·
Jan 8, 2024

Navigating Chemical-Linguistic Sharing Space with Heterogeneous Molecular Encoding

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+37.8\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

  • 8 authors
·
Dec 30, 2024

G2PTL: A Pre-trained Model for Delivery Address and its Applications in Logistics System

Text-based delivery addresses, as the data foundation for logistics systems, contain abundant and crucial location information. How to effectively encode the delivery address is a core task to boost the performance of downstream tasks in the logistics system. Pre-trained Models (PTMs) designed for Natural Language Process (NLP) have emerged as the dominant tools for encoding semantic information in text. Though promising, those NLP-based PTMs fall short of encoding geographic knowledge in the delivery address, which considerably trims down the performance of delivery-related tasks in logistic systems such as Cainiao. To tackle the above problem, we propose a domain-specific pre-trained model, named G2PTL, a Geography-Graph Pre-trained model for delivery address in Logistics field. G2PTL combines the semantic learning capabilities of text pre-training with the geographical-relationship encoding abilities of graph modeling. Specifically, we first utilize real-world logistics delivery data to construct a large-scale heterogeneous graph of delivery addresses, which contains abundant geographic knowledge and delivery information. Then, G2PTL is pre-trained with subgraphs sampled from the heterogeneous graph. Comprehensive experiments are conducted to demonstrate the effectiveness of G2PTL through four downstream tasks in logistics systems on real-world datasets. G2PTL has been deployed in production in Cainiao's logistics system, which significantly improves the performance of delivery-related tasks.

  • 8 authors
·
Apr 4, 2023

GUS-Net: Social Bias Classification in Text with Generalizations, Unfairness, and Stereotypes

The detection of bias in natural language processing (NLP) is a critical challenge, particularly with the increasing use of large language models (LLMs) in various domains. This paper introduces GUS-Net, an innovative approach to bias detection that focuses on three key types of biases: (G)eneralizations, (U)nfairness, and (S)tereotypes. GUS-Net leverages generative AI and automated agents to create a comprehensive synthetic dataset, enabling robust multi-label token classification. Our methodology enhances traditional bias detection methods by incorporating the contextual encodings of pre-trained models, resulting in improved accuracy and depth in identifying biased entities. Through extensive experiments, we demonstrate that GUS-Net outperforms state-of-the-art techniques, achieving superior performance in terms of accuracy, F1-score, and Hamming Loss. The findings highlight GUS-Net's effectiveness in capturing a wide range of biases across diverse contexts, making it a valuable tool for social bias detection in text. This study contributes to the ongoing efforts in NLP to address implicit bias, providing a pathway for future research and applications in various fields. The Jupyter notebooks used to create the dataset and model are available at: https://github.com/Ethical-Spectacle/fair-ly/tree/main/resources. Warning: This paper contains examples of harmful language, and reader discretion is recommended.

  • 5 authors
·
Oct 10, 2024

Let Models Speak Ciphers: Multiagent Debate through Embeddings

Discussion and debate among Large Language Models (LLMs) have gained considerable attention due to their potential to enhance the reasoning ability of LLMs. Although natural language is an obvious choice for communication due to LLM's language understanding capability, the token sampling step needed when generating natural language poses a potential risk of information loss, as it uses only one token to represent the model's belief across the entire vocabulary. In this paper, we introduce a communication regime named CIPHER (Communicative Inter-Model Protocol Through Embedding Representation) to address this issue. Specifically, we remove the token sampling step from LLMs and let them communicate their beliefs across the vocabulary through the expectation of the raw transformer output embeddings. Remarkably, by deviating from natural language, CIPHER offers an advantage of encoding a broader spectrum of information without any modification to the model weights, outperforming the state-of-the-art LLM debate methods using natural language by 0.5-5.0% across five reasoning tasks and multiple open-source LLMs of varying sizes. This showcases the superiority and robustness of embeddings as an alternative "language" for communication among LLMs. We anticipate that CIPHER will inspire further exploration for the design of interactions within LLM agent systems, offering a new direction that could significantly influence future developments in the field.

  • 9 authors
·
Oct 9, 2023

FocalLens: Instruction Tuning Enables Zero-Shot Conditional Image Representations

Visual understanding is inherently contextual -- what we focus on in an image depends on the task at hand. For instance, given an image of a person holding a bouquet of flowers, we may focus on either the person such as their clothing, or the type of flowers, depending on the context of interest. Yet, most existing image encoding paradigms represent an image as a fixed, generic feature vector, overlooking the potential needs of prioritizing varying visual information for different downstream use cases. In this work, we introduce FocalLens, a conditional visual encoding method that produces different representations for the same image based on the context of interest, expressed flexibly through natural language. We leverage vision instruction tuning data and contrastively finetune a pretrained vision encoder to take natural language instructions as additional inputs for producing conditional image representations. Extensive experiments validate that conditional image representation from FocalLens better pronounce the visual features of interest compared to generic features produced by standard vision encoders like CLIP. In addition, we show FocalLens further leads to performance improvements on a range of downstream tasks including image-image retrieval, image classification, and image-text retrieval, with an average gain of 5 and 10 points on the challenging SugarCrepe and MMVP-VLM benchmarks, respectively.

  • 8 authors
·
Apr 11, 2025

CellCLIP -- Learning Perturbation Effects in Cell Painting via Text-Guided Contrastive Learning

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

  • 4 authors
·
May 16, 2025

MatterGPT: A Generative Transformer for Multi-Property Inverse Design of Solid-State Materials

Inverse design of solid-state materials with desired properties represents a formidable challenge in materials science. Although recent generative models have demonstrated potential, their adoption has been hindered by limitations such as inefficiency, architectural constraints and restricted open-source availability. The representation of crystal structures using the SLICES (Simplified Line-Input Crystal-Encoding System) notation as a string of characters enables the use of state-of-the-art natural language processing models, such as Transformers, for crystal design. Drawing inspiration from the success of GPT models in generating coherent text, we trained a generative Transformer on the next-token prediction task to generate solid-state materials with targeted properties. We demonstrate MatterGPT's capability to generate de novo crystal structures with targeted single properties, including both lattice-insensitive (formation energy) and lattice-sensitive (band gap) properties. Furthermore, we extend MatterGPT to simultaneously target multiple properties, addressing the complex challenge of multi-objective inverse design of crystals. Our approach showcases high validity, uniqueness, and novelty in generated structures, as well as the ability to generate materials with properties beyond the training data distribution. This work represents a significant step forward in computational materials discovery, offering a powerful and open tool for designing materials with tailored properties for various applications in energy, electronics, and beyond.

  • 8 authors
·
Aug 14, 2024

VoxCPM2 Technical Report

We present VoxCPM2, a https://info.arxiv.org/help/prep#abstractsfully open-source multilingual and controllable speech generation foundation model that extends the hierarchical diffusion-autoregressive modeling paradigm of VoxCPM. VoxCPM2 advances the framework in three key dimensions: (i) capability, by unifying 30 languages, 9 Chinese dialects, natural-language voice design, style-controllable voice cloning, and high-fidelity continuation cloning within a single backbone; (ii) quality, through an asymmetric AudioVAE that encodes at 16 kHz and reconstructs at 48 kHz, enabling implicit super-resolution with high encoding efficiency; and (iii) scale, by jointly scaling the model to 2B parameters and the training data to over 2 million hours of multilingual speech. To support these diverse capabilities within one model, we introduce a unified sequence organization that expresses all generation modes through different arrangements of the same input building blocks, allowing joint training under a single set of parameters and objective. VoxCPM2 achieves state-of-the-art or competitive performance on public zero-shot and instruction-following TTS benchmarks. On our internal 30-language evaluation set, it attains an average WER of 1.68%. These results demonstrate that hierarchical continuous-latent modeling, without relying on any external discrete speech tokenizer, offers a viable and powerful foundation for large-scale multilingual and controllable speech generation. The model weights, fine-tuning code, and inference tools are publicly released under the Apache 2.0 license to foster community research and development.

  • 18 authors
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Jun 4

From Flat to Hierarchical: Extracting Sparse Representations with Matching Pursuit

Motivated by the hypothesis that neural network representations encode abstract, interpretable features as linearly accessible, approximately orthogonal directions, sparse autoencoders (SAEs) have become a popular tool in interpretability. However, recent work has demonstrated phenomenology of model representations that lies outside the scope of this hypothesis, showing signatures of hierarchical, nonlinear, and multi-dimensional features. This raises the question: do SAEs represent features that possess structure at odds with their motivating hypothesis? If not, does avoiding this mismatch help identify said features and gain further insights into neural network representations? To answer these questions, we take a construction-based approach and re-contextualize the popular matching pursuits (MP) algorithm from sparse coding to design MP-SAE -- an SAE that unrolls its encoder into a sequence of residual-guided steps, allowing it to capture hierarchical and nonlinearly accessible features. Comparing this architecture with existing SAEs on a mixture of synthetic and natural data settings, we show: (i) hierarchical concepts induce conditionally orthogonal features, which existing SAEs are unable to faithfully capture, and (ii) the nonlinear encoding step of MP-SAE recovers highly meaningful features, helping us unravel shared structure in the seemingly dichotomous representation spaces of different modalities in a vision-language model, hence demonstrating the assumption that useful features are solely linearly accessible is insufficient. We also show that the sequential encoder principle of MP-SAE affords an additional benefit of adaptive sparsity at inference time, which may be of independent interest. Overall, we argue our results provide credence to the idea that interpretability should begin with the phenomenology of representations, with methods emerging from assumptions that fit it.

  • 5 authors
·
Jun 3, 2025

Do not copy and paste! Rewriting strategies for code retrieval

Embedding-based code retrieval often suffers when encoders overfit to surface syntax. Prior work mitigates this by using LLMs to rephrase queries and corpora into a normalized style, but leaves two questions open: how much representational shift helps, and when is the per-query LLM call justified? We study a hierarchy of three rewriting strategies: stylistic rephrasing, NL-enriched PseudoCode, and full Natural-Language transcription, under joint query-corpus (QC, online) and corpus-only (C, offline) augmentation, across six CoIR benchmarks, five encoders, and three rewriters spanning independent model families (Qwen, DeepSeek, Mistral). We are the first to evaluate NL-enriched PseudoCode and snippet-level Natural Language as direct retrieval representations, rather than as transient intermediates. Full NL rewriting with QC yields the largest gains (+0.51 absolute NDCG@10 on CT-Contest for MoSE-18), while corpus-only rewriting degrades retrieval in 56 of 90 configurations, about 62%. We introduce two diagnostics, Delta H, token entropy, and Delta s, embedding cosine, and show that Delta H predicts retrieval gain under QC across all three rewriter families: pooled Spearman rho = +0.436, p < 0.001 on DeepSeek+Codestral; rho = +0.593 on Codestral alone; rho = +0.356 on Qwen. This establishes Delta H as a cheap, rewriter-agnostic proxy for deciding when rewriting pays off before running retrieval. Our analysis reframes LLM rewriting as a cost-benefit decision: it is most effective as a remediation layer for lightweight encoders on code-dominant queries, with diminishing returns for strong encoders or NL-heavy queries.

  • 3 authors
·
May 7 1

From Word Vectors to Multimodal Embeddings: Techniques, Applications, and Future Directions For Large Language Models

Word embeddings and language models have transformed natural language processing (NLP) by facilitating the representation of linguistic elements in continuous vector spaces. This review visits foundational concepts such as the distributional hypothesis and contextual similarity, tracing the evolution from sparse representations like one-hot encoding to dense embeddings including Word2Vec, GloVe, and fastText. We examine both static and contextualized embeddings, underscoring advancements in models such as ELMo, BERT, and GPT and their adaptations for cross-lingual and personalized applications. The discussion extends to sentence and document embeddings, covering aggregation methods and generative topic models, along with the application of embeddings in multimodal domains, including vision, robotics, and cognitive science. Advanced topics such as model compression, interpretability, numerical encoding, and bias mitigation are analyzed, addressing both technical challenges and ethical implications. Additionally, we identify future research directions, emphasizing the need for scalable training techniques, enhanced interpretability, and robust grounding in non-textual modalities. By synthesizing current methodologies and emerging trends, this survey offers researchers and practitioners an in-depth resource to push the boundaries of embedding-based language models.

  • 15 authors
·
Nov 6, 2024

AST-Probe: Recovering abstract syntax trees from hidden representations of pre-trained language models

The objective of pre-trained language models is to learn contextual representations of textual data. Pre-trained language models have become mainstream in natural language processing and code modeling. Using probes, a technique to study the linguistic properties of hidden vector spaces, previous works have shown that these pre-trained language models encode simple linguistic properties in their hidden representations. However, none of the previous work assessed whether these models encode the whole grammatical structure of a programming language. In this paper, we prove the existence of a syntactic subspace, lying in the hidden representations of pre-trained language models, which contain the syntactic information of the programming language. We show that this subspace can be extracted from the models' representations and define a novel probing method, the AST-Probe, that enables recovering the whole abstract syntax tree (AST) of an input code snippet. In our experimentations, we show that this syntactic subspace exists in five state-of-the-art pre-trained language models. In addition, we highlight that the middle layers of the models are the ones that encode most of the AST information. Finally, we estimate the optimal size of this syntactic subspace and show that its dimension is substantially lower than those of the models' representation spaces. This suggests that pre-trained language models use a small part of their representation spaces to encode syntactic information of the programming languages.

  • 4 authors
·
Jun 23, 2022

Compression Represents Intelligence Linearly

There is a belief that learning to compress well will lead to intelligence. Recently, language modeling has been shown to be equivalent to compression, which offers a compelling rationale for the success of large language models (LLMs): the development of more advanced language models is essentially enhancing compression which facilitates intelligence. Despite such appealing discussions, little empirical evidence is present for the interplay between compression and intelligence. In this work, we examine their relationship in the context of LLMs, treating LLMs as data compressors. Given the abstract concept of "intelligence", we adopt the average downstream benchmark scores as a surrogate, specifically targeting intelligence related to knowledge and commonsense, coding, and mathematical reasoning. Across 12 benchmarks, our study brings together 30 public LLMs that originate from diverse organizations. Remarkably, we find that LLMs' intelligence -- reflected by average benchmark scores -- almost linearly correlates with their ability to compress external text corpora. These results provide concrete evidence supporting the belief that superior compression indicates greater intelligence. Furthermore, our findings suggest that compression efficiency, as an unsupervised metric derived from raw text corpora, serves as a reliable evaluation measure that is linearly associated with the model capabilities. We open-source our compression datasets as well as our data collection pipelines to facilitate future researchers to assess compression properly.

  • 4 authors
·
Apr 15, 2024 1

IndicSentEval: How Effectively do Multilingual Transformer Models encode Linguistic Properties for Indic Languages?

Transformer-based models have revolutionized the field of natural language processing. To understand why they perform so well and to assess their reliability, several studies have focused on questions such as: Which linguistic properties are encoded by these models, and to what extent? How robust are these models in encoding linguistic properties when faced with perturbations in the input text? However, these studies have mainly focused on BERT and the English language. In this paper, we investigate similar questions regarding encoding capability and robustness for 8 linguistic properties across 13 different perturbations in 6 Indic languages, using 9 multilingual Transformer models (7 universal and 2 Indic-specific). To conduct this study, we introduce a novel multilingual benchmark dataset, IndicSentEval, containing approximately sim47K sentences. Surprisingly, our probing analysis of surface, syntactic, and semantic properties reveals that while almost all multilingual models demonstrate consistent encoding performance for English, they show mixed results for Indic languages. As expected, Indic-specific multilingual models capture linguistic properties in Indic languages better than universal models. Intriguingly, universal models broadly exhibit better robustness compared to Indic-specific models, particularly under perturbations such as dropping both nouns and verbs, dropping only verbs, or keeping only nouns. Overall, this study provides valuable insights into probing and perturbation-specific strengths and weaknesses of popular multilingual Transformer-based models for different Indic languages. We make our code and dataset publicly available [https://github.com/aforakhilesh/IndicBertology].

  • 5 authors
·
Oct 31, 2025

From Tokens to Thoughts: How LLMs and Humans Trade Compression for Meaning

Humans organize knowledge into compact categories through semantic compression by mapping diverse instances to abstract representations while preserving meaning (e.g., robin and blue jay are both birds; most birds can fly). These concepts reflect a trade-off between expressive fidelity and representational simplicity. Large Language Models (LLMs) demonstrate remarkable linguistic abilities, yet whether their internal representations strike a human-like trade-off between compression and semantic fidelity is unclear. We introduce a novel information-theoretic framework, drawing from Rate-Distortion Theory and the Information Bottleneck principle, to quantitatively compare these strategies. Analyzing token embeddings from a diverse suite of LLMs against seminal human categorization benchmarks, we uncover key divergences. While LLMs form broad conceptual categories that align with human judgment, they struggle to capture the fine-grained semantic distinctions crucial for human understanding. More fundamentally, LLMs demonstrate a strong bias towards aggressive statistical compression, whereas human conceptual systems appear to prioritize adaptive nuance and contextual richness, even if this results in lower compressional efficiency by our measures. These findings illuminate critical differences between current AI and human cognitive architectures, guiding pathways toward LLMs with more human-aligned conceptual representations.

  • 4 authors
·
May 21, 2025