GenAI4ELab/papercli-papers huggingface dataset:
Representational Similarity via Interpretable Visual Concepts
Authors: Neehar Kondapaneni; Oisin Mac Aodha; Pietro Perona
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: How do two deep neural networks differ in how they arrive at a decision? Measuring  the similarity of deep networks has been a long-standing open question. Most existing methods provide a single number to measure the similarity of two networks at a given layer, but give no insight into what makes them similar or dissimilar. We introduce an interpretable representational similarity method (RSVC) to compare two networks. We use RSVC to discover shared and unique visual concepts between two models. We show that some aspects of model differences can be attributed to unique concepts discovered by one model that are not well represented in the other. Finally, we conduct extensive evaluation across different vision model architectures and training protocols to demonstrate its effectiveness.
DRoC: Elevating Large Language Models for Complex Vehicle Routing via Decomposed Retrieval of Constraints
Authors: Xia Jiang; Yaoxin Wu; Chenhao Zhang; Yingqian Zhang
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: This paper proposes Decomposed Retrieval of Constraints (DRoC), a novel framework aimed at enhancing large language models (LLMs) in exploiting solvers to tackle vehicle routing problems (VRPs) with intricate constraints. While LLMs have shown promise in solving simple VRPs, their potential in addressing complex VRP variants is still suppressed, due to the limited embedded internal knowledge that is required to accurately reflect diverse VRP constraints. Our approach mitigates the issue by integrating external knowledge via a novel retrieval-augmented generation (RAG) approach. More specifically, the DRoC decomposes VRP constraints, externally retrieves information relevant to each constraint, and synergistically combines internal and external knowledge to benefit the program generation for solving VRPs. The DRoC also allows LLMs to dynamically select between RAG and self-debugging mechanisms, thereby optimizing program generation without the need for additional training. Experiments across 48 VRP variants exhibit the superiority of DRoC, with significant improvements in the accuracy rate and runtime error rate delivered by the generated programs. The DRoC framework has the potential to elevate LLM performance in complex optimization tasks, fostering the applicability of LLMs in industries such as transportation and logistics.
Topological Schrödinger Bridge Matching
Authors: Maosheng Yang
Venue: ICLR 2025 (ICLR 2025 Spotlight)

Abstract: Given two boundary distributions, the \emph{Schrödinger Bridge} (SB) problem seeks the “most likely” random evolution between them with respect to a reference process. It has revealed rich connections to recent machine learning methods for generative modeling and distribution matching. While these methods perform well in Euclidean domains, they are not directly applicable to topological domains such as graphs and simplicial complexes, which are crucial for data defined over network entities, such as node signals and edge flows. In this work, we propose the \emph{Topological Schrödinger Bridge problem} ($\mathcal{T}$SBP) for matching signal distributions on a topological domain. We set the reference process to follow some linear tractable \emph{topology-aware} stochastic dynamics such as topological heat diffusion. For the case of Gaussian boundary distributions, we derive a \emph{closed-form} topological SB ($\mathcal{T}$SB) in terms of its time-marginal and stochastic differential. In the general case, leveraging the well-known result, we show that the optimal process follows the forward-backward topological dynamics governed by some unknowns. Building on these results, we develop $\mathcal{T}$SB-based models for matching topological signals by parameterizing the unknowns in the optimal process as \emph{(topological) neural networks} and learning them through \emph{likelihood training}. We validate the theoretical results and demonstrate the practical applications of $\mathcal{T}$SB-based models on both synthetic and real-world networks, emphasizing the role of topology. Additionally, we discuss the connections of $\mathcal{T}$SB-based models to other emerging models, and outline future directions for topological signal matching.
On Minimizing Adversarial Counterfactual Error in Adversarial Reinforcement Learning
Authors: Roman Belaire; Arunesh Sinha; Pradeep Varakantham
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Deep Reinforcement Learning (DRL) policies are highly susceptible to adversarial noise in observations, which poses significant risks in safety-critical scenarios. The challenge inherent to adversarial perturbations is that by altering the information observed by the agent, the state becomes only partially observable. Existing approaches address this by either enforcing consistent actions across nearby states or maximizing the worst-case value within adversarially perturbed observations. However, the former suffers from performance degradation when attacks succeed, while the latter tends to be overly conservative, leading to suboptimal performance in benign settings. We hypothesize that these limitations stem from their failing to account for partial observability directly. To this end, we introduce a novel objective called Adversarial Counterfactual Error (ACoE), defined on the beliefs about the true state and balancing value optimization with robustness. To make ACoE scalable in model-free settings, we propose the theoretically-grounded surrogate objective Cumulative-ACoE (C-ACoE). Our empirical evaluations on standard benchmarks (MuJoCo, Atari, and Highway) demonstrate that our method significantly outperforms current state-of-the-art approaches for addressing adversarial RL challenges, offering a promising direction for improving robustness in DRL under adversarial conditions. Our code is available at https://github.com/romanbelaire/acoe-robust-rl.
ToolDial: Multi-turn Dialogue Generation Method for Tool-Augmented Language Models
Authors: Jeonghoon Shim; Gyuhyeon Seo; Cheongsu Lim; Yohan Jo
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Tool-Augmented Language Models (TALMs) leverage external APIs to answer user queries across various domains. However, existing benchmark datasets for TALM research often feature simplistic dialogues that do not reflect real-world scenarios, such as the need for models to ask clarifying questions or proactively call additional APIs when essential information is missing. To address these limitations, we construct and release ToolDial, a dataset comprising 11,111 multi-turn dialogues, with an average of 8.95 turns per dialogue, based on APIs from RapidAPI. ToolDial has two key characteristics. First, the dialogues incorporate 16 user and system actions (e.g., request, clarify, fail inform) to capture the rich dynamics of real-world interactions. Second, we simulate dialogues where the system requests necessary information from the user based on API documentation and seeks additional APIs if the user fails to provide the required information. To facilitate this process, we introduce a method for generating an API graph that represents input and output compatibility between APIs. Using ToolDial, we evaluate a suite of language models on their ability to predict correct actions and extract input parameter values for API calls from the dialogue history. Modern language models achieve accuracy scores below 70\%, indicating substantial room for improvement. We provide a detailed analysis of the areas where these models fall short.
3D-MolT5: Leveraging Discrete Structural Information for Molecule-Text Modeling
Authors: Qizhi Pei; Rui Yan; Kaiyuan Gao; Jinhua Zhu; Lijun Wu
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: The integration of molecular and natural language representations has emerged as a focal point in molecular science, with recent advancements in Language Models (LMs) demonstrating significant potential for comprehensive modeling of both domains. However, existing approaches face notable limitations, particularly in their neglect of three-dimensional (3D) information, which is crucial for understanding molecular structures and functions. While some efforts have been made to incorporate 3D molecular information into LMs using external structure encoding modules, significant difficulties remain, such as insufficient interaction across modalities in pre-training and challenges in modality alignment. To address the limitations, we propose \textbf{3D-MolT5}, a unified framework designed to model molecule in both sequence and 3D structure spaces. The key innovation of our approach lies in mapping fine-grained 3D substructure representations into a specialized 3D token vocabulary. This methodology facilitates the seamless integration of sequence and structure representations in a tokenized format, enabling 3D-MolT5 to encode molecular sequences, molecular structures, and text sequences within a unified architecture. Leveraging this tokenized input strategy, we build a foundation model that unifies the sequence and structure data formats. We then conduct joint pre-training with multi-task objectives to enhance the model's comprehension of these diverse modalities within a shared representation space. Thus, our approach significantly improves cross-modal interaction and alignment, addressing key challenges in previous work. Further instruction tuning demonstrated that our 3D-MolT5 has strong generalization ability and surpasses existing methods with superior performance in multiple downstream tasks, such as nearly 70\% improvement on the molecular property prediction task compared to state-of-the-art methods. Our code is available at \url{https://github.com/QizhiPei/3D-MolT5}.
ParFam -- (Neural Guided) Symbolic Regression via Continuous Global Optimization
Authors: Philipp Scholl; Katharina Bieker; Hillary Hauger; Gitta Kutyniok
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: The problem of symbolic regression (SR) arises in many different applications, such as identifying physical laws or deriving mathematical equations describing the behavior of financial markets from given data. Various methods exist to address the problem of SR, often based on genetic programming. However, these methods are usually complicated and involve various hyperparameters. In this paper, we present our new approach ParFam that utilizes parametric families of suitable symbolic functions to translate the discrete symbolic regression problem into a continuous one, resulting in a more straightforward setup compared to current state-of-the-art methods. In combination with a global optimizer, this approach results in a highly effective method to tackle the problem of SR. We theoretically analyze the expressivity of ParFam and demonstrate its performance with extensive numerical experiments based on the common SR benchmark suit SRBench, showing that we achieve state-of-the-art results. Moreover, we present an extension incorporating a pre-trained transformer network (DL-ParFam) to guide ParFam, accelerating the optimization process by up to two magnitudes. Our code and results can be found at https://github.com/Philipp238/parfam.
Taming Transformer Without Using Learning Rate Warmup
Authors: Xianbiao Qi; Yelin He; Jiaquan Ye; Chun-Guang Li; Bojia Zi; Xili Dai; Qin Zou; Rong Xiao
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Scaling Transformer to a large scale without using some technical tricks  such as learning rate warump and an obviously lower learning rate, is an extremely challenging task, and is increasingly gaining more attention. In this paper, we provide a theoretical analysis for the process of training Transformer and reveal a key problem behind model crash phenomenon in the training process, termed *spectral energy concentration* of ${W_q}^{\top} W_k$, which is the reason for a malignant entropy collapse, where ${W_q}$ and $W_k$ are the projection matrices for the query and the key in Transformer, respectively. 
To remedy this problem, motivated by *Weyl's Inequality*, we present a novel optimization strategy, \ie, making the weight updating in successive steps steady---if the ratio $\frac{\sigma_{1}(\nabla W_t)}{\sigma_{1}(W_{t-1})}$ is larger than a threshold, we will automatically bound the learning rate to a weighted multiple of $\frac{\sigma_{1}(W_{t-1})}{\sigma_{1}(\nabla W_t)}$, where $\nabla W_t$ is the updating quantity in step $t$. Such an optimization strategy can prevent spectral energy concentration to only a few directions, and thus can avoid malignant entropy collapse which will trigger the model crash. We conduct extensive experiments using ViT, Swin-Transformer and GPT, showing that our optimization strategy can effectively and stably train these (Transformer) models without using learning rate warmup.
Redefining the task of Bioactivity Prediction
Authors: Yanwen Huang; Bowen Gao; Yinjun Jia; Hongbo Ma; Wei-Ying Ma; Ya-Qin Zhang; Yanyan Lan
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Small molecules are vital to modern medicine, and accurately predicting their bioactivity against protein targets is crucial for therapeutic discovery and development. However, current machine learning models often rely on spurious features, leading to biased outcomes. Notably, a simple pocket-only baseline can achieve results comparable to, and sometimes better than, more complex models that incorporate both the protein pockets and the small molecules. Our analysis reveals that this phenomenon arises from insufficient training data and an improper evaluation process, which is typically conducted at the pocket level rather than the small molecule level. To address these issues, we redefine the bioactivity prediction task by introducing the SIU dataset-a million-scale Structural small molecule-protein Interaction dataset for Unbiased bioactivity prediction task, which is 50 times larger than the widely used PDBbind. The bioactivity labels in SIU are derived from wet experiments and organized by label types, ensuring greater accuracy and comparability. The complexes in SIU are constructed using a majority vote from three commonly used docking software programs, enhancing their reliability. Additionally, the structure of SIU allows for multiple small molecules to be associated with each protein pocket, enabling the redefinition of evaluation metrics like Pearson and Spearman correlations across different small molecules targeting the same protein pocket. Experimental results demonstrate that this new task provides a more challenging and meaningful benchmark for training and evaluating bioactivity prediction models, ultimately offering a more robust assessment of model performance.
Boltzmann priors for Implicit Transfer Operators
Authors: Juan Viguera Diez; Mathias Jacob Schreiner; Ola Engkvist; Simon Olsson
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Accurate prediction of thermodynamic properties is essential in drug discovery and materials science. Molecular dynamics (MD) simulations provide a principled approach to this task, yet they typically rely on prohibitively long sequential simulations. Implicit Transfer Operator (ITO) Learning offers a promising approach to address this limitation by enabling stable simulation with time steps orders of magnitude larger than MD. However, to train ITOs, we need extensive, unbiased MD data, limiting the scope of this framework. Here, we introduce Boltzmann Priors for ITO (BoPITO) to enhance ITO learning in two ways. First, BoPITO enables more efficient data generation, and second, it embeds inductive biases for long-term dynamical behavior, simultaneously improving sample efficiency by one order of magnitude and guaranteeing asymptotically unbiased equilibrium statistics. Furthermore, we showcase the use of BoPITO in a new tunable sampling protocol interpolating between ITOs trained on off-equilibrium simulations and an equilibrium model by incorporating unbiased correlation functions. Code is available at https://github.com/olsson-group/bopito.
ThunderKittens: Simple, Fast, and $\textit{Adorable}$ Kernels
Authors: Benjamin Frederick Spector; Simran Arora; Aaryan Singhal; Arjun Parthasarathy; Daniel Y Fu; Christopher Re
Venue: ICLR 2025 (ICLR 2025 Spotlight)

Abstract: The challenge of mapping AI architectures to GPU hardware is creating a critical bottleneck in AI progress. Despite substantial efforts, hand-written custom kernels fail to meet their theoretical performance thresholds, even on well-established operations like linear attention. The diverse capabilities of GPUs suggests we might we need a wide variety of techniques to achieve high performance. However, our work explores if a small number of key abstractions can drastically simplify the process. We present ThunderKittens (TK), a framework for writing performant AI kernels while remaining easy to use. Our abstractions map to the three levels of the GPU hierarchy: (1) at the warp-level, we provide 16x16 matrix tiles as basic data structures and PyTorch-like operations, (2) at the thread-block level, we provide templates for asynchronously overlapping operations, and (3) at the grid-level, TK helps hide block launch, tear-down, and memory costs. We show the value of TK by providing simple & diverse kernels that match or outperform prior art. We match CuBLAS and FlashAttention-3 on GEMM and attention inference performance and outperform the strongest baselines by $10-40$\% on attention backwards, $8\times$ on state space models, and $14\times$ on linear attention.
Can In-context Learning Really Generalize to Out-of-distribution Tasks?
Authors: Qixun Wang; Yifei Wang; Xianghua Ying; Yisen Wang
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: In this work, we explore the mechanism of in-context learning (ICL) on out-of-distribution (OOD) tasks that were not encountered during training. To achieve this, we conduct synthetic experiments where the objective is to learn OOD mathematical functions through ICL using a GPT-2 model. We reveal that Transformers may struggle to learn OOD task functions through ICL. Specifically, ICL performance resembles implementing a function within the pretraining hypothesis space and optimizing it with gradient descent based on the in-context examples. Additionally, we investigate ICL's well-documented ability to learn unseen abstract labels in context. We demonstrate that such ability only manifests in the scenarios without distributional shifts and, therefore, may not serve as evidence of new-task-learning ability. Furthermore, we assess ICL's performance on OOD tasks when the model is pretrained on multiple tasks. Both empirical and theoretical analyses demonstrate the existence of the \textbf{low-test-error preference} of ICL, where it tends to implement the pretraining function that yields low test error in the testing context. We validate this through numerical experiments. This new theoretical result, combined with our empirical findings, elucidates the mechanism of ICL in addressing OOD tasks.
CAKE: Cascading and Adaptive KV Cache Eviction with Layer Preferences
Authors: Ziran Qin; Yuchen Cao; Mingbao Lin; Wen Hu; Shixuan Fan; Ke Cheng; Weiyao Lin; Jianguo Li
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Large language models (LLMs) excel at processing long sequences, boosting demand for key-value (KV) caching. While recent efforts to evict KV cache have alleviated the inference burden, they often fail to allocate resources rationally across layers with different attention patterns. In this paper, we introduce Cascading and Adaptive KV cache Eviction (CAKE), a novel approach that frames KV cache eviction as a ``cake-slicing problem.''
CAKE assesses layer-specific preferences by considering attention dynamics in both spatial and temporal dimensions, allocates rational cache size for layers accordingly, and manages memory constraints in a cascading manner. This approach enables a global view of cache allocation, adaptively distributing resources across diverse attention mechanisms while maintaining memory budgets.
CAKE also employs a new eviction indicator that considers the shifting importance of tokens over time, addressing limitations in existing methods that overlook temporal dynamics.
Comprehensive experiments on LongBench and NeedleBench show that CAKE maintains model performance with only 3.2\% of the KV cache and consistently outperforms current baselines across various models and memory constraints, particularly in low-memory settings. Additionally, CAKE achieves over 10$\times$ speedup in decoding latency compared to full cache when processing contexts of 128K tokens with FlashAttention-2. Our code is available at https://github.com/antgroup/cakekv.
gRNAde: Geometric Deep Learning for 3D RNA inverse design
Authors: Chaitanya K. Joshi; Arian Rokkum Jamasb; Ramon Viñas Torné; Charles Harris; Simon V Mathis; Alex Morehead; Rishabh Anand; Pietro Lio
Venue: ICLR 2025 (ICLR 2025 Spotlight)

Abstract: Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. gRNAde uses a multi-state Graph Neural Network and autoregressive decoding to generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. (2010), gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent ribozyme. Experimental wet lab validation on 10 different structured RNA backbones finds that gRNAde has a success rate of 50% at designing pseudoknotted RNA structures, a significant advance over 35% for Rosetta. Open source code and tutorials are available at: github.com/chaitjo/geometric-rna-design
Toward Guidance-Free AR Visual Generation via Condition Contrastive Alignment
Authors: Huayu Chen; Hang Su; Peize Sun; Jun Zhu
Venue: ICLR 2025 (ICLR 2025 Oral)

Abstract: Classifier-Free Guidance (CFG) is a critical technique for enhancing the sample quality of visual generative models. However, in autoregressive (AR) multi-modal generation, CFG introduces design inconsistencies between language and visual content, contradicting the design philosophy of unifying different modalities for visual AR. Motivated by language model alignment methods, we propose Condition Contrastive Alignment (CCA) to facilitate guidance-free AR visual generation. Unlike guidance methods that alter the sampling process to achieve the ideal sampling distribution, CCA directly fine-tunes pretrained models to fit the same distribution target. Experimental results show that CCA can significantly enhance the guidance-free performance of all tested models with just one epoch of fine-tuning (1% of pretraining epochs) on the pretraining dataset. This largely removes the need for guided sampling in AR visual generation and cuts the sampling cost by half. Moreover, by adjusting training parameters, CCA can achieve trade-offs between sample diversity and fidelity similar to CFG. This experimentally confirms the strong theoretical connection between language-targeted alignment and visual-targeted guidance methods, unifying two previously independent research fields.