Daily Papers

Protein language models (PLMs) encode rich biological information, yet their internal neuron representations are poorly understood. We introduce the first automated framework for labeling every neuron in a PLM with biologically grounded natural language descriptions. Unlike prior approaches relying on sparse autoencoders or manual annotation, our method scales to hundreds of thousands of neurons, revealing individual neurons are selectively sensitive to diverse biochemical and structural properties. We then develop a novel neuron activation-guided steering method to generate proteins with desired traits, enabling convergence to target biochemical properties like molecular weight and instability index as well as secondary and tertiary structural motifs, including alpha helices and canonical Zinc Fingers. We finally show that analysis of labeled neurons in different model sizes reveals PLM scaling laws and a structured neuron space distribution.

Related works used indexes like CKA and variants of CCA to measure the similarity of cross-lingual representations in multilingual language models. In this paper, we argue that assumptions of CKA/CCA align poorly with one of the motivating goals of cross-lingual learning analysis, i.e., explaining zero-shot cross-lingual transfer. We highlight what valuable aspects of cross-lingual similarity these indexes fail to capture and provide a motivating case study demonstrating the problem empirically. Then, we introduce Average Neuron-Wise Correlation (ANC) as a straightforward alternative that is exempt from the difficulties of CKA/CCA and is good specifically in a cross-lingual context. Finally, we use ANC to construct evidence that the previously introduced ``first align, then predict'' pattern takes place not only in masked language models (MLMs) but also in multilingual models with causal language modeling objectives (CLMs). Moreover, we show that the pattern extends to the scaled versions of the MLMs and CLMs (up to 85x original mBERT).Our code is publicly available at \url{https://github.com/TartuNLP/xsim}

Artificial neural networks (ANN) were inspired by the architecture and functions of the human brain and have revolutionised the field of artificial intelligence (AI). Inspired by studies on the latent geometry of the brain we posit that an increase in the research and application of hyperbolic geometry in machine learning will lead to increased accuracy, improved feature space representations and more efficient models across a range of tasks. We look at the structure and functions of the human brain, highlighting the alignment between the brain's hierarchical nature and hyperbolic geometry. By examining the brain's complex network of neuron connections and its cognitive processes, we illustrate how hyperbolic geometry plays a pivotal role in human intelligence. Empirical evidence indicates that hyperbolic neural networks outperform Euclidean models for tasks including natural language processing, computer vision and complex network analysis, requiring fewer parameters and exhibiting better generalisation. Despite its nascent adoption, hyperbolic geometry holds promise for improving machine learning models and advancing the field toward AGI.

Language Models (LMs) have become widely used in software engineering, especially for tasks such as code generation, where they are referred to as code LMs. These models have proven effective in generating code, making it easier for developers to automate coding activities. However, research has highlighted a significant limitation: despite their effectiveness, LMs often produce code that is incorrect, buggy, or not fully functional. Updating these models with limited data can be prohibitively challenging, yet it is essential to maximize their utility. This may require hot-fix techniques (updating models with limited data) to resolve. In this paper, we propose Model Improvement via Neuron Targeting (MINT), a novel approach for repairing code LMs. MINT leverages the semantic property of language models to perform neuron-level repairs in a novel way. Further, by analyzing the relationships between the model's latent representations, the incorrect outputs, and the desired outputs, MINT determines which neurons are worth updating. This approach ensures that only the neurons crucial to the model's failure are targeted, avoiding unnecessary changes and allowing for a more efficient and precise repair process. MINT is effective, efficient, and reliable, capable of correcting a neural model by patching a minimum number of neurons (usually one or two neurons). Our approach is evaluated on three coding tasks: line-level code generation, shellcode generation, and intent-to-bash translation. The experimental results demonstrate that the proposed approach significantly outperforms the state-of-the-art in both effectiveness and efficiency measures. In addition, we analyze and discuss the side effects of model repair techniques, including the balance between generalization and specificity, and the performance after multiple repairs in succession.

What is the right supervisory signal to train visual representations? Current approaches in computer vision use category labels from datasets such as ImageNet to train ConvNets. However, in case of biological agents, visual representation learning does not require millions of semantic labels. We argue that biological agents use physical interactions with the world to learn visual representations unlike current vision systems which just use passive observations (images and videos downloaded from web). For example, babies push objects, poke them, put them in their mouth and throw them to learn representations. Towards this goal, we build one of the first systems on a Baxter platform that pushes, pokes, grasps and observes objects in a tabletop environment. It uses four different types of physical interactions to collect more than 130K datapoints, with each datapoint providing supervision to a shared ConvNet architecture allowing us to learn visual representations. We show the quality of learned representations by observing neuron activations and performing nearest neighbor retrieval on this learned representation. Quantitatively, we evaluate our learned ConvNet on image classification tasks and show improvements compared to learning without external data. Finally, on the task of instance retrieval, our network outperforms the ImageNet network on recall@1 by 3%

Large Language Models (LLMs) demonstrate human-level or even superior language abilities, effectively modeling syntactic structures, yet the specific computational modules responsible remain unclear. A key question is whether LLM behavioral capabilities stem from mechanisms akin to those in the human brain. To address these questions, we introduce the Hierarchical Frequency Tagging Probe (HFTP), a tool that utilizes frequency-domain analysis to identify neuron-wise components of LLMs (e.g., individual Multilayer Perceptron (MLP) neurons) and cortical regions (via intracranial recordings) encoding syntactic structures. Our results show that models such as GPT-2, Gemma, Gemma 2, Llama 2, Llama 3.1, and GLM-4 process syntax in analogous layers, while the human brain relies on distinct cortical regions for different syntactic levels. Representational similarity analysis reveals a stronger alignment between LLM representations and the left hemisphere of the brain (dominant in language processing). Notably, upgraded models exhibit divergent trends: Gemma 2 shows greater brain similarity than Gemma, while Llama 3.1 shows less alignment with the brain compared to Llama 2. These findings offer new insights into the interpretability of LLM behavioral improvements, raising questions about whether these advancements are driven by human-like or non-human-like mechanisms, and establish HFTP as a valuable tool bridging computational linguistics and cognitive neuroscience. This project is available at https://github.com/LilTiger/HFTP.

Selecting appropriate datasets is critical in modern computer vision. However, no general-purpose tools exist to evaluate the extent to which two datasets differ. For this, we propose representing images - and by extension datasets - using Distributions of Neuron Activations (DNAs). DNAs fit distributions, such as histograms or Gaussians, to activations of neurons in a pre-trained feature extractor through which we pass the image(s) to represent. This extractor is frozen for all datasets, and we rely on its generally expressive power in feature space. By comparing two DNAs, we can evaluate the extent to which two datasets differ with granular control over the comparison attributes of interest, providing the ability to customise the way distances are measured to suit the requirements of the task at hand. Furthermore, DNAs are compact, representing datasets of any size with less than 15 megabytes. We demonstrate the value of DNAs by evaluating their applicability on several tasks, including conditional dataset comparison, synthetic image evaluation, and transfer learning, and across diverse datasets, ranging from synthetic cat images to celebrity faces and urban driving scenes.

We propose a formal mathematical model for sparse representations and active dendrites in neocortex. Our model is inspired by recent experimental findings on active dendritic processing and NMDA spikes in pyramidal neurons. These experimental and modeling studies suggest that the basic unit of pattern memory in the neocortex is instantiated by small clusters of synapses operated on by localized non-linear dendritic processes. We derive a number of scaling laws that characterize the accuracy of such dendrites in detecting activation patterns in a neuronal population under adverse conditions. We introduce the union property which shows that synapses for multiple patterns can be randomly mixed together within a segment and still lead to highly accurate recognition. We describe simulation results that provide further insight into sparse representations as well as two primary results. First we show that pattern recognition by a neuron with active dendrites can be extremely accurate and robust with high dimensional sparse inputs even when using a tiny number of synapses to recognize large patterns. Second, equations representing recognition accuracy of a dendrite predict optimal NMDA spiking thresholds under a generous set of assumptions. The prediction tightly matches NMDA spiking thresholds measured in the literature. Our model matches many of the known properties of pyramidal neurons. As such the theory provides a mathematical framework for understanding the benefits and limits of sparse representations in cortical networks.

Large language models (LLMs) exhibit strong multilingual abilities, yet the neural mechanisms behind language-specific processing remain unclear. We analyze language-specific neurons in Llama-3.1-8B, Mistral-Nemo-12B, and Aya-Expanse-8B & 32B across 21 typologically diverse languages, identifying neurons that control language behavior. Using the Language Activation Probability Entropy (LAPE) method, we show that these neurons cluster in deeper layers, with non-Latin scripts showing greater specialization. Related languages share overlapping neurons, reflecting internal representations of linguistic proximity. Through language arithmetics, i.e. systematic activation addition and multiplication, we steer models to deactivate unwanted languages and activate desired ones, outperforming simpler replacement approaches. These interventions effectively guide behavior across five multilingual tasks: language forcing, translation, QA, comprehension, and NLI. Manipulation is more successful for high-resource languages, while typological similarity improves effectiveness. We also demonstrate that cross-lingual neuron steering enhances downstream performance and reveal internal "fallback" mechanisms for language selection when neurons are progressively deactivated. Our code is made publicly available at https://github.com/d-gurgurov/Language-Neurons-Manipulation.

Individual neurons participate in the representation of multiple high-level concepts. To what extent can different interpretability methods successfully disentangle these roles? To help address this question, we introduce RAVEL (Resolving Attribute-Value Entanglements in Language Models), a dataset that enables tightly controlled, quantitative comparisons between a variety of existing interpretability methods. We use the resulting conceptual framework to define the new method of Multi-task Distributed Alignment Search (MDAS), which allows us to find distributed representations satisfying multiple causal criteria. With Llama2-7B as the target language model, MDAS achieves state-of-the-art results on RAVEL, demonstrating the importance of going beyond neuron-level analyses to identify features distributed across activations. We release our benchmark at https://github.com/explanare/ravel.

The alignment of vision-language representations endows current Vision-Language Models (VLMs) with strong multi-modal reasoning capabilities. However, the interpretability of the alignment component remains uninvestigated due to the difficulty in mapping the semantics of multi-modal representations into a unified concept set. To address this problem, we propose VL-SAE, a sparse autoencoder that encodes vision-language representations into its hidden activations. Each neuron in its hidden layer correlates to a concept represented by semantically similar images and texts, thereby interpreting these representations with a unified concept set. To establish the neuron-concept correlation, we encourage semantically similar representations to exhibit consistent neuron activations during self-supervised training. First, to measure the semantic similarity of multi-modal representations, we perform their alignment in an explicit form based on cosine similarity. Second, we construct the VL-SAE with a distance-based encoder and two modality-specific decoders to ensure the activation consistency of semantically similar representations. Experiments across multiple VLMs (e.g., CLIP, LLaVA) demonstrate the superior capability of VL-SAE in interpreting and enhancing the vision-language alignment. For interpretation, the alignment between vision and language representations can be understood by comparing their semantics with concepts. For enhancement, the alignment can be strengthened by aligning vision-language representations at the concept level, contributing to performance improvements in downstream tasks, including zero-shot image classification and hallucination elimination. Codes are available at https://github.com/ssfgunner/VL-SAE.

This paper describes MAIA, a Multimodal Automated Interpretability Agent. MAIA is a system that uses neural models to automate neural model understanding tasks like feature interpretation and failure mode discovery. It equips a pre-trained vision-language model with a set of tools that support iterative experimentation on subcomponents of other models to explain their behavior. These include tools commonly used by human interpretability researchers: for synthesizing and editing inputs, computing maximally activating exemplars from real-world datasets, and summarizing and describing experimental results. Interpretability experiments proposed by MAIA compose these tools to describe and explain system behavior. We evaluate applications of MAIA to computer vision models. We first characterize MAIA's ability to describe (neuron-level) features in learned representations of images. Across several trained models and a novel dataset of synthetic vision neurons with paired ground-truth descriptions, MAIA produces descriptions comparable to those generated by expert human experimenters. We then show that MAIA can aid in two additional interpretability tasks: reducing sensitivity to spurious features, and automatically identifying inputs likely to be mis-classified.

Large language models (LLMs) have demonstrated prowess in a wide range of tasks. However, many LLMs exhibit significant performance discrepancies between high- and low-resource languages. To mitigate this challenge, we present FuxiTranyu, an open-source multilingual LLM, which is designed to satisfy the need of the research community for balanced and high-performing multilingual capabilities. FuxiTranyu-8B, the base model with 8 billion parameters, is trained from scratch on a meticulously balanced multilingual data repository that contains 600 billion tokens covering 43 natural languages and 16 programming languages. In addition to the base model, we also develop two instruction-tuned models: FuxiTranyu-8B-SFT that is fine-tuned on a diverse multilingual instruction dataset, and FuxiTranyu-8B-DPO that is further refined with DPO on a preference dataset for enhanced alignment ability. Extensive experiments on a wide range of multilingual benchmarks demonstrate the competitive performance of FuxiTranyu against existing multilingual LLMs, e.g., BLOOM-7B, PolyLM-13B, Llama-2-Chat-7B and Mistral-7B-Instruct. Interpretability analyses at both the neuron and representation level suggest that FuxiTranyu is able to learn consistent multilingual representations across different languages. To promote further research into multilingual LLMs and their working mechanisms, we release both the base and instruction-tuned FuxiTranyu models together with 58 pretraining checkpoints at HuggingFace and Github.

Despite their remarkable success and deployment across diverse workflows, language models sometimes produce untruthful responses. Our limited understanding of how truthfulness is mechanistically encoded within these models jeopardizes their reliability and safety. In this paper, we propose a method for identifying representations of truthfulness at the neuron level. We show that language models contain truth neurons, which encode truthfulness in a subject-agnostic manner. Experiments conducted across models of varying scales validate the existence of truth neurons, confirming that the encoding of truthfulness at the neuron level is a property shared by many language models. The distribution patterns of truth neurons over layers align with prior findings on the geometry of truthfulness. Selectively suppressing the activations of truth neurons found through the TruthfulQA dataset degrades performance both on TruthfulQA and on other benchmarks, showing that the truthfulness mechanisms are not tied to a specific dataset. Our results offer novel insights into the mechanisms underlying truthfulness in language models and highlight potential directions toward improving their trustworthiness and reliability.

Large Language Models have demonstrated impressive fluency across diverse tasks, yet their tendency to produce toxic content remains a critical challenge for AI safety and public trust. Existing toxicity mitigation approaches primarily manipulate individual neuron activations, but these methods suffer from instability, context dependence, and often compromise the model's core language abilities. To address these shortcomings, we investigate three key questions: the stability of neuron-level toxicity indicators, the advantages of structural (layer-wise) representations, and the interpretability of mechanisms driving toxic generation. Through extensive experiments on Jigsaw and ToxiCN datasets, we show that aggregated layer-wise features provide more robust signals than single neurons. Moreover, we observe conceptual limitations in prior works that conflate toxicity detection experts and generation experts within neuron-based interventions. To mitigate this, we propose a novel principled intervention technique, EigenShift, based on eigen-decomposition of the language model's final output layer. This method selectively targets generation-aligned components, enabling precise toxicity suppression without impairing linguistic competence. Our method requires no additional training or fine-tuning, incurs minimal computational cost, and is grounded in rigorous theoretical analysis.

Ambiguity is pervasive in real-world questions, yet large language models (LLMs) often respond with confident answers rather than seeking clarification. In this work, we show that question ambiguity is linearly encoded in the internal representations of LLMs and can be both detected and controlled at the neuron level. During the model's pre-filling stage, we identify that a small number of neurons, as few as one, encode question ambiguity information. Probes trained on these Ambiguity-Encoding Neurons (AENs) achieve strong performance on ambiguity detection and generalize across datasets, outperforming prompting-based and representation-based baselines. Layerwise analysis reveals that AENs emerge from shallow layers, suggesting early encoding of ambiguity signals in the model's processing pipeline. Finally, we show that through manipulating AENs, we can control LLM's behavior from direct answering to abstention. Our findings reveal that LLMs form compact internal representations of question ambiguity, enabling interpretable and controllable behavior.

A growing intuition in machine learning suggests a link between sparsity and interpretability. We introduce a novel self-ablation mechanism to investigate this connection ante-hoc in the context of language transformers. Our approach dynamically enforces a k-winner-takes-all constraint, forcing the model to demonstrate selective activation across neuron and attention units. Unlike post-hoc methods that analyze already-trained models, our approach integrates interpretability directly into model training, promoting feature localization from inception. Training small models on the TinyStories dataset and employing interpretability tests, we find that self-ablation leads to more localized circuits, concentrated feature representations, and increased neuron specialization without compromising language modelling performance. Surprisingly, our method also decreased overall sparsity, indicating that self-ablation promotes specialization rather than widespread inactivity. This reveals a complex interplay between sparsity and interpretability, where decreased global sparsity can coexist with increased local specialization, leading to enhanced interpretability. To facilitate reproducibility, we make our code available at https://github.com/keenanpepper/self-ablating-transformers.

Self-supervised models have revolutionized speech processing, achieving new levels of performance in a wide variety of tasks with limited resources. However, the inner workings of these models are still opaque. In this paper, we aim to analyze the encoded contextual representation of these foundation models based on their inter- and intra-model similarity, independent of any external annotation and task-specific constraint. We examine different SSL models varying their training paradigm -- Contrastive (Wav2Vec2.0) and Predictive models (HuBERT); and model sizes (base and large). We explore these models on different levels of localization/distributivity of information including (i) individual neurons; (ii) layer representation; (iii) attention weights and (iv) compare the representations with their finetuned counterparts.Our results highlight that these models converge to similar representation subspaces but not to similar neuron-localized concepts\footnote{A concept represents a coherent fragment of knowledge, such as ``a class containing certain objects as elements, where the objects have certain properties. We made the code publicly available for facilitating further research, we publicly released our code.