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Jan 7

Multi-scale Iterative Refinement towards Robust and Versatile Molecular Docking

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep learning-based approaches leading to improvements in blind docking efficiency, these methods have encountered notable challenges, such as limited generalization performance on unseen proteins, the inability to concurrently address the settings of blind docking and site-specific docking, and the frequent occurrence of physical implausibilities such as inter-molecular steric clash. In this study, we introduce DeltaDock, a robust and versatile framework designed for efficient molecular docking to overcome these challenges. DeltaDock operates in a two-step process: rapid initial complex structures sampling followed by multi-scale iterative refinement of the initial structures. In the initial stage, to sample accurate structures with high efficiency, we develop a ligand-dependent binding site prediction model founded on large protein models and graph neural networks. This model is then paired with GPU-accelerated sampling algorithms. The sampled structures are updated using a multi-scale iterative refinement module that captures both protein-ligand atom-atom interactions and residue-atom interactions in the following stage. Distinct from previous geometric deep learning methods that are conditioned on the blind docking setting, DeltaDock demonstrates superior performance in both blind docking and site-specific docking settings. Comprehensive experimental results reveal that DeltaDock consistently surpasses baseline methods in terms of docking accuracy. Furthermore, it displays remarkable generalization capabilities and proficiency for predicting physically valid structures, thereby attesting to its robustness and reliability in various scenarios.

  • 4 authors
·
Nov 30, 2023

Exploring Geometry of Blind Spots in Vision Models

Despite the remarkable success of deep neural networks in a myriad of settings, several works have demonstrated their overwhelming sensitivity to near-imperceptible perturbations, known as adversarial attacks. On the other hand, prior works have also observed that deep networks can be under-sensitive, wherein large-magnitude perturbations in input space do not induce appreciable changes to network activations. In this work, we study in detail the phenomenon of under-sensitivity in vision models such as CNNs and Transformers, and present techniques to study the geometry and extent of "equi-confidence" level sets of such networks. We propose a Level Set Traversal algorithm that iteratively explores regions of high confidence with respect to the input space using orthogonal components of the local gradients. Given a source image, we use this algorithm to identify inputs that lie in the same equi-confidence level set as the source image despite being perceptually similar to arbitrary images from other classes. We further observe that the source image is linearly connected by a high-confidence path to these inputs, uncovering a star-like structure for level sets of deep networks. Furthermore, we attempt to identify and estimate the extent of these connected higher-dimensional regions over which the model maintains a high degree of confidence. The code for this project is publicly available at https://github.com/SriramB-98/blindspots-neurips-sub

  • 4 authors
·
Oct 30, 2023

BlindHarmony: "Blind" Harmonization for MR Images via Flow model

In MRI, images of the same contrast (e.g., T_1) from the same subject can exhibit noticeable differences when acquired using different hardware, sequences, or scan parameters. These differences in images create a domain gap that needs to be bridged by a step called image harmonization, to process the images successfully using conventional or deep learning-based image analysis (e.g., segmentation). Several methods, including deep learning-based approaches, have been proposed to achieve image harmonization. However, they often require datasets from multiple domains for deep learning training and may still be unsuccessful when applied to images from unseen domains. To address this limitation, we propose a novel concept called `Blind Harmonization', which utilizes only target domain data for training but still has the capability to harmonize images from unseen domains. For the implementation of blind harmonization, we developed BlindHarmony using an unconditional flow model trained on target domain data. The harmonized image is optimized to have a correlation with the input source domain image while ensuring that the latent vector of the flow model is close to the center of the Gaussian distribution. BlindHarmony was evaluated on both simulated and real datasets and compared to conventional methods. BlindHarmony demonstrated noticeable performance on both datasets, highlighting its potential for future use in clinical settings. The source code is available at: https://github.com/SNU-LIST/BlindHarmony

  • 4 authors
·
May 18, 2023

Words or Vision: Do Vision-Language Models Have Blind Faith in Text?

Vision-Language Models (VLMs) excel in integrating visual and textual information for vision-centric tasks, but their handling of inconsistencies between modalities is underexplored. We investigate VLMs' modality preferences when faced with visual data and varied textual inputs in vision-centered settings. By introducing textual variations to four vision-centric tasks and evaluating ten Vision-Language Models (VLMs), we discover a ``blind faith in text'' phenomenon: VLMs disproportionately trust textual data over visual data when inconsistencies arise, leading to significant performance drops under corrupted text and raising safety concerns. We analyze factors influencing this text bias, including instruction prompts, language model size, text relevance, token order, and the interplay between visual and textual certainty. While certain factors, such as scaling up the language model size, slightly mitigate text bias, others like token order can exacerbate it due to positional biases inherited from language models. To address this issue, we explore supervised fine-tuning with text augmentation and demonstrate its effectiveness in reducing text bias. Additionally, we provide a theoretical analysis suggesting that the blind faith in text phenomenon may stem from an imbalance of pure text and multi-modal data during training. Our findings highlight the need for balanced training and careful consideration of modality interactions in VLMs to enhance their robustness and reliability in handling multi-modal data inconsistencies.

  • 4 authors
·
Mar 3, 2025 2

INFWIDE: Image and Feature Space Wiener Deconvolution Network for Non-blind Image Deblurring in Low-Light Conditions

Under low-light environment, handheld photography suffers from severe camera shake under long exposure settings. Although existing deblurring algorithms have shown promising performance on well-exposed blurry images, they still cannot cope with low-light snapshots. Sophisticated noise and saturation regions are two dominating challenges in practical low-light deblurring. In this work, we propose a novel non-blind deblurring method dubbed image and feature space Wiener deconvolution network (INFWIDE) to tackle these problems systematically. In terms of algorithm design, INFWIDE proposes a two-branch architecture, which explicitly removes noise and hallucinates saturated regions in the image space and suppresses ringing artifacts in the feature space, and integrates the two complementary outputs with a subtle multi-scale fusion network for high quality night photograph deblurring. For effective network training, we design a set of loss functions integrating a forward imaging model and backward reconstruction to form a close-loop regularization to secure good convergence of the deep neural network. Further, to optimize INFWIDE's applicability in real low-light conditions, a physical-process-based low-light noise model is employed to synthesize realistic noisy night photographs for model training. Taking advantage of the traditional Wiener deconvolution algorithm's physically driven characteristics and arisen deep neural network's representation ability, INFWIDE can recover fine details while suppressing the unpleasant artifacts during deblurring. Extensive experiments on synthetic data and real data demonstrate the superior performance of the proposed approach.

  • 5 authors
·
Jul 17, 2022

Misaligned Roles, Misplaced Images: Structural Input Perturbations Expose Multimodal Alignment Blind Spots

Multimodal Language Models (MMLMs) typically undergo post-training alignment to prevent harmful content generation. However, these alignment stages focus primarily on the assistant role, leaving the user role unaligned, and stick to a fixed input prompt structure of special tokens, leaving the model vulnerable when inputs deviate from these expectations. We introduce Role-Modality Attacks (RMA), a novel class of adversarial attacks that exploit role confusion between the user and assistant and alter the position of the image token to elicit harmful outputs. Unlike existing attacks that modify query content, RMAs manipulate the input structure without altering the query itself. We systematically evaluate these attacks across multiple Vision Language Models (VLMs) on eight distinct settings, showing that they can be composed to create stronger adversarial prompts, as also evidenced by their increased projection in the negative refusal direction in the residual stream, a property observed in prior successful attacks. Finally, for mitigation, we propose an adversarial training approach that makes the model robust against input prompt perturbations. By training the model on a range of harmful and benign prompts all perturbed with different RMA settings, it loses its sensitivity to Role Confusion and Modality Manipulation attacks and is trained to only pay attention to the content of the query in the input prompt structure, effectively reducing Attack Success Rate (ASR) while preserving the model's general utility.

  • 6 authors
·
Mar 31, 2025

Comparing the Efficacy of GPT-4 and Chat-GPT in Mental Health Care: A Blind Assessment of Large Language Models for Psychological Support

Background: Rapid advancements in natural language processing have led to the development of large language models with the potential to revolutionize mental health care. These models have shown promise in assisting clinicians and providing support to individuals experiencing various psychological challenges. Objective: This study aims to compare the performance of two large language models, GPT-4 and Chat-GPT, in responding to a set of 18 psychological prompts, to assess their potential applicability in mental health care settings. Methods: A blind methodology was employed, with a clinical psychologist evaluating the models' responses without knowledge of their origins. The prompts encompassed a diverse range of mental health topics, including depression, anxiety, and trauma, to ensure a comprehensive assessment. Results: The results demonstrated a significant difference in performance between the two models (p > 0.05). GPT-4 achieved an average rating of 8.29 out of 10, while Chat-GPT received an average rating of 6.52. The clinical psychologist's evaluation suggested that GPT-4 was more effective at generating clinically relevant and empathetic responses, thereby providing better support and guidance to potential users. Conclusions: This study contributes to the growing body of literature on the applicability of large language models in mental health care settings. The findings underscore the importance of continued research and development in the field to optimize these models for clinical use. Further investigation is necessary to understand the specific factors underlying the performance differences between the two models and to explore their generalizability across various populations and mental health conditions.

  • 1 authors
·
May 15, 2024

A Careful Examination of Large Behavior Models for Multitask Dexterous Manipulation

Robot manipulation has seen tremendous progress in recent years, with imitation learning policies enabling successful performance of dexterous and hard-to-model tasks. Concurrently, scaling data and model size has led to the development of capable language and vision foundation models, motivating large-scale efforts to create general-purpose robot foundation models. While these models have garnered significant enthusiasm and investment, meaningful evaluation of real-world performance remains a challenge, limiting both the pace of development and inhibiting a nuanced understanding of current capabilities. In this paper, we rigorously evaluate multitask robot manipulation policies, referred to as Large Behavior Models (LBMs), by extending the Diffusion Policy paradigm across a corpus of simulated and real-world robot data. We propose and validate an evaluation pipeline to rigorously analyze the capabilities of these models with statistical confidence. We compare against single-task baselines through blind, randomized trials in a controlled setting, using both simulation and real-world experiments. We find that multi-task pretraining makes the policies more successful and robust, and enables teaching complex new tasks more quickly, using a fraction of the data when compared to single-task baselines. Moreover, performance predictably increases as pretraining scale and diversity grows. Project page: https://toyotaresearchinstitute.github.io/lbm1/

  • 82 authors
·
Jul 7, 2025

MixAT: Combining Continuous and Discrete Adversarial Training for LLMs

Despite recent efforts in Large Language Models (LLMs) safety and alignment, current adversarial attacks on frontier LLMs are still able to force harmful generations consistently. Although adversarial training has been widely studied and shown to significantly improve the robustness of traditional machine learning models, its strengths and weaknesses in the context of LLMs are less understood. Specifically, while existing discrete adversarial attacks are effective at producing harmful content, training LLMs with concrete adversarial prompts is often computationally expensive, leading to reliance on continuous relaxations. As these relaxations do not correspond to discrete input tokens, such latent training methods often leave models vulnerable to a diverse set of discrete attacks. In this work, we aim to bridge this gap by introducing MixAT, a novel method that combines stronger discrete and faster continuous attacks during training. We rigorously evaluate MixAT across a wide spectrum of state-of-the-art attacks, proposing the At Least One Attack Success Rate (ALO-ASR) metric to capture the worst-case vulnerability of models. We show MixAT achieves substantially better robustness (ALO-ASR < 20%) compared to prior defenses (ALO-ASR > 50%), while maintaining a runtime comparable to methods based on continuous relaxations. We further analyze MixAT in realistic deployment settings, exploring how chat templates, quantization, low-rank adapters, and temperature affect both adversarial training and evaluation, revealing additional blind spots in current methodologies. Our results demonstrate that MixAT's discrete-continuous defense offers a principled and superior robustness-accuracy tradeoff with minimal computational overhead, highlighting its promise for building safer LLMs. We provide our code and models at https://github.com/insait-institute/MixAT.

  • 5 authors
·
May 22, 2025

Evaluating language models as risk scores

Current question-answering benchmarks predominantly focus on accuracy in realizable prediction tasks. Conditioned on a question and answer-key, does the most likely token match the ground truth? Such benchmarks necessarily fail to evaluate LLMs' ability to quantify ground-truth outcome uncertainty. In this work, we focus on the use of LLMs as risk scores for unrealizable prediction tasks. We introduce folktexts, a software package to systematically generate risk scores using LLMs, and evaluate them against US Census data products. A flexible API enables the use of different prompting schemes, local or web-hosted models, and diverse census columns that can be used to compose custom prediction tasks. We evaluate 17 recent LLMs across five proposed benchmark tasks. We find that zero-shot risk scores produced by multiple-choice question-answering have high predictive signal but are widely miscalibrated. Base models consistently overestimate outcome uncertainty, while instruction-tuned models underestimate uncertainty and produce over-confident risk scores. In fact, instruction-tuning polarizes answer distribution regardless of true underlying data uncertainty. This reveals a general inability of instruction-tuned LLMs to express data uncertainty using multiple-choice answers. A separate experiment using verbalized chat-style risk queries yields substantially improved calibration across instruction-tuned models. These differences in ability to quantify data uncertainty cannot be revealed in realizable settings, and highlight a blind-spot in the current evaluation ecosystem that folktexts covers.

  • 3 authors
·
Jul 19, 2024

PointArena: Probing Multimodal Grounding Through Language-Guided Pointing

Pointing serves as a fundamental and intuitive mechanism for grounding language within visual contexts, with applications spanning robotics, assistive technologies, and interactive AI systems. While recent multimodal models have started to support pointing capabilities, existing benchmarks typically focus only on referential object localization tasks. We introduce PointArena, a comprehensive platform for evaluating multimodal pointing across diverse reasoning scenarios. PointArena comprises three components: (1) Point-Bench, a curated dataset containing approximately 1,000 pointing tasks across five reasoning categories; (2) Point-Battle, an interactive, web-based arena facilitating blind, pairwise model comparisons, which has already gathered over 4,500 anonymized votes; and (3) Point-Act, a real-world robotic manipulation system allowing users to directly evaluate multimodal model pointing capabilities in practical settings. We conducted extensive evaluations of both state-of-the-art open-source and proprietary multimodal models. Results indicate that Molmo-72B consistently outperforms other models, though proprietary models increasingly demonstrate comparable performance. Additionally, we find that supervised training specifically targeting pointing tasks significantly enhances model performance. Across our multi-stage evaluation pipeline, we also observe strong correlations, underscoring the critical role of precise pointing capabilities in enabling multimodal models to effectively bridge abstract reasoning with concrete, real-world actions. Project page: https://pointarena.github.io/

  • 15 authors
·
May 15, 2025 2