new

Get trending papers in your email inbox!

Subscribe

byAK and the research community

Mar 13

ProFSA: Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment

Pocket representations play a vital role in various biomedical applications, such as druggability estimation, ligand affinity prediction, and de novo drug design. While existing geometric features and pretrained representations have demonstrated promising results, they usually treat pockets independent of ligands, neglecting the fundamental interactions between them. However, the limited pocket-ligand complex structures available in the PDB database (less than 100 thousand non-redundant pairs) hampers large-scale pretraining endeavors for interaction modeling. To address this constraint, we propose a novel pocket pretraining approach that leverages knowledge from high-resolution atomic protein structures, assisted by highly effective pretrained small molecule representations. By segmenting protein structures into drug-like fragments and their corresponding pockets, we obtain a reasonable simulation of ligand-receptor interactions, resulting in the generation of over 5 million complexes. Subsequently, the pocket encoder is trained in a contrastive manner to align with the representation of pseudo-ligand furnished by some pretrained small molecule encoders. Our method, named ProFSA, achieves state-of-the-art performance across various tasks, including pocket druggability prediction, pocket matching, and ligand binding affinity prediction. Notably, ProFSA surpasses other pretraining methods by a substantial margin. Moreover, our work opens up a new avenue for mitigating the scarcity of protein-ligand complex data through the utilization of high-quality and diverse protein structure databases.

SimpleToM: Exposing the Gap between Explicit ToM Inference and Implicit ToM Application in LLMs

While prior work has explored whether large language models (LLMs) possess a "theory of mind" (ToM) - the ability to attribute mental states to oneself and others - there has been little work testing whether LLMs can implicitly apply such knowledge to predict behavior, or to judge whether an observed behavior is rational. Such skills are critical for appropriate interaction in social environments. We create a new dataset, SimpleTom, containing concise, diverse stories (e.g., "The can of Pringles has moldy chips in it. Mary picks up the can in the supermarket and walks to the cashier."), each with three questions that test different degrees of ToM reasoning, asking models to predict (a) mental state ("Is Mary aware of the mold?"), (b) behavior ("Will Mary pay for the chips or report the mold?"), and (c) judgment ("Mary paid for the chips. Was that reasonable?"). To our knowledge, SimpleToM is the first dataset to systematically explore downstream reasoning requiring knowledge of mental states in realistic scenarios. Our experimental results are intriguing: While most models can reliably predict mental state on our dataset (a), they often fail to correctly predict the behavior (b), and fare even worse at judging whether given behaviors are reasonable (c), despite being correctly aware of the protagonist's mental state should make such secondary predictions obvious. We further show that we can help models do better at (b) and (c) via interventions such as reminding the model of its earlier mental state answer and mental-state-specific chain-of-thought prompting, raising the action prediction accuracies (e.g., from 49.5% to 93.5% for GPT-4o) and judgment accuracies (e.g., from 15.3% to 94.7% in GPT-4o). While this shows that models can be coaxed to perform well, it requires task-specific interventions, and the natural model performances remain low, a cautionary tale for LLM deployment.

WildGuard: Open One-Stop Moderation Tools for Safety Risks, Jailbreaks, and Refusals of LLMs

We introduce WildGuard -- an open, light-weight moderation tool for LLM safety that achieves three goals: (1) identifying malicious intent in user prompts, (2) detecting safety risks of model responses, and (3) determining model refusal rate. Together, WildGuard serves the increasing needs for automatic safety moderation and evaluation of LLM interactions, providing a one-stop tool with enhanced accuracy and broad coverage across 13 risk categories. While existing open moderation tools such as Llama-Guard2 score reasonably well in classifying straightforward model interactions, they lag far behind a prompted GPT-4, especially in identifying adversarial jailbreaks and in evaluating models' refusals, a key measure for evaluating safety behaviors in model responses. To address these challenges, we construct WildGuardMix, a large-scale and carefully balanced multi-task safety moderation dataset with 92K labeled examples that cover vanilla (direct) prompts and adversarial jailbreaks, paired with various refusal and compliance responses. WildGuardMix is a combination of WildGuardTrain, the training data of WildGuard, and WildGuardTest, a high-quality human-annotated moderation test set with 5K labeled items covering broad risk scenarios. Through extensive evaluations on WildGuardTest and ten existing public benchmarks, we show that WildGuard establishes state-of-the-art performance in open-source safety moderation across all the three tasks compared to ten strong existing open-source moderation models (e.g., up to 26.4% improvement on refusal detection). Importantly, WildGuard matches and sometimes exceeds GPT-4 performance (e.g., up to 3.9% improvement on prompt harmfulness identification). WildGuard serves as a highly effective safety moderator in an LLM interface, reducing the success rate of jailbreak attacks from 79.8% to 2.4%.

DriveDreamer: Towards Real-world-driven World Models for Autonomous Driving

World models, especially in autonomous driving, are trending and drawing extensive attention due to their capacity for comprehending driving environments. The established world model holds immense potential for the generation of high-quality driving videos, and driving policies for safe maneuvering. However, a critical limitation in relevant research lies in its predominant focus on gaming environments or simulated settings, thereby lacking the representation of real-world driving scenarios. Therefore, we introduce DriveDreamer, a pioneering world model entirely derived from real-world driving scenarios. Regarding that modeling the world in intricate driving scenes entails an overwhelming search space, we propose harnessing the powerful diffusion model to construct a comprehensive representation of the complex environment. Furthermore, we introduce a two-stage training pipeline. In the initial phase, DriveDreamer acquires a deep understanding of structured traffic constraints, while the subsequent stage equips it with the ability to anticipate future states. The proposed DriveDreamer is the first world model established from real-world driving scenarios. We instantiate DriveDreamer on the challenging nuScenes benchmark, and extensive experiments verify that DriveDreamer empowers precise, controllable video generation that faithfully captures the structural constraints of real-world traffic scenarios. Additionally, DriveDreamer enables the generation of realistic and reasonable driving policies, opening avenues for interaction and practical applications.

Carbon and Silicon, Coexist or Compete? A Survey on Human-AI Interactions in Agent-based Modeling and Simulation

Recent interest in human-AI interactions in agent-based modeling and simulation (ABMS) has grown rapidly due to the widespread utilization of large language models (LLMs). ABMS is an intelligent approach that simulates autonomous agents' behaviors within a defined environment to research emergent phenomena. Integrating LLMs into ABMS enables natural language interaction between humans and models. Meanwhile, it introduces new challenges that rely on human interaction to address. Human involvement can assist ABMS in adapting to flexible and complex research demands. However, systematic reviews of interactions that examine how humans and AI interact in ABMS are lacking. In this paper, we investigate existing works and propose a novel taxonomy to categorize the interactions derived from them. Specifically, human users refer to researchers who utilize ABMS tools to conduct their studies in our survey. We decompose interactions into five dimensions: the goals that users want to achieve (Why), the phases that users are involved (When), the components of the system (What), the roles of users (Who), and the means of interactions (How). Our analysis summarizes the findings that reveal existing interaction patterns. They provide researchers who develop interactions with comprehensive guidance on how humans and AI interact. We further discuss the unexplored interactions and suggest future research directions.

Exploring the cloud of feature interaction scores in a Rashomon set

Interactions among features are central to understanding the behavior of machine learning models. Recent research has made significant strides in detecting and quantifying feature interactions in single predictive models. However, we argue that the feature interactions extracted from a single pre-specified model may not be trustworthy since: a well-trained predictive model may not preserve the true feature interactions and there exist multiple well-performing predictive models that differ in feature interaction strengths. Thus, we recommend exploring feature interaction strengths in a model class of approximately equally accurate predictive models. In this work, we introduce the feature interaction score (FIS) in the context of a Rashomon set, representing a collection of models that achieve similar accuracy on a given task. We propose a general and practical algorithm to calculate the FIS in the model class. We demonstrate the properties of the FIS via synthetic data and draw connections to other areas of statistics. Additionally, we introduce a Halo plot for visualizing the feature interaction variance in high-dimensional space and a swarm plot for analyzing FIS in a Rashomon set. Experiments with recidivism prediction and image classification illustrate how feature interactions can vary dramatically in importance for similarly accurate predictive models. Our results suggest that the proposed FIS can provide valuable insights into the nature of feature interactions in machine learning models.

Rethinking Explainability as a Dialogue: A Practitioner's Perspective

As practitioners increasingly deploy machine learning models in critical domains such as health care, finance, and policy, it becomes vital to ensure that domain experts function effectively alongside these models. Explainability is one way to bridge the gap between human decision-makers and machine learning models. However, most of the existing work on explainability focuses on one-off, static explanations like feature importances or rule lists. These sorts of explanations may not be sufficient for many use cases that require dynamic, continuous discovery from stakeholders. In the literature, few works ask decision-makers about the utility of existing explanations and other desiderata they would like to see in an explanation going forward. In this work, we address this gap and carry out a study where we interview doctors, healthcare professionals, and policymakers about their needs and desires for explanations. Our study indicates that decision-makers would strongly prefer interactive explanations in the form of natural language dialogues. Domain experts wish to treat machine learning models as "another colleague", i.e., one who can be held accountable by asking why they made a particular decision through expressive and accessible natural language interactions. Considering these needs, we outline a set of five principles researchers should follow when designing interactive explanations as a starting place for future work. Further, we show why natural language dialogues satisfy these principles and are a desirable way to build interactive explanations. Next, we provide a design of a dialogue system for explainability and discuss the risks, trade-offs, and research opportunities of building these systems. Overall, we hope our work serves as a starting place for researchers and engineers to design interactive explainability systems.

Truthful AI: Developing and governing AI that does not lie

In many contexts, lying -- the use of verbal falsehoods to deceive -- is harmful. While lying has traditionally been a human affair, AI systems that make sophisticated verbal statements are becoming increasingly prevalent. This raises the question of how we should limit the harm caused by AI "lies" (i.e. falsehoods that are actively selected for). Human truthfulness is governed by social norms and by laws (against defamation, perjury, and fraud). Differences between AI and humans present an opportunity to have more precise standards of truthfulness for AI, and to have these standards rise over time. This could provide significant benefits to public epistemics and the economy, and mitigate risks of worst-case AI futures. Establishing norms or laws of AI truthfulness will require significant work to: (1) identify clear truthfulness standards; (2) create institutions that can judge adherence to those standards; and (3) develop AI systems that are robustly truthful. Our initial proposals for these areas include: (1) a standard of avoiding "negligent falsehoods" (a generalisation of lies that is easier to assess); (2) institutions to evaluate AI systems before and after real-world deployment; and (3) explicitly training AI systems to be truthful via curated datasets and human interaction. A concerning possibility is that evaluation mechanisms for eventual truthfulness standards could be captured by political interests, leading to harmful censorship and propaganda. Avoiding this might take careful attention. And since the scale of AI speech acts might grow dramatically over the coming decades, early truthfulness standards might be particularly important because of the precedents they set.

Dispider: Enabling Video LLMs with Active Real-Time Interaction via Disentangled Perception, Decision, and Reaction

Active Real-time interaction with video LLMs introduces a new paradigm for human-computer interaction, where the model not only understands user intent but also responds while continuously processing streaming video on the fly. Unlike offline video LLMs, which analyze the entire video before answering questions, active real-time interaction requires three capabilities: 1) Perception: real-time video monitoring and interaction capturing. 2) Decision: raising proactive interaction in proper situations, 3) Reaction: continuous interaction with users. However, inherent conflicts exist among the desired capabilities. The Decision and Reaction require a contrary Perception scale and grain, and the autoregressive decoding blocks the real-time Perception and Decision during the Reaction. To unify the conflicted capabilities within a harmonious system, we present Dispider, a system that disentangles Perception, Decision, and Reaction. Dispider features a lightweight proactive streaming video processing module that tracks the video stream and identifies optimal moments for interaction. Once the interaction is triggered, an asynchronous interaction module provides detailed responses, while the processing module continues to monitor the video in the meantime. Our disentangled and asynchronous design ensures timely, contextually accurate, and computationally efficient responses, making Dispider ideal for active real-time interaction for long-duration video streams. Experiments show that Dispider not only maintains strong performance in conventional video QA tasks, but also significantly surpasses previous online models in streaming scenario responses, thereby validating the effectiveness of our architecture. The code and model are released at https://github.com/Mark12Ding/Dispider.

GLEE: A Unified Framework and Benchmark for Language-based Economic Environments

Large Language Models (LLMs) show significant potential in economic and strategic interactions, where communication via natural language is often prevalent. This raises key questions: Do LLMs behave rationally? Can they mimic human behavior? Do they tend to reach an efficient and fair outcome? What is the role of natural language in the strategic interaction? How do characteristics of the economic environment influence these dynamics? These questions become crucial concerning the economic and societal implications of integrating LLM-based agents into real-world data-driven systems, such as online retail platforms and recommender systems. While the ML community has been exploring the potential of LLMs in such multi-agent setups, varying assumptions, design choices and evaluation criteria across studies make it difficult to draw robust and meaningful conclusions. To address this, we introduce a benchmark for standardizing research on two-player, sequential, language-based games. Inspired by the economic literature, we define three base families of games with consistent parameterization, degrees of freedom and economic measures to evaluate agents' performance (self-gain), as well as the game outcome (efficiency and fairness). We develop an open-source framework for interaction simulation and analysis, and utilize it to collect a dataset of LLM vs. LLM interactions across numerous game configurations and an additional dataset of human vs. LLM interactions. Through extensive experimentation, we demonstrate how our framework and dataset can be used to: (i) compare the behavior of LLM-based agents to human players in various economic contexts; (ii) evaluate agents in both individual and collective performance measures; and (iii) quantify the effect of the economic characteristics of the environments on the behavior of agents.

Multimodal Learning Without Labeled Multimodal Data: Guarantees and Applications

In many machine learning systems that jointly learn from multiple modalities, a core research question is to understand the nature of multimodal interactions: the emergence of new task-relevant information during learning from both modalities that was not present in either alone. We study this challenge of interaction quantification in a semi-supervised setting with only labeled unimodal data and naturally co-occurring multimodal data (e.g., unlabeled images and captions, video and corresponding audio) but when labeling them is time-consuming. Using a precise information-theoretic definition of interactions, our key contributions are the derivations of lower and upper bounds to quantify the amount of multimodal interactions in this semi-supervised setting. We propose two lower bounds based on the amount of shared information between modalities and the disagreement between separately trained unimodal classifiers, and derive an upper bound through connections to approximate algorithms for min-entropy couplings. We validate these estimated bounds and show how they accurately track true interactions. Finally, two semi-supervised multimodal applications are explored based on these theoretical results: (1) analyzing the relationship between multimodal performance and estimated interactions, and (2) self-supervised learning that embraces disagreement between modalities beyond agreement as is typically done.

Critical-Questions-of-Thought: Steering LLM reasoning with Argumentative Querying

Studies have underscored how, regardless of the recent breakthrough and swift advances in AI research, even state-of-the-art Large Language models (LLMs) continue to struggle when performing logical and mathematical reasoning. The results seem to suggest that LLMs still work as (highly advanced) data pattern identifiers, scoring poorly when attempting to generalise and solve reasoning problems the models have never previously seen or that are not close to samples presented in their training data. To address this compelling concern, this paper makes use of the notion of critical questions from the literature on argumentation theory, focusing in particular on Toulmin's model of argumentation. We show that employing these critical questions can improve the reasoning capabilities of LLMs. By probing the rationale behind the models' reasoning process, the LLM can assess whether some logical mistake is occurring and correct it before providing the final reply to the user prompt. The underlying idea is drawn from the gold standard of any valid argumentative procedure: the conclusion is valid if it is entailed by accepted premises. Or, to paraphrase such Aristotelian principle in a real-world approximation, characterised by incomplete information and presumptive logic, the conclusion is valid if not proved otherwise. This approach successfully steers the models' output through a reasoning pipeline, resulting in better performance against the baseline and its Chain-of-Thought (CoT) implementation. To this end, an extensive evaluation of the proposed approach on the MT-Bench Reasoning and Math tasks across a range of LLMs is provided.