Diffusion Transformers (DiTs) have demonstrated strong performance in generative modeling, particularly in image synthesis, making them a compelling choice for molecular conformer generation. However, applying DiTs to molecules introduces novel challenges, such as integrating discrete molecular graph information with continuous 3D geometry, handling Euclidean symmetries, and designing conditioning mechanisms that generalize across molecules of varying sizes and structures. We propose DiTMC, a framework that adapts DiTs to address these challenges through a modular architecture that separates the processing of 3D coordinates from conditioning on atomic connectivity. To this end, we introduce two complementary graph-based conditioning strategies that integrate seamlessly with the DiT architecture. These are combined with different attention mechanisms, including both standard non-equivariant and SO(3)-equivariant formulations, enabling flexible control over the trade-off between between accuracy and computational efficiency. Experiments on standard conformer generation benchmarks (GEOM-QM9, -DRUGS, -XL) demonstrate that DiTMC achieves state-of-the-art precision and physical validity. Our results highlight how architectural choices and symmetry priors affect sample quality and efficiency, suggesting promising directions for large-scale generative modeling of molecular structures. Code is available at https://github.com/ML4MolSim/dit_mc.

Despite its empirical success, the theoretical foundations of self-supervised contrastive learning (CL) are not yet fully established. In this work, we address this gap by showing that standard CL objectives implicitly approximate a supervised variant we call the negatives-only supervised contrastive loss (NSCL), which excludes same-class contrasts. We prove that the gap between the CL and NSCL losses vanishes as the number of semantic classes increases, under a bound that is both label-agnostic and architecture-independent. We characterize the geometric structure of the global minimizers of the NSCL loss: the learned representations exhibit augmentation collapse, within-class collapse, and class centers that form a simplex equiangular tight frame. We further introduce a new bound on the few-shot error of linear-probing. This bound depends on two measures of feature variability--within-class dispersion and variation along the line between class centers. We show that directional variation dominates the bound and that the within-class dispersion's effect diminishes as the number of labeled samples increases. These properties enable CL and NSCL-trained representations to support accurate few-shot label recovery using simple linear probes. Finally, we empirically validate our theoretical findings: the gap between CL and NSCL losses decays at a rate of $\mathcal{O}(\frac{1}{\#\text{classes}})$; the two losses are highly correlated; minimizing the CL loss implicitly brings the NSCL loss close to the value achieved by direct minimization; and the proposed few-shot error bound provides a tight estimate of probing performance in practice. The code and project page of the paper are available at [\href{https://github.com/DLFundamentals/understanding-ssl}{code}, \href{https://dlfundamentals.github.io/ssl-is-approximately-sl/}{project page}].

Emotions are a fundamental facet of human experience, varying across individuals, cultural contexts, and nationalities. Given the recent success of Large Language Models (LLMs) as role-playing agents, we examine whether LLMs exhibit emotional stereotypes when assigned nationality-specific personas. Specifically, we investigate how different countries are represented in pre-trained LLMs through emotion attributions and whether these attributions align with cultural norms. To provide a deeper interpretive lens, we incorporate four key cultural dimensions, namely Power Distance, Uncertainty Avoidance, Long-Term Orientation, and Individualism, derived from Hofstedes cross-cultural framework. Our analysis reveals significant nationality-based differences, with emotions such as shame, fear, and joy being disproportionately assigned across regions. Furthermore, we observe notable misalignment between LLM-generated and human emotional responses, particularly for negative emotions, highlighting the presence of reductive and potentially biased stereotypes in LLM outputs.

Multi-label classification is prevalent in real-world settings, but the behavior of Large Language Models (LLMs) in this setting is understudied. We investigate how autoregressive LLMs perform multi-label classification, focusing on subjective tasks, by analyzing the output distributions of the models at each label generation step. We find that the initial probability distribution for the first label often does not reflect the eventual final output, even in terms of relative order and find LLMs tend to suppress all but one label at each generation step. We further observe that as model scale increases, their token distributions exhibit lower entropy and higher single-label confidence, but the internal relative ranking of the labels improves. Finetuning methods such as supervised finetuning and reinforcement learning amplify this phenomenon. We introduce the task of distribution alignment for multi-label settings: aligning LLM-derived label distributions with empirical distributions estimated from annotator responses in subjective tasks. We propose both zero-shot and supervised methods which improve both alignment and predictive performance over existing approaches. We find one method -- taking the max probability over all label generation distributions instead of just using the initial probability distribution -- improves both distribution alignment and overall F1 classification without adding any additional computation.

Modeling complex subjective tasks in Natural Language Processing, such as recognizing emotion and morality, is considerably challenging due to significant variation in human annotations. This variation often reflects reasonable differences in semantic interpretations rather than mere noise, necessitating methods to distinguish between legitimate subjectivity and error. We address this challenge by exploring label verification in these contexts using Large Language Models (LLMs). First, we propose a simple In-Context Learning binary filtering baseline that estimates the reasonableness of a document-label pair. We then introduce the Label-in-a-Haystack setting: the query and its label(s) are included in the demonstrations shown to LLMs, which are prompted to predict the label(s) again, while receiving task-specific instructions (e.g., emotion recognition) rather than label copying. We show how the failure to copy the label(s) to the output of the LLM are task-relevant and informative. Building on this, we propose the Label-in-a-Haystack Rectification (LiaHR) framework for subjective label correction: when the model outputs diverge from the reference gold labels, we assign the generated labels to the example instead of discarding it. This approach can be integrated into annotation pipelines to enhance signal-to-noise ratios. Comprehensive analyses, human evaluations, and ecological validity studies verify the utility of LiaHR for label correction. Code is available at https://github.com/gchochla/liahr.

Traditional Retrieval-Augmented Generation (RAG) struggles with complex queries that lack strong signals to retrieve the most relevant context, forcing a trade-off between choosing a small context that misses key information and a large context that confuses the LLM. To address this, we propose Forward-Backward RAG (FB-RAG), a new training-free framework based on a simple yet powerful forward-looking strategy. FB-RAG employs a light-weight LLM to peek into potential future generations, using evidence from multiple sampled outputs to precisely identify the most relevant context for a final, more powerful generator. This improves performance without complex finetuning or Reinforcement Learning common in prior work. Across $9$ datasets from LongBench and $\infty$Bench, FB-RAG consistently delivers strong results. Further, the performance gains can be achieved with reduced latency due to a shorter, more focused prompt for the powerful generator. On EN.QA dataset, FB-RAG matches the leading baseline with over $48$% latency reduction or achieves an $8$% performance improvement with a $10$% latency reduction. Our analysis finds cases where even when the forward-looking LLM fails to generate correct answers, its attempts are sufficient to guide the final model to an accurate response, demonstrating how smaller LLMs can systematically improve the performance and efficiency of larger ones.

We have only limited understanding of how and why large language models (LLMs) respond in the ways that they do. Their neural networks have proven challenging to interpret, and we are only beginning to tease out the function of individual neurons and circuits within them. However, another path to understanding these systems is to investigate and develop their capacity to explain their own functioning. Here, we show that i) LLMs can accurately describe quantitative features of their own internal processes during certain kinds of decision-making and ii) that it is possible to improve these capabilities through training. To do so, we fine-tuned GPT-4o and GPT-4o-mini to make decisions in a wide variety of complex contexts (e.g., choosing between condos, loans, vacations, etc.) according to randomly-generated, quantitative preferences about how to weigh different attributes (e.g., the relative importance of natural light versus quiet surroundings for condos). We demonstrate that the LLMs can accurately report these preferences (i.e., the weights that they learned to give to different attributes during decision-making). Next, we demonstrate that these LLMs can be fine-tuned to explain their decision-making even more accurately. Finally, we demonstrate that this training generalizes: It improves the ability of the models to accurately explain how they make other complex decisions, not just decisions they have been fine-tuned to make. This work is a step towards training LLMs to accurately and broadly report on their own internal processes -- a possibility that would yield substantial benefits for interpretability, control, and safety.

Reinforcement learning-based post-training of large language models (LLMs) has recently gained attention, particularly following the release of DeepSeek R1, which applied GRPO for fine-tuning. Amid the growing hype around improved reasoning abilities attributed to RL post-training, we critically examine the formulation and assumptions underlying these methods. We start by highlighting the popular structural assumptions made in modeling LLM training as a Markov Decision Process (MDP), and show how they lead to a degenerate MDP that doesn't quite need the RL/GRPO apparatus. The two critical structural assumptions include (1) making the MDP states be just a concatenation of the actions-with states becoming the context window and the actions becoming the tokens in LLMs and (2) splitting the reward of a state-action trajectory uniformly across the trajectory. Through a comprehensive analysis, we demonstrate that these simplifying assumptions make the approach effectively equivalent to an outcome-driven supervised learning. Our experiments on benchmarks including GSM8K and Countdown using Qwen-2.5 base models show that iterative supervised fine-tuning, incorporating both positive and negative samples, achieves performance comparable to GRPO-based training. We will also argue that the structural assumptions indirectly incentivize the RL to generate longer sequences of intermediate tokens-which in turn feeds into the narrative of "RL generating longer thinking traces." While RL may well be a very useful technique for improving the reasoning abilities of LLMs, our analysis shows that the simplistic structural assumptions made in modeling the underlying MDP render the popular LLM RL frameworks and their interpretations questionable.

Model editing aims to enhance the accuracy and reliability of large language models (LLMs) by efficiently adjusting their internal parameters. Currently, most LLM editing datasets are confined to narrow knowledge domains and cover a limited range of editing evaluation. They often overlook the broad scope of editing demands and the diversity of ripple effects resulting from edits. In this context, we introduce UniEdit, a unified benchmark for LLM editing grounded in open-domain knowledge. First, we construct editing samples by selecting entities from 25 common domains across five major categories, utilizing the extensive triple knowledge available in open-domain knowledge graphs to ensure comprehensive coverage of the knowledge domains. To address the issues of generality and locality in editing, we design an Neighborhood Multi-hop Chain Sampling (NMCS) algorithm to sample subgraphs based on a given knowledge piece to entail comprehensive ripple effects to evaluate. Finally, we employ proprietary LLMs to convert the sampled knowledge subgraphs into natural language text, guaranteeing grammatical accuracy and syntactical diversity. Extensive statistical analysis confirms the scale, comprehensiveness, and diversity of our UniEdit benchmark. We conduct comprehensive experiments across multiple LLMs and editors, analyzing their performance to highlight strengths and weaknesses in editing across open knowledge domains and various evaluation criteria, thereby offering valuable insights for future research endeavors.

Model Context Protocol (MCP) standardizes interface mapping for large language models (LLMs) to access external data and tools, which revolutionizes the paradigm of tool selection and facilitates the rapid expansion of the LLM agent tool ecosystem. However, as the MCP is increasingly adopted, third-party customized versions of the MCP server expose potential security vulnerabilities. In this paper, we first introduce a novel security threat, which we term the MCP Preference Manipulation Attack (MPMA). An attacker deploys a customized MCP server to manipulate LLMs, causing them to prioritize it over other competing MCP servers. This can result in economic benefits for attackers, such as revenue from paid MCP services or advertising income generated from free servers. To achieve MPMA, we first design a Direct Preference Manipulation Attack (DPMA) that achieves significant effectiveness by inserting the manipulative word and phrases into the tool name and description. However, such a direct modification is obvious to users and lacks stealthiness. To address these limitations, we further propose Genetic-based Advertising Preference Manipulation Attack (GAPMA). GAPMA employs four commonly used strategies to initialize descriptions and integrates a Genetic Algorithm (GA) to enhance stealthiness. The experiment results demonstrate that GAPMA balances high effectiveness and stealthiness. Our study reveals a critical vulnerability of the MCP in open ecosystems, highlighting an urgent need for robust defense mechanisms to ensure the fairness of the MCP ecosystem.