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Apr 20

White-Box Diffusion Transformer for single-cell RNA-seq generation

As a powerful tool for characterizing cellular subpopulations and cellular heterogeneity, single cell RNA sequencing (scRNA-seq) technology offers advantages of high throughput and multidimensional analysis. However, the process of data acquisition is often constrained by high cost and limited sample availability. To overcome these limitations, we propose a hybrid model based on Diffusion model and White-Box transformer that aims to generate synthetic and biologically plausible scRNA-seq data. Diffusion model progressively introduce noise into the data and then recover the original data through a denoising process, a forward and reverse process that is particularly suitable for generating complex data distributions. White-Box transformer is a deep learning architecture that emphasizes mathematical interpretability. By minimizing the encoding rate of the data and maximizing the sparsity of the representation, it not only reduces the computational burden, but also provides clear insight into underlying structure. Our White-Box Diffusion Transformer combines the generative capabilities of Diffusion model with the mathematical interpretability of White-Box transformer. Through experiments using six different single-cell RNA-Seq datasets, we visualize both generated and real data using t-SNE dimensionality reduction technique, as well as quantify similarity between generated and real data using various metrics to demonstrate comparable performance of White-Box Diffusion Transformer and Diffusion Transformer in generating scRNA-seq data alongside significant improvements in training efficiency and resource utilization. Our code is available at https://github.com/lingximamo/White-Box-Diffusion-Transformer

  • 3 authors
·
Nov 11, 2024

White-Box Transformers via Sparse Rate Reduction: Compression Is All There Is?

In this paper, we contend that a natural objective of representation learning is to compress and transform the distribution of the data, say sets of tokens, towards a low-dimensional Gaussian mixture supported on incoherent subspaces. The goodness of such a representation can be evaluated by a principled measure, called sparse rate reduction, that simultaneously maximizes the intrinsic information gain and extrinsic sparsity of the learned representation. From this perspective, popular deep network architectures, including transformers, can be viewed as realizing iterative schemes to optimize this measure. Particularly, we derive a transformer block from alternating optimization on parts of this objective: the multi-head self-attention operator compresses the representation by implementing an approximate gradient descent step on the coding rate of the features, and the subsequent multi-layer perceptron sparsifies the features. This leads to a family of white-box transformer-like deep network architectures, named CRATE, which are mathematically fully interpretable. We show, by way of a novel connection between denoising and compression, that the inverse to the aforementioned compressive encoding can be realized by the same class of CRATE architectures. Thus, the so-derived white-box architectures are universal to both encoders and decoders. Experiments show that these networks, despite their simplicity, indeed learn to compress and sparsify representations of large-scale real-world image and text datasets, and achieve performance very close to highly engineered transformer-based models: ViT, MAE, DINO, BERT, and GPT2. We believe the proposed computational framework demonstrates great potential in bridging the gap between theory and practice of deep learning, from a unified perspective of data compression. Code is available at: https://ma-lab-berkeley.github.io/CRATE .

  • 10 authors
·
Nov 21, 2023

Adversarial Attacks on Multimodal Agents

Vision-enabled language models (VLMs) are now used to build autonomous multimodal agents capable of taking actions in real environments. In this paper, we show that multimodal agents raise new safety risks, even though attacking agents is more challenging than prior attacks due to limited access to and knowledge about the environment. Our attacks use adversarial text strings to guide gradient-based perturbation over one trigger image in the environment: (1) our captioner attack attacks white-box captioners if they are used to process images into captions as additional inputs to the VLM; (2) our CLIP attack attacks a set of CLIP models jointly, which can transfer to proprietary VLMs. To evaluate the attacks, we curated VisualWebArena-Adv, a set of adversarial tasks based on VisualWebArena, an environment for web-based multimodal agent tasks. Within an L-infinity norm of 16/256 on a single image, the captioner attack can make a captioner-augmented GPT-4V agent execute the adversarial goals with a 75% success rate. When we remove the captioner or use GPT-4V to generate its own captions, the CLIP attack can achieve success rates of 21% and 43%, respectively. Experiments on agents based on other VLMs, such as Gemini-1.5, Claude-3, and GPT-4o, show interesting differences in their robustness. Further analysis reveals several key factors contributing to the attack's success, and we also discuss the implications for defenses as well. Project page: https://chenwu.io/attack-agent Code and data: https://github.com/ChenWu98/agent-attack

  • 5 authors
·
Jun 18, 2024 1

Flexible Non-intrusive Dynamic Instrumentation for WebAssembly

A key strength of managed runtimes over hardware is the ability to gain detailed insight into the dynamic execution of programs with instrumentation. Analyses such as code coverage, execution frequency, tracing, and debugging, are all made easier in a virtual setting. As a portable, low-level bytecode, WebAssembly offers inexpensive in-process sandboxing with high performance. Yet to date, Wasm engines have not offered much insight into executing programs, supporting at best bytecode-level stepping and basic source maps, but no instrumentation capabilities. In this paper, we show the first non-intrusive dynamic instrumentation system for WebAssembly in the open-source Wizard Research Engine. Our innovative design offers a flexible, complete hierarchy of instrumentation primitives that support building high-level, complex analyses in terms of low-level, programmable probes. In contrast to emulation or machine code instrumentation, injecting probes at the bytecode level increases expressiveness and vastly simplifies the implementation by reusing the engine's JIT compiler, interpreter, and deoptimization mechanism rather than building new ones. Wizard supports both dynamic instrumentation insertion and removal while providing consistency guarantees, which is key to composing multiple analyses without interference. We detail a fully-featured implementation in a high-performance multi-tier Wasm engine, show novel optimizations specifically designed to minimize instrumentation overhead, and evaluate performance characteristics under load from various analyses. This design is well-suited for production engine adoption as probes can be implemented to have no impact on production performance when not in use.

  • 6 authors
·
Mar 12, 2024

Building Production-Ready Probes For Gemini

Frontier language model capabilities are improving rapidly. We thus need stronger mitigations against bad actors misusing increasingly powerful systems. Prior work has shown that activation probes may be a promising misuse mitigation technique, but we identify a key remaining challenge: probes fail to generalize under important production distribution shifts. In particular, we find that the shift from short-context to long-context inputs is difficult for existing probe architectures. We propose several new probe architecture that handle this long-context distribution shift. We evaluate these probes in the cyber-offensive domain, testing their robustness against various production-relevant shifts, including multi-turn conversations, static jailbreaks, and adaptive red teaming. Our results demonstrate that while multimax addresses context length, a combination of architecture choice and training on diverse distributions is required for broad generalization. Additionally, we show that pairing probes with prompted classifiers achieves optimal accuracy at a low cost due to the computational efficiency of probes. These findings have informed the successful deployment of misuse mitigation probes in user-facing instances of Gemini, Google's frontier language model. Finally, we find early positive results using AlphaEvolve to automate improvements in both probe architecture search and adaptive red teaming, showing that automating some AI safety research is already possible.

  • 7 authors
·
Jan 16 3

Learning on LLM Output Signatures for gray-box LLM Behavior Analysis

Large Language Models (LLMs) have achieved widespread adoption, yet our understanding of their behavior remains limited, particularly in detecting data contamination and hallucinations. While recently proposed probing techniques provide insights through activation analysis, they require "white-box" access to model internals, often unavailable. Current "gray-box" approaches typically analyze only the probability of the actual tokens in the sequence with simple task-specific heuristics. Importantly, these methods overlook the rich information contained in the full token distribution at each processing step. To address these limitations, we propose that gray-box analysis should leverage the complete observable output of LLMs, consisting of both the previously used token probabilities as well as the complete token distribution sequences - a unified data type we term LOS (LLM Output Signature). To this end, we develop a transformer-based approach to process LOS that theoretically guarantees approximation of existing techniques while enabling more nuanced analysis. Our approach achieves superior performance on hallucination and data contamination detection in gray-box settings, significantly outperforming existing baselines. Furthermore, it demonstrates strong transfer capabilities across datasets and LLMs, suggesting that LOS captures fundamental patterns in LLM behavior. Our code is available at: https://github.com/BarSGuy/LLM-Output-Signatures-Network.

  • 8 authors
·
Mar 18, 2025

ReCreate: Reasoning and Creating Domain Agents Driven by Experience

Large Language Model agents are reshaping the industrial landscape. However, most practical agents remain human-designed because tasks differ widely, making them labor-intensive to build. This situation poses a central question: can we automatically create and adapt domain agents in the wild? While several recent approaches have sought to automate agent creation, they typically treat agent generation as a black-box procedure and rely solely on final performance metrics to guide the process. Such strategies overlook critical evidence explaining why an agent succeeds or fails, and often require high computational costs. To address these limitations, we propose ReCreate, an experience-driven framework for the automatic creation of domain agents. ReCreate systematically leverages agent interaction histories, which provide rich concrete signals on both the causes of success or failure and the avenues for improvement. Specifically, we introduce an agent-as-optimizer paradigm that effectively learns from experience via three key components: (i) an experience storage and retrieval mechanism for on-demand inspection; (ii) a reasoning-creating synergy pipeline that maps execution experience into scaffold edits; and (iii) hierarchical updates that abstract instance-level details into reusable domain patterns. In experiments across diverse domains, ReCreate consistently outperforms human-designed agents and existing automated agent generation methods, even when starting from minimal seed scaffolds.

  • 9 authors
·
Jan 16

Understanding Disparities in Post Hoc Machine Learning Explanation

Previous work has highlighted that existing post-hoc explanation methods exhibit disparities in explanation fidelity (across 'race' and 'gender' as sensitive attributes), and while a large body of work focuses on mitigating these issues at the explanation metric level, the role of the data generating process and black box model in relation to explanation disparities remains largely unexplored. Accordingly, through both simulations as well as experiments on a real-world dataset, we specifically assess challenges to explanation disparities that originate from properties of the data: limited sample size, covariate shift, concept shift, omitted variable bias, and challenges based on model properties: inclusion of the sensitive attribute and appropriate functional form. Through controlled simulation analyses, our study demonstrates that increased covariate shift, concept shift, and omission of covariates increase explanation disparities, with the effect pronounced higher for neural network models that are better able to capture the underlying functional form in comparison to linear models. We also observe consistent findings regarding the effect of concept shift and omitted variable bias on explanation disparities in the Adult income dataset. Overall, results indicate that disparities in model explanations can also depend on data and model properties. Based on this systematic investigation, we provide recommendations for the design of explanation methods that mitigate undesirable disparities.

  • 4 authors
·
Jan 25, 2024

Learning on Model Weights using Tree Experts

The number of publicly available models is rapidly increasing, yet most remain undocumented. Users looking for suitable models for their tasks must first determine what each model does. Training machine learning models to infer missing documentation directly from model weights is challenging, as these weights often contain significant variation unrelated to model functionality (denoted nuisance). Here, we identify a key property of real-world models: most public models belong to a small set of Model Trees, where all models within a tree are fine-tuned from a common ancestor (e.g., a foundation model). Importantly, we find that within each tree there is less nuisance variation between models. Concretely, while learning across Model Trees requires complex architectures, even a linear classifier trained on a single model layer often works within trees. While effective, these linear classifiers are computationally expensive, especially when dealing with larger models that have many parameters. To address this, we introduce Probing Experts (ProbeX), a theoretically motivated and lightweight method. Notably, ProbeX is the first probing method specifically designed to learn from the weights of a single hidden model layer. We demonstrate the effectiveness of ProbeX by predicting the categories in a model's training dataset based only on its weights. Excitingly, ProbeX can map the weights of Stable Diffusion into a weight-language embedding space, enabling model search via text, i.e., zero-shot model classification.

  • 4 authors
·
Oct 17, 2024

RAPTOR: Ridge-Adaptive Logistic Probes

Probing studies what information is encoded in a frozen LLM's layer representations by training a lightweight predictor on top of them. Beyond analysis, probes are often used operationally in probe-then-steer pipelines: a learned concept vector is extracted from a probe and injected via additive activation steering by adding it to a layer representation during the forward pass. The effectiveness of this pipeline hinges on estimating concept vectors that are accurate, directionally stable under ablation, and inexpensive to obtain. Motivated by these desiderata, we propose RAPTOR (Ridge-Adaptive Logistic Probe), a simple L2-regularized logistic probe whose validation-tuned ridge strength yields concept vectors from normalized weights. Across extensive experiments on instruction-tuned LLMs and human-written concept datasets, RAPTOR matches or exceeds strong baselines in accuracy while achieving competitive directional stability and substantially lower training cost; these quantitative results are supported by qualitative downstream steering demonstrations. Finally, using the Convex Gaussian Min-max Theorem (CGMT), we provide a mechanistic characterization of ridge logistic regression in an idealized Gaussian teacher-student model in the high-dimensional few-shot regime, explaining how penalty strength mediates probe accuracy and concept-vector stability and yielding structural predictions that qualitatively align with trends observed on real LLM embeddings.

Neural Probe-Based Hallucination Detection for Large Language Models

Large language models(LLMs) excel at text generation and knowledge question-answering tasks, but they are prone to generating hallucinated content, severely limiting their application in high-risk domains. Current hallucination detection methods based on uncertainty estimation and external knowledge retrieval suffer from the limitation that they still produce erroneous content at high confidence levels and rely heavily on retrieval efficiency and knowledge coverage. In contrast, probe methods that leverage the model's hidden-layer states offer real-time and lightweight advantages. However, traditional linear probes struggle to capture nonlinear structures in deep semantic spaces.To overcome these limitations, we propose a neural network-based framework for token-level hallucination detection. By freezing language model parameters, we employ lightweight MLP probes to perform nonlinear modeling of high-level hidden states. A multi-objective joint loss function is designed to enhance detection stability and semantic disambiguity. Additionally, we establish a layer position-probe performance response model, using Bayesian optimization to automatically search for optimal probe insertion layers and achieve superior training results.Experimental results on LongFact, HealthBench, and TriviaQA demonstrate that MLP probes significantly outperform state-of-the-art methods in accuracy, recall, and detection capability under low false-positive conditions.

  • 2 authors
·
Dec 24, 2025