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Nov 4

Reddit-Impacts: A Named Entity Recognition Dataset for Analyzing Clinical and Social Effects of Substance Use Derived from Social Media

Substance use disorders (SUDs) are a growing concern globally, necessitating enhanced understanding of the problem and its trends through data-driven research. Social media are unique and important sources of information about SUDs, particularly since the data in such sources are often generated by people with lived experiences. In this paper, we introduce Reddit-Impacts, a challenging Named Entity Recognition (NER) dataset curated from subreddits dedicated to discussions on prescription and illicit opioids, as well as medications for opioid use disorder. The dataset specifically concentrates on the lesser-studied, yet critically important, aspects of substance use--its clinical and social impacts. We collected data from chosen subreddits using the publicly available Application Programming Interface for Reddit. We manually annotated text spans representing clinical and social impacts reported by people who also reported personal nonmedical use of substances including but not limited to opioids, stimulants and benzodiazepines. Our objective is to create a resource that can enable the development of systems that can automatically detect clinical and social impacts of substance use from text-based social media data. The successful development of such systems may enable us to better understand how nonmedical use of substances affects individual health and societal dynamics, aiding the development of effective public health strategies. In addition to creating the annotated data set, we applied several machine learning models to establish baseline performances. Specifically, we experimented with transformer models like BERT, and RoBERTa, one few-shot learning model DANN by leveraging the full training dataset, and GPT-3.5 by using one-shot learning, for automatic NER of clinical and social impacts. The dataset has been made available through the 2024 SMM4H shared tasks.

  • 6 authors
·
May 9, 2024

Substrate Prediction for RiPP Biosynthetic Enzymes via Masked Language Modeling and Transfer Learning

Ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic enzymes often exhibit promiscuous substrate preferences that cannot be reduced to simple rules. Large language models are promising tools for predicting such peptide fitness landscapes. However, state-of-the-art protein language models are trained on relatively few peptide sequences. A previous study comprehensively profiled the peptide substrate preferences of LazBF (a two-component serine dehydratase) and LazDEF (a three-component azole synthetase) from the lactazole biosynthetic pathway. We demonstrated that masked language modeling of LazBF substrate preferences produced language model embeddings that improved downstream classification models of both LazBF and LazDEF substrates. Similarly, masked language modeling of LazDEF substrate preferences produced embeddings that improved the performance of classification models of both LazBF and LazDEF substrates. Our results suggest that the models learned functional forms that are transferable between distinct enzymatic transformations that act within the same biosynthetic pathway. Our transfer learning method improved performance and data efficiency in data-scarce scenarios. We then fine-tuned models on each data set and showed that the fine-tuned models provided interpretable insight that we anticipate will facilitate the design of substrate libraries that are compatible with desired RiPP biosynthetic pathways.

  • 4 authors
·
Feb 23, 2024

Are You Getting What You Pay For? Auditing Model Substitution in LLM APIs

The proliferation of Large Language Models (LLMs) accessed via black-box APIs introduces a significant trust challenge: users pay for services based on advertised model capabilities (e.g., size, performance), but providers may covertly substitute the specified model with a cheaper, lower-quality alternative to reduce operational costs. This lack of transparency undermines fairness, erodes trust, and complicates reliable benchmarking. Detecting such substitutions is difficult due to the black-box nature, typically limiting interaction to input-output queries. This paper formalizes the problem of model substitution detection in LLM APIs. We systematically evaluate existing verification techniques, including output-based statistical tests, benchmark evaluations, and log probability analysis, under various realistic attack scenarios like model quantization, randomized substitution, and benchmark evasion. Our findings reveal the limitations of methods relying solely on text outputs, especially against subtle or adaptive attacks. While log probability analysis offers stronger guarantees when available, its accessibility is often limited. We conclude by discussing the potential of hardware-based solutions like Trusted Execution Environments (TEEs) as a pathway towards provable model integrity, highlighting the trade-offs between security, performance, and provider adoption. Code is available at https://github.com/sunblaze-ucb/llm-api-audit

  • 4 authors
·
Apr 6 2

EnzyControl: Adding Functional and Substrate-Specific Control for Enzyme Backbone Generation

Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but face limitations in binding data, substrate-specific control, and flexibility for de novo enzyme backbone generation. To address this, we introduce EnzyBind, a dataset with 11,100 experimentally validated enzyme-substrate pairs specifically curated from PDBbind. Building on this, we propose EnzyControl, a method that enables functional and substrate-specific control in enzyme backbone generation. Our approach generates enzyme backbones conditioned on MSA-annotated catalytic sites and their corresponding substrates, which are automatically extracted from curated enzyme-substrate data. At the core of EnzyControl is EnzyAdapter, a lightweight, modular component integrated into a pretrained motif-scaffolding model, allowing it to become substrate-aware. A two-stage training paradigm further refines the model's ability to generate accurate and functional enzyme structures. Experiments show that our EnzyControl achieves the best performance across structural and functional metrics on EnzyBind and EnzyBench benchmarks, with particularly notable improvements of 13\% in designability and 13\% in catalytic efficiency compared to the baseline models. The code is released at https://github.com/Vecteur-libre/EnzyControl.

Fast and Interpretable Protein Substructure Alignment via Optimal Transport

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. For a pair of input protein structures, PLASMA outputs a clear alignment matrix with an interpretable overall similarity score. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Reproducibility is ensured via our official implementation at https://github.com/ZW471/PLASMA-Protein-Local-Alignment.git.

  • 7 authors
·
Oct 12

Gradient-Based Word Substitution for Obstinate Adversarial Examples Generation in Language Models

In this paper, we study the problem of generating obstinate (over-stability) adversarial examples by word substitution in NLP, where input text is meaningfully changed but the model's prediction does not, even though it should. Previous word substitution approaches have predominantly focused on manually designed antonym-based strategies for generating obstinate adversarial examples, which hinders its application as these strategies can only find a subset of obstinate adversarial examples and require human efforts. To address this issue, in this paper, we introduce a novel word substitution method named GradObstinate, a gradient-based approach that automatically generates obstinate adversarial examples without any constraints on the search space or the need for manual design principles. To empirically evaluate the efficacy of GradObstinate, we conduct comprehensive experiments on five representative models (Electra, ALBERT, Roberta, DistillBERT, and CLIP) finetuned on four NLP benchmarks (SST-2, MRPC, SNLI, and SQuAD) and a language-grounding benchmark (MSCOCO). Extensive experiments show that our proposed GradObstinate generates more powerful obstinate adversarial examples, exhibiting a higher attack success rate compared to antonym-based methods. Furthermore, to show the transferability of obstinate word substitutions found by GradObstinate, we replace the words in four representative NLP benchmarks with their obstinate substitutions. Notably, obstinate substitutions exhibit a high success rate when transferred to other models in black-box settings, including even GPT-3 and ChatGPT. Examples of obstinate adversarial examples found by GradObstinate are available at https://huggingface.co/spaces/anonauthors/SecretLanguage.

  • 3 authors
·
Jul 23, 2023

Style Over Substance: Evaluation Biases for Large Language Models

As large language models (LLMs) continue to advance, accurately and comprehensively evaluating their performance becomes increasingly challenging. Human evaluations are conventionally considered the gold standard in natural language generation, but recent advancements incorporate state-of-the-art LLMs as proxies for human judges in evaluation processes. However, the extent to which humans and LLMs are capable evaluators remains uncertain. This study investigates the behavior of crowd-sourced and expert annotators, as well as LLMs, when comparing outputs from different models. To achieve this, we curate a dataset of intentionally flawed machine-generated answers. Our findings reveal a concerning bias in the evaluation process, as answers with factual errors are rated more favorably than answers that are too short or contained grammatical errors. To address this issue, we propose independently evaluating machine-generated text across multiple dimensions, rather than merging all the evaluation aspects into a single score. We instantiate this idea with the Elo rating system, resulting in the Multi-Elo Rating System. Empirical results from our study reveal that this proposed approach significantly enhances the quality of LLM-based evaluations, particularly in terms of factual accuracy. However, there is no significant improvement in crowd-sourced-based evaluations, indicating the need for further investigation and refinement.

  • 2 authors
·
Jul 6, 2023

Certified Robustness to Word Substitution Ranking Attack for Neural Ranking Models

Neural ranking models (NRMs) have achieved promising results in information retrieval. NRMs have also been shown to be vulnerable to adversarial examples. A typical Word Substitution Ranking Attack (WSRA) against NRMs was proposed recently, in which an attacker promotes a target document in rankings by adding human-imperceptible perturbations to its text. This raises concerns when deploying NRMs in real-world applications. Therefore, it is important to develop techniques that defend against such attacks for NRMs. In empirical defenses adversarial examples are found during training and used to augment the training set. However, such methods offer no theoretical guarantee on the models' robustness and may eventually be broken by other sophisticated WSRAs. To escape this arms race, rigorous and provable certified defense methods for NRMs are needed. To this end, we first define the Certified Top-K Robustness for ranking models since users mainly care about the top ranked results in real-world scenarios. A ranking model is said to be Certified Top-K Robust on a ranked list when it is guaranteed to keep documents that are out of the top K away from the top K under any attack. Then, we introduce a Certified Defense method, named CertDR, to achieve certified top-K robustness against WSRA, based on the idea of randomized smoothing. Specifically, we first construct a smoothed ranker by applying random word substitutions on the documents, and then leverage the ranking property jointly with the statistical property of the ensemble to provably certify top-K robustness. Extensive experiments on two representative web search datasets demonstrate that CertDR can significantly outperform state-of-the-art empirical defense methods for ranking models.

  • 7 authors
·
Sep 14, 2022

Autoregressive Search Engines: Generating Substrings as Document Identifiers

Knowledge-intensive language tasks require NLP systems to both provide the correct answer and retrieve supporting evidence for it in a given corpus. Autoregressive language models are emerging as the de-facto standard for generating answers, with newer and more powerful systems emerging at an astonishing pace. In this paper we argue that all this (and future) progress can be directly applied to the retrieval problem with minimal intervention to the models' architecture. Previous work has explored ways to partition the search space into hierarchical structures and retrieve documents by autoregressively generating their unique identifier. In this work we propose an alternative that doesn't force any structure in the search space: using all ngrams in a passage as its possible identifiers. This setup allows us to use an autoregressive model to generate and score distinctive ngrams, that are then mapped to full passages through an efficient data structure. Empirically, we show this not only outperforms prior autoregressive approaches but also leads to an average improvement of at least 10 points over more established retrieval solutions for passage-level retrieval on the KILT benchmark, establishing new state-of-the-art downstream performance on some datasets, while using a considerably lighter memory footprint than competing systems. Code and pre-trained models at https://github.com/facebookresearch/SEAL.

  • 6 authors
·
Apr 22, 2022

LexiMark: Robust Watermarking via Lexical Substitutions to Enhance Membership Verification of an LLM's Textual Training Data

Large language models (LLMs) can be trained or fine-tuned on data obtained without the owner's consent. Verifying whether a specific LLM was trained on particular data instances or an entire dataset is extremely challenging. Dataset watermarking addresses this by embedding identifiable modifications in training data to detect unauthorized use. However, existing methods often lack stealth, making them relatively easy to detect and remove. In light of these limitations, we propose LexiMark, a novel watermarking technique designed for text and documents, which embeds synonym substitutions for carefully selected high-entropy words. Our method aims to enhance an LLM's memorization capabilities on the watermarked text without altering the semantic integrity of the text. As a result, the watermark is difficult to detect, blending seamlessly into the text with no visible markers, and is resistant to removal due to its subtle, contextually appropriate substitutions that evade automated and manual detection. We evaluated our method using baseline datasets from recent studies and seven open-source models: LLaMA-1 7B, LLaMA-3 8B, Mistral 7B, Pythia 6.9B, as well as three smaller variants from the Pythia family (160M, 410M, and 1B). Our evaluation spans multiple training settings, including continued pretraining and fine-tuning scenarios. The results demonstrate significant improvements in AUROC scores compared to existing methods, underscoring our method's effectiveness in reliably verifying whether unauthorized watermarked data was used in LLM training.

  • 5 authors
·
Jun 17

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

Hardwired-Neurons Language Processing Units as General-Purpose Cognitive Substrates

The rapid advancement of Large Language Models (LLMs) has established language as a core general-purpose cognitive substrate, driving the demand for specialized Language Processing Units (LPUs) tailored for LLM inference. To overcome the growing energy consumption of LLM inference systems, this paper proposes a Hardwired-Neurons Language Processing Unit (HNLPU), which physically hardwires LLM weight parameters into the computational fabric, achieving several orders of magnitude computational efficiency improvement by extreme specialization. However, a significant challenge still lies in the scale of modern LLMs. An ideal estimation on hardwiring gpt-oss 120 B requires fabricating at least 6 billion dollars of photomask sets, rendering the straightforward solution economically impractical. Addressing this challenge, we propose the novel Metal-Embedding methodology. Instead of embedding weights in a 2D grid of silicon device cells, Metal-Embedding embeds weight parameters into the 3D topology of metal wires. This brings two benefits: (1) a 15x increase in density, and (2) 60 out of 70 layers of photomasks are made homogeneous across chips, including all EUV photomasks. In total, Metal-Embedding reduced the photomask cost by 112x, bringing the Non-Recurring Engineering (NRE) cost of HNLPU into an economically viable range. Experimental results show that HNLPU achieved 249,960 tokens/s (5,555x/85x of GPU/WSE), 36 tokens/J (1,047x/283x of GPU/WSE), 13,232 mm2 total die area (29% inscribed rectangular area in a 300 mm wafer), \$184M estimated NRE at 5 nm technology. Analysis shows that HNLPU achieved 8.57x cost-effectiveness and 230x carbon footprint reduction compared to H100 clusters, under an annual weight updating assumption.

  • 27 authors
·
Aug 22

Can Sound Replace Vision in LLaVA With Token Substitution?

What happens when we push audio-visual alignment to its absolute limits? To systematically investigate this question, we needed datasets with granular alignment quality annotations, but existing datasets treat alignment as binary, either synchronized or not. To address this limitation, we developed a comprehensive dataset featuring detailed alignment scores that reveal the hidden spectrum of audio-visual perceptual correspondence. Using these precise scores, we create "superaligned" representations by training exclusively on the most perfectly matched audio-visual pairs, then conduct our systematic investigation into how this extreme alignment transforms perceptual model behavior across retrieval and generation tasks. The encoders under study fall into two main groups consisting of image-centric encoders that were pretrained using visual modalities as intermediary hubs for connecting modalities, and text-centric encoders that were pretrained with direct audio-language alignment. We first measure the baseline performance of these encoders on two key tasks, namely cross-modal retrieval and text description generation in vision-language models. Subsequently, we realign all encoders with the CLIP space using highly coherent audio-visual data and observe the performance changes. Our findings reveal that the initial architectural type of the encoder determines how it responds to the alignment process. Image-centric encoders, which are inherently designed for alignment, demonstrate exceptional performance in cross-modal retrieval, but this intensive alignment causes compression of unique linguistic information and reduces the quality of their text description generation in vision-language models. In contrast, text-centric encoders, which possess stronger linguistic authenticity, are able to maintain a better balance between the two objectives.

  • 5 authors
·
Jun 12

Towards Robustness of Text-to-SQL Models against Synonym Substitution

Recently, there has been significant progress in studying neural networks to translate text descriptions into SQL queries. Despite achieving good performance on some public benchmarks, existing text-to-SQL models typically rely on the lexical matching between words in natural language (NL) questions and tokens in table schemas, which may render the models vulnerable to attacks that break the schema linking mechanism. In this work, we investigate the robustness of text-to-SQL models to synonym substitution. In particular, we introduce Spider-Syn, a human-curated dataset based on the Spider benchmark for text-to-SQL translation. NL questions in Spider-Syn are modified from Spider, by replacing their schema-related words with manually selected synonyms that reflect real-world question paraphrases. We observe that the accuracy dramatically drops by eliminating such explicit correspondence between NL questions and table schemas, even if the synonyms are not adversarially selected to conduct worst-case adversarial attacks. Finally, we present two categories of approaches to improve the model robustness. The first category of approaches utilizes additional synonym annotations for table schemas by modifying the model input, while the second category is based on adversarial training. We demonstrate that both categories of approaches significantly outperform their counterparts without the defense, and the first category of approaches are more effective.

  • 7 authors
·
Jun 2, 2021