Deep Learning
Conformal Risk Training: End-to-End Optimization of Conformal Risk Control
While deep learning models often achieve high predictive accuracy, their predictions typically do not come with any provable guarantees on risk or reliability, which are critical for deployment in high-stakes applications. The framework of conformal risk control (CRC) provides a distribution-free, finite-sample method for controlling the expected value of any bounded monotone loss function and can be conveniently applied post-hoc to any pre-trained deep learning model. However, many realworld applications are sensitive to tail risks, as opposed to just expected loss. In this work, we develop a method for controlling the general class of Optimized CertaintyEquivalent (OCE) risks, a broad class of risk measures which includes as special cases the expected loss (generalizing the original CRC method) and common tail risks like the conditional value-at-risk (CVaR).
Collapse and simplex ETF
Neural collapse [26] is an intuitive observation that happens at the terminal phase of a well-trained model on a balanced dataset that last-layer features converge to within-class mean, and all within-class means and their corresponding classifier vectors converge to ETF as shown in Figure 6. The main results can be concluded as follows: (NC1) Variability of the last-layer features ฮฃ:= Avgi,c{(hic hc)(hic hc)T} collapse within-class: ฮฃ 0, where hic is the last-layer feature of the i-th sample in the c-th class, and hc is the within-class mean of c-th class's features. Last-layer features converge to within-class mean, and all within-class means and their corresponding classifier vectors converge to a simplex ETF. To analyze this phenomenon, some studies simplify deep neural networks as last-layer features and classifier (layer-peeled model)[9, 12, 40, 53] with proper constraints or regularizations. In the view of layer-peeled model (LPM), training W with constraints on the weights can be seen as training the C-class classification head WL = {W1,...,WC} and features H = {h1,...,hN} of all n samples output by last layer of backbone with constraints EW and EH respectively. EH. (6) In the balanced dataset, as described in Lemma 1, any solutions to this model merge neural collapse and form a simplex equiangular tight frame (ETF), which means ETF is optimal classifier in the balanced case of LPM.
Cross City Traffic Flow Generation via Retrieval Augmented Diffusion Model
Traffic flow data are of great value in smart city applications. However, limited by data collection costs and privacy sensitivity, it is rather difficult to obtain large-scale traffic flow data. Therefore, various data generation methods have been proposed in the literature. Nevertheless, these methods often require data from a specific city for training and are difficult to directly apply to new cities lacking data. To address this problem, this paper proposes a retrieval-augmented diffusion generation model with geographic representation alignment. We use data from multiple source cities for training, extract consistent representations across multiple cities, and leverage retrieval-augmented generation (RAG) technology to incorporate dynamic traffic flow patterns into the condition, aiming to improve the accuracy of data generation in the target city. Experiments on four real-world datasets demonstrate that, compared to existing generation methods, our method achieves best cross-city zero-shot performance.
Dual-Flow: Transferable Multi-Target, Instance-Agnostic Attacks via In-the-wild Cascading Flow Optimization
Adversarial attacks are widely used to evaluate model robustness, and in black-box scenarios, the transferability of these attacks becomes crucial. Existing generatorbased attacks have excellent generalization and transferability due to their instanceagnostic nature. However, when training generators for multi-target tasks, the success rate of transfer attacks is relatively low due to the limitations of the model's capacity. To address these challenges, we propose a novel Dual-Flow framework for multi-target instance-agnostic adversarial attacks, utilizing Cascading Distribution Shift Training to develop an adversarial velocity function. Extensive experiments demonstrate that Dual-Flow significantly improves transferability over previous multi-target generative attacks. For example, it increases the success rate from Inception-v3 to ResNet-152 by 34.58%. Furthermore, our attack method shows substantially stronger robustness against defense mechanisms, such as adversarially trained models. The code of Dual-Flow is available at: https://github.com/Chyxx/Dual-Flow.
Direct Alignment with Heterogeneous Preferences
Alignment with human preferences is commonly framed using a universal reward function, even though human preferences are inherently heterogeneous. We formalize this heterogeneity by introducing user types and examine the limits of the homogeneity assumption. We show that aligning to heterogeneous preferences with a single policy is best achieved using the average reward across user types. However, this requires additional information about annotators. We examine improvements under different information settings, focusing on direct alignment methods. We find that minimal information can yield first-order improvements, while full feedback from each user type leads to consistent learning of the optimal policy. Surprisingly, however, no sample-efficient consistent direct loss exists in this latter setting. These results reveal a fundamental tension between consistency and sample efficiency in direct policy alignment.
Efficient Multi-modal Large Language Models via Progressive Consistency Distillation
Visual tokens consume substantial computational resources in multi-modal large models (MLLMs), significantly compromising their efficiency. Recent works have attempted to improve efficiency by compressing visual tokens during training, either through modifications to model components or by introducing additional parameters. However, they often overlook the increased learning difficulty caused by such compression, as the model's parameter space struggles to quickly adapt to the substantial perturbations in the feature space induced by token compression. In this work, we propose to develop Efficient MLLMs via ProgressIve Consistency Distillation (EPIC), a progressive learning framework. Specifically, by decomposing the feature space perturbations introduced by token compression along the token-wise and layer-wise dimensions, we introduce token consistency distillation and layer consistency distillation, respectively, aiming to reduce the training difficulty by leveraging guidance from a teacher model and following a progressive learning trajectory. Extensive experiments demonstrate the superior effectiveness, robustness, and generalization capabilities of our proposed framework.
Bifrost-1: Bridging Multimodal LLMs and Diffusion Models with Patch-level CLIP Latents
There is growing interest in integrating high-fidelity visual synthesis capabilities into large language models (LLMs) without compromising their strong reasoning capabilities. Existing methods that directly train LLMs or bridge LLMs and diffusion models usually suffer from costly training since the backbone LLMs have not seen image representations during pretraining. We present BIFROST-1, a unified framework that bridges pretrained multimodal LLMs (MLLMs) and diffusion models using patch-level CLIP image embeddings as latent variables, which are natively aligned with the MLLM's CLIP visual encoder. These patch-level image embeddings are integrated into the diffusion model with a lightweight adaptation of its ControlNet. To retain the original multimodal reasoning capabilities of MLLMs, we equip the MLLM with a visual generation branch initialized from the original MLLM parameters when predicting the patch-level image embeddings. By seamlessly integrating pretrained MLLMs and diffusion models with patch-level CLIP latents, our framework enables high-fidelity controllable image generation with significant training efficiency. Our experiments demonstrate that BIFROST-1 achieves comparable or better performance than previous methods in terms of visual fidelity and multimodal understanding, with substantially lower compute during training. We also provide comprehensive ablation studies showing the effectiveness of our design choices.
Unified all-atom molecule generation with neural fields
Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate targetconditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs scorebased generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation*.
Bi-linearFactored/Block Diag.Bi-linearComplex DiagonalReal DiagonalPositive DiagonalParityArbitraryState MachinesModular AdditionAbelian Groups(e.g., Mamba)
The role of hidden units in recurrent neural networks is typically seen as modeling memory, with research focusing on enhancing information retention through gating mechanisms. A less explored perspective views hidden units as active participants in the computation performed by the network, rather than passive memory stores. In this work, we revisit bilinear operations, which involve multiplicative interactions between hidden units and input embeddings. We demonstrate theoretically and empirically that they constitute a natural inductive bias for representing the evolution of hidden states in state tracking tasks. These are the simplest type of tasks that require hidden units to actively contribute to the behavior of the network. We also show that bilinear state updates form a natural hierarchy corresponding to state tracking tasks of increasing complexity, with popular linear recurrent networks such as Mamba residing at the lowest-complexity center of that hierarchy.
Towards Precision Protein-Ligand Affinity Prediction Benchmark: AComplete and Modification-Aware DAVISDataset
Advancements in AI for science unlocks capabilities for critical drug discovery tasks such as protein-ligand binding affinity prediction. However, current models overfit to existing oversimplified datasets that does not represent naturally occurring and biologically relevant proteins with modifications. In this work, we curate a complete and modification-aware version of the widely used DAVIS dataset by incorporating 4,032 kinase-ligand pairs involving substitutions, insertions, deletions, and phosphorylation events. This enriched dataset enables benchmarking of predictive models under biologically realistic conditions. Based on this new dataset, we propose three benchmark settings--Augmented Dataset Prediction, Wild-Type to Modification Generalization, and Few-Shot Modification Generalization--designed to assess model robustness in the presence of protein modifications. Through extensive evaluation of both docking-free and docking-based methods, we find that docking-based model generalize better in zero-shot settings. In contrast, docking-free models tend to overfit to wild-type proteins and struggle with unseen modifications but show notable improvement when fine-tuned on a small set of modified examples. We anticipate that the curated dataset and benchmarks offer a valuable foundation for developing models that better generalize to protein modifications, ultimately advancing precision medicine in drug discovery.