Daily Papers

The success of Transformer language models is widely credited to their dot-product attention mechanism, which interweaves a set of key design principles: mixing information across positions (enabling multi-token interactions), sequence-dependent activations (where attention weights adapt to each input), a specific mathematical form (dot-product similarities plus softmax weighting), and coupling of queries and keys to evolving hidden states (grounding attention in the current layer). However, the necessity of each of these principles remains largely untested. In this work, we systematically deconstruct attention by designing controlled variants that selectively relax these principles, applied both uniformly across all layers and in hybrid architectures where only some layers retain standard attention. Our empirical analysis reveals that mechanisms for mixing tokens are indispensable, as their absence collapses models to near-random behavior, while the exact mathematical form and sequence dependency can be substantially relaxed, especially when preserved in just a subset of layers. Surprisingly, even variants that fail in isolation can achieve robust performance when interleaved with standard attention, highlighting a cooperative effect. These findings deepen our understanding of what truly underpins attention's effectiveness and open new avenues for simplifying language models without sacrificing performance.

Recent advancements in Large Language Models (LLMs) such as GPT4 have displayed exceptional multi-modal capabilities in following open-ended instructions given images. However, the performance of these models heavily relies on design choices such as network structures, training data, and training strategies, and these choices have not been extensively discussed in the literature, making it difficult to quantify progress in this field. To address this issue, this paper presents a systematic and comprehensive study, quantitatively and qualitatively, on training such models. We implement over 20 variants with controlled settings. Concretely, for network structures, we compare different LLM backbones and model designs. For training data, we investigate the impact of data and sampling strategies. For instructions, we explore the influence of diversified prompts on the instruction-following ability of the trained models. For benchmarks, we contribute the first, to our best knowledge, comprehensive evaluation set including both image and video tasks through crowd-sourcing. Based on our findings, we present Lynx, which performs the most accurate multi-modal understanding while keeping the best multi-modal generation ability compared to existing open-sourced GPT4-style models.

We empirically study the scaling properties of various Diffusion Transformers (DiTs) for text-to-image generation by performing extensive and rigorous ablations, including training scaled DiTs ranging from 0.3B upto 8B parameters on datasets up to 600M images. We find that U-ViT, a pure self-attention based DiT model provides a simpler design and scales more effectively in comparison with cross-attention based DiT variants, which allows straightforward expansion for extra conditions and other modalities. We identify a 2.3B U-ViT model can get better performance than SDXL UNet and other DiT variants in controlled setting. On the data scaling side, we investigate how increasing dataset size and enhanced long caption improve the text-image alignment performance and the learning efficiency.

A human author can write any length of story without losing coherence. Also, they always bring the story to a proper ending, an ability that current language models lack. In this work, we present the LongStory for coherent, complete, and length-controlled long story generation. LongStory introduces two novel methodologies: (1) the long and short-term contexts weight calibrator (CWC) and (2) long story structural positions (LSP). The CWC adjusts weights for long-term context Memory and short-term context Cheating, acknowledging their distinct roles. The LSP employs discourse tokens to convey the structural positions of a long story. Trained on three datasets with varied average story lengths, LongStory outperforms other baselines, including the strong story generator Plotmachine, in coherence, completeness, relevance, and repetitiveness. We also perform zero-shot tests on each dataset to assess the model's ability to predict outcomes beyond its training data and validate our methodology by comparing its performance with variants of our model.

For federated learning (FL) algorithms such as FedSAM, their generalization capability is crucial for real-word applications. In this paper, we revisit the generalization problem in FL and investigate the impact of data heterogeneity on FL generalization. We find that FedSAM usually performs worse than FedAvg in the case of highly heterogeneous data, and thus propose a novel and effective federated learning algorithm with Stochastic Weight Averaging (called FedSWA), which aims to find flatter minima in the setting of highly heterogeneous data. Moreover, we introduce a new momentum-based stochastic controlled weight averaging FL algorithm (FedMoSWA), which is designed to better align local and global models. Theoretically, we provide both convergence analysis and generalization bounds for FedSWA and FedMoSWA. We also prove that the optimization and generalization errors of FedMoSWA are smaller than those of their counterparts, including FedSAM and its variants. Empirically, experimental results on CIFAR10/100 and Tiny ImageNet demonstrate the superiority of the proposed algorithms compared to their counterparts. Open source code at: https://github.com/junkangLiu0/FedSWA.

Structured knowledge grounding (SKG) leverages structured knowledge to complete user requests, such as semantic parsing over databases and question answering over knowledge bases. Since the inputs and outputs of SKG tasks are heterogeneous, they have been studied separately by different communities, which limits systematic and compatible research on SKG. In this paper, we overcome this limitation by proposing the UnifiedSKG framework, which unifies 21 SKG tasks into a text-to-text format, aiming to promote systematic SKG research, instead of being exclusive to a single task, domain, or dataset. We use UnifiedSKG to benchmark T5 with different sizes and show that T5, with simple modifications when necessary, achieves state-of-the-art performance on almost all of the 21 tasks. We further demonstrate that multi-task prefix-tuning improves the performance on most tasks, largely improving the overall performance. UnifiedSKG also facilitates the investigation of zero-shot and few-shot learning, and we show that T0, GPT-3, and Codex struggle in zero-shot and few-shot learning for SKG. We also use UnifiedSKG to conduct a series of controlled experiments on structured knowledge encoding variants across SKG tasks. UnifiedSKG is easily extensible to more tasks, and it is open-sourced at https://github.com/hkunlp/unifiedskg.

We present Hubble, a suite of fully open-source large language models (LLMs) for the scientific study of LLM memorization. Hubble models come in standard and perturbed variants: standard models are pretrained on a large English corpus, and perturbed models are trained in the same way but with controlled insertion of text (e.g., book passages, biographies, and test sets) designed to emulate key memorization risks. Our core release includes 8 models -- standard and perturbed models with 1B or 8B parameters, pretrained on 100B or 500B tokens -- establishing that memorization risks are determined by the frequency of sensitive data relative to size of the training corpus (i.e., a password appearing once in a smaller corpus is memorized better than the same password in a larger corpus). Our release also includes 6 perturbed models with text inserted at different pretraining phases, showing that sensitive data without continued exposure can be forgotten. These findings suggest two best practices for addressing memorization risks: to dilute sensitive data by increasing the size of the training corpus, and to order sensitive data to appear earlier in training. Beyond these general empirical findings, Hubble enables a broad range of memorization research; for example, analyzing the biographies reveals how readily different types of private information are memorized. We also demonstrate that the randomized insertions in Hubble make it an ideal testbed for membership inference and machine unlearning, and invite the community to further explore, benchmark, and build upon our work.

Large language models (LLMs) have garnered significant attention in both the AI community and beyond. Among these, the Generative Pre-trained Transformer (GPT) has emerged as the dominant architecture, spawning numerous variants. However, these variants have undergone pre-training under diverse conditions, including variations in input data, data preprocessing, and training methodologies, resulting in a lack of controlled comparative studies. Here we meticulously examine two prominent open-sourced GPT architectures, GPT-NeoX and LLaMA, leveraging the computational power of Frontier, the world's first Exascale supercomputer. Employing the same materials science text corpus and a comprehensive end-to-end pipeline, we conduct a comparative analysis of their training and downstream performance. Our efforts culminate in achieving state-of-the-art performance on a challenging materials science benchmark. Furthermore, we investigate the computation and energy efficiency, and propose a computationally efficient method for architecture design. To our knowledge, these pre-trained models represent the largest available for materials science. Our findings provide practical guidance for building LLMs on HPC platforms.

Large Language Models (LLMs) have become a milestone in the field of artificial intelligence and natural language processing. However, their large-scale deployment remains constrained by the need for significant computational resources. This work proposes starting from a base model to explore and combine data processing and careful data selection techniques, training strategies, and architectural adjustments to improve the efficiency of LLMs in resource-constrained environments and within a delimited knowledge base. The methodological approach included defining criteria for building reliable datasets, conducting controlled experiments with different configurations, and systematically evaluating the resulting variants in terms of capability, versatility, response time, and safety. Finally, comparative tests were conducted to measure the performance of the developed variants and to validate the effectiveness of the proposed strategies. This work is based on the master's thesis in Systems and Computer Engineering titled "Efficient Strategy for Improving the Capabilities of Large Language Models (LLMs)".

Genome-wide association study (GWAS) tests single nucleotide polymorphism (SNP) markers across the genome to localize the underlying causal variant of a trait. Because causal variants are seldom observed directly, a surrogate model based on genotyped markers are widely considered. Although many methods estimating the parameters of the surrogate model have been proposed, the connection between the surrogate model and the true causal model is yet investigated. In this work, we establish the connection between the surrogate model and the true causal model. The connection shows that population structure is accounted in GWAS by modelling the variant of interest and not the trait. Such observation explains how environmental confounding can be partially corrected using genetic covariates and why the previously claimed connection between PC correction and linear mixed models is incorrect.

Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein structure and function. The effectiveness of these models on diverse set of tasks suggests that they learn meaningful representations of fitness landscape that can be useful for downstream clinical applications. Here, we interrogate the use of these language models in characterizing known pathogenic mutations in curated, medically actionable genes through an exhaustive search of putative compensatory mutations on each variant's genetic background. Systematic analysis of the predicted effects of these compensatory mutations reveal unappreciated structural features of proteins that are missed by other structure predictors like AlphaFold. While deep mutational scan experiments provide an unbiased estimate of the mutational landscape, we encourage the community to generate and curate rescue mutation experiments to inform the design of more sophisticated co-masking strategies and leverage large language models more effectively for downstream clinical prediction tasks.

We consider controllable DNA sequence design, where sequences are generated by conditioning on specific biological properties. While language models (LMs) such as GPT and BERT have achieved remarkable success in natural language generation, their application to DNA sequence generation remains largely underexplored. In this work, we introduce ATGC-Gen, an Automated Transformer Generator for Controllable Generation, which leverages cross-modal encoding to integrate diverse biological signals. ATGC-Gen is instantiated with both decoder-only and encoder-only transformer architectures, allowing flexible training and generation under either autoregressive or masked recovery objectives. We evaluate ATGC-Gen on representative tasks including promoter and enhancer sequence design, and further introduce a new dataset based on ChIP-Seq experiments for modeling protein binding specificity. Our experiments demonstrate that ATGC-Gen can generate fluent, diverse, and biologically relevant sequences aligned with the desired properties. Compared to prior methods, our model achieves notable improvements in controllability and functional relevance, highlighting the potential of language models in advancing programmable genomic design. The source code is released at (https://github.com/divelab/AIRS/blob/main/OpenBio/ATGC_Gen).

Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel fine-tuning approach to improve the performance of PLMs with experimental maps of variant effects from Deep Mutational Scanning (DMS) assays using a Normalised Log-odds Ratio (NLR) head. We find consistent improvements in a held-out protein test set, and on independent DMS and clinical variant annotation benchmarks from ProteinGym and ClinVar. These findings demonstrate that DMS is a promising source of sequence diversity and supervised training data for improving the performance of PLMs for variant effect prediction.

We study the problem of extrapolative controlled generation, i.e., generating sequences with attribute values beyond the range seen in training. This task is of significant importance in automated design, especially drug discovery, where the goal is to design novel proteins that are better (e.g., more stable) than existing sequences. Thus, by definition, the target sequences and their attribute values are out of the training distribution, posing challenges to existing methods that aim to directly generate the target sequence. Instead, in this work, we propose Iterative Controlled Extrapolation (ICE) which iteratively makes local edits to a sequence to enable extrapolation. We train the model on synthetically generated sequence pairs that demonstrate small improvement in the attribute value. Results on one natural language task (sentiment analysis) and two protein engineering tasks (ACE2 stability and AAV fitness) show that ICE considerably outperforms state-of-the-art approaches despite its simplicity. Our code and models are available at: https://github.com/vishakhpk/iter-extrapolation.

Previous studies have shown that automated text-mining tools are becoming increasingly important for successfully unlocking variant information in scientific literature at large scale. Despite multiple attempts in the past, existing tools are still of limited recognition scope and precision. We propose tmVar 3.0: an improved variant recognition and normalization tool. Compared to its predecessors, tmVar 3.0 is able to recognize a wide spectrum of variant related entities (e.g., allele and copy number variants), and to group different variant mentions belonging to the same concept in an article for improved accuracy. Moreover, tmVar3 provides additional variant normalization options such as allele-specific identifiers from the ClinGen Allele Registry. tmVar3 exhibits a state-of-the-art performance with over 90% accuracy in F-measure in variant recognition and normalization, when evaluated on three independent benchmarking datasets. tmVar3 is freely available for download. We have also processed the entire PubMed and PMC with tmVar3 and released its annotations on our FTP. Availability: ftp://ftp.ncbi.nlm.nih.gov/pub/lu/tmVar3

Behavior Cloning (BC) on curated (or filtered) data is the predominant paradigm for supervised fine-tuning (SFT) of large language models; as well as for imitation learning of control policies. Here, we draw on a connection between this successful strategy and the theory and practice of finding optimal policies via Reinforcement Learning (RL). Building on existing literature, we clarify that SFT can be understood as maximizing a lower bound on the RL objective in a sparse reward setting. Giving support to its often observed good performance. From this viewpoint, we realize that a small modification to SFT leads to an importance weighted variant that behaves closer to training with RL as it: i) optimizes a tighter bound to the RL objective and, ii) can improve performance compared to SFT on curated data. We refer to this variant as importance weighted supervised fine-tuning (iw-SFT). We show that it is easy to implement and can be further generalized to training with quality scored data. The resulting SFT variants are competitive with more advanced RL algorithms for large language models and for training policies in continuous control tasks. For example achieving 66.7% on the AIME 2024 dataset.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Conditional visual generation has witnessed remarkable progress with the advent of diffusion models (DMs), especially in tasks like control-to-image generation. However, challenges such as expensive computational cost, high inference latency, and difficulties of integration with large language models (LLMs) have necessitated exploring alternatives to DMs. This paper introduces ControlVAR, a novel framework that explores pixel-level controls in visual autoregressive (VAR) modeling for flexible and efficient conditional generation. In contrast to traditional conditional models that learn the conditional distribution, ControlVAR jointly models the distribution of image and pixel-level conditions during training and imposes conditional controls during testing. To enhance the joint modeling, we adopt the next-scale AR prediction paradigm and unify control and image representations. A teacher-forcing guidance strategy is proposed to further facilitate controllable generation with joint modeling. Extensive experiments demonstrate the superior efficacy and flexibility of ControlVAR across various conditional generation tasks against popular conditional DMs, \eg, ControlNet and T2I-Adaptor. Code: https://github.com/lxa9867/ControlVAR.

Large language models are being widely used across industries to generate content that contributes directly to key performance metrics, such as conversion rates. Pretrained models, however, often fall short when it comes to aligning with human preferences or optimizing for business objectives. As a result, fine-tuning with good-quality labeled data is essential to guide models to generate content that achieves better results. Controlled experiments, like A/B tests, can provide such data, but they are often expensive and come with significant engineering and logistical challenges. Meanwhile, companies have access to a vast amount of historical (observational) data that remains underutilized. In this work, we study the challenges and opportunities of fine-tuning LLMs using observational data. We show that while observational outcomes can provide valuable supervision, directly fine-tuning models on such data can lead them to learn spurious correlations. We present empirical evidence of this issue using various real-world datasets and propose DeconfoundLM, a method that explicitly removes the effect of known confounders from reward signals. Using simulation experiments, we demonstrate that DeconfoundLM improves the recovery of causal relationships and mitigates failure modes found in fine-tuning methods that ignore or naively incorporate confounding variables. Our findings highlight that while observational data presents risks, with the right causal corrections, it can be a powerful source of signal for LLM alignment. Please refer to the project page for code and related resources.

The controllable generation of diffusion models aims to steer the model to generate samples that optimize some given objective functions. It is desirable for a variety of applications including image generation, molecule generation, and DNA/sequence generation. Reinforcement Learning (RL) based fine-tuning of the base model is a popular approach but it can overfit the reward function while requiring significant resources. We frame controllable generation as a problem of finding a distribution that optimizes a KL-regularized objective function. We present SLCD -- Supervised Learning based Controllable Diffusion, which iteratively generates online data and trains a small classifier to guide the generation of the diffusion model. Similar to the standard classifier-guided diffusion, SLCD's key computation primitive is classification and does not involve any complex concepts from RL or control. Via a reduction to no-regret online learning analysis, we show that under KL divergence, the output from SLCD provably converges to the optimal solution of the KL-regularized objective. Further, we empirically demonstrate that SLCD can generate high quality samples with nearly the same inference time as the base model in both image generation with continuous diffusion and biological sequence generation with discrete diffusion. Our code is available at https://github.com/Owen-Oertell/slcd

The objective of personalized medicine is to tailor interventions to an individual patient's unique characteristics. A key technology for this purpose involves medical digital twins, computational models of human biology that can be personalized and dynamically updated to incorporate patient-specific data collected over time. Certain aspects of human biology, such as the immune system, are not easily captured with physics-based models, such as differential equations. Instead, they are often multi-scale, stochastic, and hybrid. This poses a challenge to existing model-based control and optimization approaches that cannot be readily applied to such models. Recent advances in automatic differentiation and neural-network control methods hold promise in addressing complex control problems. However, the application of these approaches to biomedical systems is still in its early stages. This work introduces dynamics-informed neural-network controllers as an alternative approach to control of medical digital twins. As a first use case for this method, the focus is on agent-based models, a versatile and increasingly common modeling platform in biomedicine. The effectiveness of the proposed neural-network control method is illustrated and benchmarked against other methods with two widely-used agent-based model types. The relevance of the method introduced here extends beyond medical digital twins to other complex dynamical systems.

We study regressions with multiple treatments and a set of controls that is flexible enough to purge omitted variable bias. We show that these regressions generally fail to estimate convex averages of heterogeneous treatment effects -- instead, estimates of each treatment's effect are contaminated by non-convex averages of the effects of other treatments. We discuss three estimation approaches that avoid such contamination bias, including the targeting of easiest-to-estimate weighted average effects. A re-analysis of nine empirical applications finds economically and statistically meaningful contamination bias in observational studies; contamination bias in experimental studies is more limited due to smaller variability in propensity scores.

Controllable text generation systems often leverage control codes to direct various properties of the output like style and length. Inspired by recent work on causal inference for NLP, this paper reveals a previously overlooked flaw in these control code-based conditional text generation algorithms. Spurious correlations in the training data can lead models to incorrectly rely on parts of the input other than the control code for attribute selection, significantly undermining downstream generation quality and controllability. We demonstrate the severity of this issue with a series of case studies and then propose two simple techniques to reduce these correlations in training sets. The first technique is based on resampling the data according to an example's propensity towards each linguistic attribute (IPS). The second produces multiple counterfactual versions of each example and then uses an additional feedback mechanism to remove noisy examples (feedback aware self-training, FAST). We evaluate on 3 tasks -- news headline, meta review, and search ads generation -- and demonstrate that FAST can significantly improve the controllability and language quality of generated outputs when compared to state-of-the-art controllable text generation approaches.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

Dynamic treatment regimes (DTRs) are personalized, adaptive, multi-stage treatment plans that adapt treatment decisions both to an individual's initial features and to intermediate outcomes and features at each subsequent stage, which are affected by decisions in prior stages. Examples include personalized first- and second-line treatments of chronic conditions like diabetes, cancer, and depression, which adapt to patient response to first-line treatment, disease progression, and individual characteristics. While existing literature mostly focuses on estimating the optimal DTR from offline data such as from sequentially randomized trials, we study the problem of developing the optimal DTR in an online manner, where the interaction with each individual affect both our cumulative reward and our data collection for future learning. We term this the DTR bandit problem. We propose a novel algorithm that, by carefully balancing exploration and exploitation, is guaranteed to achieve rate-optimal regret when the transition and reward models are linear. We demonstrate our algorithm and its benefits both in synthetic experiments and in a case study of adaptive treatment of major depressive disorder using real-world data.

In this paper, we present ControlVideo, a novel method for text-driven video editing. Leveraging the capabilities of text-to-image diffusion models and ControlNet, ControlVideo aims to enhance the fidelity and temporal consistency of videos that align with a given text while preserving the structure of the source video. This is achieved by incorporating additional conditions such as edge maps, fine-tuning the key-frame and temporal attention on the source video-text pair with carefully designed strategies. An in-depth exploration of ControlVideo's design is conducted to inform future research on one-shot tuning video diffusion models. Quantitatively, ControlVideo outperforms a range of competitive baselines in terms of faithfulness and consistency while still aligning with the textual prompt. Additionally, it delivers videos with high visual realism and fidelity w.r.t. the source content, demonstrating flexibility in utilizing controls containing varying degrees of source video information, and the potential for multiple control combinations. The project page is available at https://ml.cs.tsinghua.edu.cn/controlvideo/{https://ml.cs.tsinghua.edu.cn/controlvideo/}.

Domain experts across engineering, healthcare, and education follow strict standards for producing quality content such as technical manuals, medication instructions, and children's reading materials. However, current works in controllable text generation have yet to explore using these standards as references for control. Towards this end, we introduce Standardize, a retrieval-style in-context learning-based framework to guide large language models to align with expert-defined standards. Focusing on English language standards in the education domain as a use case, we consider the Common European Framework of Reference for Languages (CEFR) and Common Core Standards (CCS) for the task of open-ended content generation. Our findings show that models can gain 40% to 100% increase in precise accuracy for Llama2 and GPT-4, respectively, demonstrating that the use of knowledge artifacts extracted from standards and integrating them in the generation process can effectively guide models to produce better standard-aligned content.

Control variates are variance reduction tools for Monte Carlo estimators. They can provide significant variance reduction, but usually require a large number of samples, which can be prohibitive when sampling or evaluating the integrand is computationally expensive. Furthermore, there are many scenarios where we need to compute multiple related integrals simultaneously or sequentially, which can further exacerbate computational costs. In this paper, we propose vector-valued control variates, an extension of control variates which can be used to reduce the variance of multiple Monte Carlo estimators jointly. This allows for the transfer of information across integration tasks, and hence reduces the need for a large number of samples. We focus on control variates based on kernel interpolants and our novel construction is obtained through a generalised Stein identity and the development of novel matrix-valued Stein reproducing kernels. We demonstrate our methodology on a range of problems including multifidelity modelling, Bayesian inference for dynamical systems, and model evidence computation through thermodynamic integration.

Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but face limitations in binding data, substrate-specific control, and flexibility for de novo enzyme backbone generation. To address this, we introduce EnzyBind, a dataset with 11,100 experimentally validated enzyme-substrate pairs specifically curated from PDBbind. Building on this, we propose EnzyControl, a method that enables functional and substrate-specific control in enzyme backbone generation. Our approach generates enzyme backbones conditioned on MSA-annotated catalytic sites and their corresponding substrates, which are automatically extracted from curated enzyme-substrate data. At the core of EnzyControl is EnzyAdapter, a lightweight, modular component integrated into a pretrained motif-scaffolding model, allowing it to become substrate-aware. A two-stage training paradigm further refines the model's ability to generate accurate and functional enzyme structures. Experiments show that our EnzyControl achieves the best performance across structural and functional metrics on EnzyBind and EnzyBench benchmarks, with particularly notable improvements of 13\% in designability and 13\% in catalytic efficiency compared to the baseline models. The code is released at https://github.com/Vecteur-libre/EnzyControl.

Controllable image synthesis, which enables fine-grained control over generated outputs, has emerged as a key focus in visual generative modeling. However, controllable generation remains challenging for Visual Autoregressive (VAR) models due to their hierarchical, next-scale prediction style. Existing VAR-based methods often suffer from inefficient control encoding and disruptive injection mechanisms that compromise both fidelity and efficiency. In this work, we present SCALAR, a controllable generation method based on VAR, incorporating a novel Scale-wise Conditional Decoding mechanism. SCALAR leverages a pretrained image encoder to extract semantic control signal encodings, which are projected into scale-specific representations and injected into the corresponding layers of the VAR backbone. This design provides persistent and structurally aligned guidance throughout the generation process. Building on SCALAR, we develop SCALAR-Uni, a unified extension that aligns multiple control modalities into a shared latent space, supporting flexible multi-conditional guidance in a single model. Extensive experiments show that SCALAR achieves superior generation quality and control precision across various tasks.

Small sample sizes are common in many disciplines, which necessitates pooling roughly similar datasets across multiple institutions to study weak but relevant associations between images and disease outcomes. Such data often manifest shift/imbalance in covariates (i.e., secondary non-imaging data). Controlling for such nuisance variables is common within standard statistical analysis, but the ideas do not directly apply to overparameterized models. Consequently, recent work has shown how strategies from invariant representation learning provides a meaningful starting point, but the current repertoire of methods is limited to accounting for shifts/imbalances in just a couple of covariates at a time. In this paper, we show how viewing this problem from the perspective of Category theory provides a simple and effective solution that completely avoids elaborate multi-stage training pipelines that would otherwise be needed. We show the effectiveness of this approach via extensive experiments on real datasets. Further, we discuss how this style of formulation offers a unified perspective on at least 5+ distinct problem settings, from self-supervised learning to matching problems in 3D reconstruction.

As large language models (LLMs) are widely deployed across various domains, the ability to control their generated outputs has become more critical. This control involves aligning LLMs outputs with human values and ethical principles or customizing LLMs on specific topics or styles for individual users. Existing controlled generation methods either require significant computational resources and extensive trial-and-error or provide coarse-grained control. In this paper, we propose Generation with Concept Activation Vector (GCAV), a lightweight model control framework that ensures accurate control without requiring resource-extensive fine-tuning. Specifically, GCAV first trains a concept activation vector for specified concepts to be controlled, such as toxicity. During inference, GCAV steers the concept vector in LLMs, for example, by removing the toxicity concept vector from the activation layers. Control experiments from different perspectives, including toxicity reduction, sentiment control, linguistic style, and topic control, demonstrate that our framework achieves state-of-the-art performance with granular control, allowing for fine-grained adjustments of both the steering layers and the steering magnitudes for individual samples.

We present Vivid-VR, a DiT-based generative video restoration method built upon an advanced T2V foundation model, where ControlNet is leveraged to control the generation process, ensuring content consistency. However, conventional fine-tuning of such controllable pipelines frequently suffers from distribution drift due to limitations in imperfect multimodal alignment, resulting in compromised texture realism and temporal coherence. To tackle this challenge, we propose a concept distillation training strategy that utilizes the pretrained T2V model to synthesize training samples with embedded textual concepts, thereby distilling its conceptual understanding to preserve texture and temporal quality. To enhance generation controllability, we redesign the control architecture with two key components: 1) a control feature projector that filters degradation artifacts from input video latents to minimize their propagation through the generation pipeline, and 2) a new ControlNet connector employing a dual-branch design. This connector synergistically combines MLP-based feature mapping with cross-attention mechanism for dynamic control feature retrieval, enabling both content preservation and adaptive control signal modulation. Extensive experiments show that Vivid-VR performs favorably against existing approaches on both synthetic and real-world benchmarks, as well as AIGC videos, achieving impressive texture realism, visual vividness, and temporal consistency. The codes and checkpoints are publicly available at https://github.com/csbhr/Vivid-VR.

Image diffusion models have been utilized in various tasks, such as text-to-image generation and controllable image synthesis. Recent research has introduced tuning methods that make subtle adjustments to the original models, yielding promising results in specific adaptations of foundational generative diffusion models. Rather than modifying the main backbone of the diffusion model, we delve into the role of skip connection in U-Net and reveal that hierarchical features aggregating long-distance information across encoder and decoder make a significant impact on the content and quality of image generation. Based on the observation, we propose an efficient generative tuning framework, dubbed SCEdit, which integrates and edits Skip Connection using a lightweight tuning module named SC-Tuner. Furthermore, the proposed framework allows for straightforward extension to controllable image synthesis by injecting different conditions with Controllable SC-Tuner, simplifying and unifying the network design for multi-condition inputs. Our SCEdit substantially reduces training parameters, memory usage, and computational expense due to its lightweight tuners, with backward propagation only passing to the decoder blocks. Extensive experiments conducted on text-to-image generation and controllable image synthesis tasks demonstrate the superiority of our method in terms of efficiency and performance. Project page: https://scedit.github.io/

Consistency Models (CMs) have showed a promise in creating visual content efficiently and with high quality. However, the way to add new conditional controls to the pretrained CMs has not been explored. In this technical report, we consider alternative strategies for adding ControlNet-like conditional control to CMs and present three significant findings. 1) ControlNet trained for diffusion models (DMs) can be directly applied to CMs for high-level semantic controls but struggles with low-level detail and realism control. 2) CMs serve as an independent class of generative models, based on which ControlNet can be trained from scratch using Consistency Training proposed by Song et al. 3) A lightweight adapter can be jointly optimized under multiple conditions through Consistency Training, allowing for the swift transfer of DMs-based ControlNet to CMs. We study these three solutions across various conditional controls, including edge, depth, human pose, low-resolution image and masked image with text-to-image latent consistency models.

Controllable layout generation refers to the process of creating a plausible visual arrangement of elements within a graphic design (e.g., document and web designs) with constraints representing design intentions. Although recent diffusion-based models have achieved state-of-the-art FID scores, they tend to exhibit more pronounced misalignment compared to earlier transformer-based models. In this work, we propose the LAyout Constraint diffusion modEl (LACE), a unified model to handle a broad range of layout generation tasks, such as arranging elements with specified attributes and refining or completing a coarse layout design. The model is based on continuous diffusion models. Compared with existing methods that use discrete diffusion models, continuous state-space design can enable the incorporation of differentiable aesthetic constraint functions in training. For conditional generation, we introduce conditions via masked input. Extensive experiment results show that LACE produces high-quality layouts and outperforms existing state-of-the-art baselines.

Diffusion models have demonstrated remarkable and robust abilities in both image and video generation. To achieve greater control over generated results, researchers introduce additional architectures, such as ControlNet, Adapters and ReferenceNet, to integrate conditioning controls. However, current controllable generation methods often require substantial additional computational resources, especially for video generation, and face challenges in training or exhibit weak control. In this paper, we propose ControlNeXt: a powerful and efficient method for controllable image and video generation. We first design a more straightforward and efficient architecture, replacing heavy additional branches with minimal additional cost compared to the base model. Such a concise structure also allows our method to seamlessly integrate with other LoRA weights, enabling style alteration without the need for additional training. As for training, we reduce up to 90% of learnable parameters compared to the alternatives. Furthermore, we propose another method called Cross Normalization (CN) as a replacement for Zero-Convolution' to achieve fast and stable training convergence. We have conducted various experiments with different base models across images and videos, demonstrating the robustness of our method.

Current text-to-image generation models often struggle to follow textual instructions, especially the ones requiring spatial reasoning. On the other hand, Large Language Models (LLMs), such as GPT-4, have shown remarkable precision in generating code snippets for sketching out text inputs graphically, e.g., via TikZ. In this work, we introduce Control-GPT to guide the diffusion-based text-to-image pipelines with programmatic sketches generated by GPT-4, enhancing their abilities for instruction following. Control-GPT works by querying GPT-4 to write TikZ code, and the generated sketches are used as references alongside the text instructions for diffusion models (e.g., ControlNet) to generate photo-realistic images. One major challenge to training our pipeline is the lack of a dataset containing aligned text, images, and sketches. We address the issue by converting instance masks in existing datasets into polygons to mimic the sketches used at test time. As a result, Control-GPT greatly boosts the controllability of image generation. It establishes a new state-of-art on the spatial arrangement and object positioning generation and enhances users' control of object positions, sizes, etc., nearly doubling the accuracy of prior models. Our work, as a first attempt, shows the potential for employing LLMs to enhance the performance in computer vision tasks.

In this white paper we introduce Helix, an AI based solution for missense pathogenicity prediction. With recent advances in the sequencing of human genomes, massive amounts of genetic data have become available. This has shifted the burden of labor for genetic diagnostics and research from the gathering of data to its interpretation. Helix presents a state of the art platform for the prediction of pathogenicity in human missense variants. In addition to offering best-in-class predictive performance, Helix offers a platform that allows researchers to analyze and interpret variants in depth that can be accessed at helixlabs.ai.

Alignment with high-resource standard languages is often assumed to aid the modeling of related low-resource varieties. We challenge this assumption by demonstrating that excessive representational entanglement with a dominant variety, such as Modern Standard Arabic (MSA) in relation to Arabic dialects, can actively hinder generative modeling. We present the first comprehensive causal study of this phenomenon by analyzing and directly intervening in the internal representation geometry of large language models (LLMs). Our key contribution is an online variational probing framework that continuously estimates the subspace of the standard variety during fine-tuning, enabling projection-based decoupling from this space. While our study uses Arabic as a case due to its unusually rich parallel resources across 25 dialects, the broader motivation is methodological: dialectal MT serves as a controlled proxy for generative tasks where comparable multi-variety corpora are unavailable. Across 25 dialects, our intervention improves generation quality by up to +4.9 chrF++ and +2.0 on average compared to standard fine-tuning, despite a measured tradeoff in standard-language performance. These results provide causal evidence that subspace dominance by high-resource varieties can restrict generative capacity for related varieties. More generally, we unify geometric and information-theoretic probing with subspace-level causal interventions, offering practical tools for improving generative modeling in closely related language families and, more broadly, for controlling representational allocation in multilingual and multi-domain LLMs. Code will be released.

Analyzing and detecting cannabis seed variants is crucial for the agriculture industry. It enables precision breeding, allowing cultivators to selectively enhance desirable traits. Accurate identification of seed variants also ensures regulatory compliance, facilitating the cultivation of specific cannabis strains with defined characteristics, ultimately improving agricultural productivity and meeting diverse market demands. This paper presents a study on cannabis seed variant detection by employing a state-of-the-art object detection model Faster R-CNN. This study implemented the model on a locally sourced cannabis seed dataset in Thailand, comprising 17 distinct classes. We evaluate six Faster R-CNN models by comparing performance on various metrics and achieving a mAP score of 94.08\% and an F1 score of 95.66\%. This paper presents the first known application of deep neural network object detection models to the novel task of visually identifying cannabis seed types.

The field of image synthesis has made tremendous strides forward in the last years. Besides defining the desired output image with text-prompts, an intuitive approach is to additionally use spatial guidance in form of an image, such as a depth map. For this, a recent and highly popular approach is to use a controlling network, such as ControlNet, in combination with a pre-trained image generation model, such as Stable Diffusion. When evaluating the design of existing controlling networks, we observe that they all suffer from the same problem of a delay in information flowing between the generation and controlling process. This, in turn, means that the controlling network must have generative capabilities. In this work we propose a new controlling architecture, called ControlNet-XS, which does not suffer from this problem, and hence can focus on the given task of learning to control. In contrast to ControlNet, our model needs only a fraction of parameters, and hence is about twice as fast during inference and training time. Furthermore, the generated images are of higher quality and the control is of higher fidelity. All code and pre-trained models will be made publicly available.

Multimodal clothing image editing refers to the precise adjustment and modification of clothing images using data such as textual descriptions and visual images as control conditions, which effectively improves the work efficiency of designers and reduces the threshold for user design. In this paper, we propose a new image editing method ControlEdit, which transfers clothing image editing to multimodal-guided local inpainting of clothing images. We address the difficulty of collecting real image datasets by leveraging the self-supervised learning approach. Based on this learning approach, we extend the channels of the feature extraction network to ensure consistent clothing image style before and after editing, and we design an inverse latent loss function to achieve soft control over the content of non-edited areas. In addition, we adopt Blended Latent Diffusion as the sampling method to make the editing boundaries transition naturally and enforce consistency of non-edited area content. Extensive experiments demonstrate that ControlEdit surpasses baseline algorithms in both qualitative and quantitative evaluations.

We propose Self-Control, a novel method utilizing suffix gradients to control the behavior of large language models (LLMs) without explicit human annotations. Given a guideline expressed in suffix string and the model's self-assessment of adherence, Self-Control computes the gradient of this self-judgment concerning the model's hidden states, directly influencing the auto-regressive generation process towards desired behaviors. To enhance efficiency, we introduce Self-Control_{prefix}, a compact module that encapsulates the learned representations from suffix gradients into a Prefix Controller, facilitating inference-time control for various LLM behaviors. Our experiments demonstrate Self-Control's efficacy across multiple domains, including emotional modulation, ensuring harmlessness, and enhancing complex reasoning. Especially, Self-Control_{prefix} enables a plug-and-play control and jointly controls multiple attributes, improving model outputs without altering model parameters or increasing inference-time costs.

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.

ControlNet offers a powerful way to guide diffusion-based generative models, yet most implementations rely on ad-hoc heuristics to choose which network blocks to control-an approach that varies unpredictably with different tasks. To address this gap, we propose FlexControl, a novel framework that copies all diffusion blocks during training and employs a trainable gating mechanism to dynamically select which blocks to activate at each denoising step. With introducing a computation-aware loss, we can encourage control blocks only to activate when it benefit the generation quality. By eliminating manual block selection, FlexControl enhances adaptability across diverse tasks and streamlines the design pipeline, with computation-aware training loss in an end-to-end training manner. Through comprehensive experiments on both UNet (e.g., SD1.5) and DiT (e.g., SD3.0), we show that our method outperforms existing ControlNet variants in certain key aspects of interest. As evidenced by both quantitative and qualitative evaluations, FlexControl preserves or enhances image fidelity while also reducing computational overhead by selectively activating the most relevant blocks. These results underscore the potential of a flexible, data-driven approach for controlled diffusion and open new avenues for efficient generative model design.

One of the most profound challenges of modern machine learning is performing well on the long-tail of rare and underrepresented features. Large general-purpose models are trained for many tasks, but work best on high-frequency use cases. After training, it is hard to adapt a model to perform well on specific use cases underrepresented in the training corpus. Relying on prompt engineering or few-shot examples to maximize the output quality on a particular test case can be frustrating, as models can be highly sensitive to small changes, react in unpredicted ways or rely on a fixed system prompt for maintaining performance. In this work, we ask: "Can we optimize our training protocols to both improve controllability and performance on underrepresented use cases at inference time?" We revisit the divide between training and inference techniques to improve long-tail performance while providing users with a set of control levers the model is trained to be responsive to. We create a detailed taxonomy of data characteristics and task provenance to explicitly control generation attributes and implicitly condition generations at inference time. We fine-tune a base model to infer these markers automatically, which makes them optional at inference time. This principled and flexible approach yields pronounced improvements in performance, especially on examples from the long tail of the training distribution. While we observe an average lift of 5.7% win rates in open-ended generation quality with our markers, we see over 9.1% gains in underrepresented domains. We also observe relative lifts of up to 14.1% on underrepresented tasks like CodeRepair and absolute improvements of 35.3% on length instruction following evaluations.

Safety performance evaluation is critical for developing and deploying connected and automated vehicles (CAVs). One prevailing way is to design testing scenarios using prior knowledge of CAVs, test CAVs in these scenarios, and then evaluate their safety performances. However, significant differences between CAVs and prior knowledge could severely reduce the evaluation efficiency. Towards addressing this issue, most existing studies focus on the adaptive design of testing scenarios during the CAV testing process, but so far they cannot be applied to high-dimensional scenarios. In this paper, we focus on the adaptive safety performance evaluation by leveraging the testing results, after the CAV testing process. It can significantly improve the evaluation efficiency and be applied to high-dimensional scenarios. Specifically, instead of directly evaluating the unknown quantity (e.g., crash rates) of CAV safety performances, we evaluate the differences between the unknown quantity and known quantity (i.e., control variates). By leveraging the testing results, the control variates could be well designed and optimized such that the differences are close to zero, so the evaluation variance could be dramatically reduced for different CAVs. To handle the high-dimensional scenarios, we propose the sparse control variates method, where the control variates are designed only for the sparse and critical variables of scenarios. According to the number of critical variables in each scenario, the control variates are stratified into strata and optimized within each stratum using multiple linear regression techniques. We justify the proposed method's effectiveness by rigorous theoretical analysis and empirical study of high-dimensional overtaking scenarios.

Controllable layout generation aims at synthesizing plausible arrangement of element bounding boxes with optional constraints, such as type or position of a specific element. In this work, we try to solve a broad range of layout generation tasks in a single model that is based on discrete state-space diffusion models. Our model, named LayoutDM, naturally handles the structured layout data in the discrete representation and learns to progressively infer a noiseless layout from the initial input, where we model the layout corruption process by modality-wise discrete diffusion. For conditional generation, we propose to inject layout constraints in the form of masking or logit adjustment during inference. We show in the experiments that our LayoutDM successfully generates high-quality layouts and outperforms both task-specific and task-agnostic baselines on several layout tasks.

The widespread applicability and increasing omnipresence of LLMs have instigated a need to align LLM responses to user and stakeholder preferences. Many preference optimization approaches have been proposed that fine-tune LLM parameters to achieve good alignment. However, such parameter tuning is known to interfere with model performance on many tasks. Moreover, keeping up with shifting user preferences is tricky in such a situation. Decoding-time alignment with reward model guidance solves these issues at the cost of increased inference time. However, most of such methods fail to strike the right balance between exploration and exploitation of reward -- often due to the conflated formulation of these two aspects - to give well-aligned responses. To remedy this we decouple these two aspects and implement them in an evolutionary fashion: exploration is enforced by decoding from mutated instructions and exploitation is represented as the periodic replacement of poorly-rewarded generations with well-rewarded ones. Empirical evidences indicate that this strategy outperforms many preference optimization and decode-time alignment approaches on two widely accepted alignment benchmarks AlpacaEval 2 and MT-Bench. Our implementation will be available at: https://darwin-alignment.github.io.

In controllable generation tasks, flexibly manipulating the generated images to attain a desired appearance or structure based on a single input image cue remains a critical and longstanding challenge. Achieving this requires the effective decoupling of key attributes within the input image data, aiming to get representations accurately. Previous research has predominantly concentrated on disentangling image attributes within feature space. However, the complex distribution present in real-world data often makes the application of such decoupling algorithms to other datasets challenging. Moreover, the granularity of control over feature encoding frequently fails to meet specific task requirements. Upon scrutinizing the characteristics of various generative models, we have observed that the input sensitivity and dynamic evolution properties of the diffusion model can be effectively fused with the explicit decomposition operation in pixel space. This integration enables the image processing operations performed in pixel space for a specific feature distribution of the input image, and can achieve the desired control effect in the generated results. Therefore, we propose FilterPrompt, an approach to enhance the model control effect. It can be universally applied to any diffusion model, allowing users to adjust the representation of specific image features in accordance with task requirements, thereby facilitating more precise and controllable generation outcomes. In particular, our designed experiments demonstrate that the FilterPrompt optimizes feature correlation, mitigates content conflicts during the generation process, and enhances the model's control capability.

We present specialized Large Language Models for theoretical High-Energy Physics, obtained as 20 fine-tuned variants of the 8-billion parameter Llama-3.1 model. Each variant was trained on arXiv abstracts (through August 2024) from different combinations of hep-th, hep-ph and gr-qc. For a comparative study, we also trained models on datasets that contained abstracts from disparate fields such as the q-bio and cs categories. All models were fine-tuned using two distinct Low-Rank Adaptation fine-tuning approaches and varying dataset sizes, and outperformed the base model on hep-th abstract completion tasks. We compare performance against leading commercial LLMs (ChatGPT, Claude, Gemini, DeepSeek) and derive insights for further developing specialized language models for High-Energy Theoretical Physics.

Text-to-image diffusion generative models can generate high quality images at the cost of tedious prompt engineering. Controllability can be improved by introducing layout conditioning, however existing methods lack layout editing ability and fine-grained control over object attributes. The concept of multi-layer generation holds great potential to address these limitations, however generating image instances concurrently to scene composition limits control over fine-grained object attributes, relative positioning in 3D space and scene manipulation abilities. In this work, we propose a novel multi-stage generation paradigm that is designed for fine-grained control, flexibility and interactivity. To ensure control over instance attributes, we devise a novel training paradigm to adapt a diffusion model to generate isolated scene components as RGBA images with transparency information. To build complex images, we employ these pre-generated instances and introduce a multi-layer composite generation process that smoothly assembles components in realistic scenes. Our experiments show that our RGBA diffusion model is capable of generating diverse and high quality instances with precise control over object attributes. Through multi-layer composition, we demonstrate that our approach allows to build and manipulate images from highly complex prompts with fine-grained control over object appearance and location, granting a higher degree of control than competing methods.

Large Language Models (LLMs) have demonstrated significant enhancements in instruction-following abilities through instruction tuning, achieving notable performances across various tasks. Previous research has focused on fine-tuning medical domain-specific LLMs using an extensive array of medical-specific data, incorporating millions of pieces of biomedical literature to augment their medical capabilities. However, existing medical instruction-tuned LLMs have been constrained by the limited scope of tasks and instructions available, restricting the efficacy of instruction tuning and adversely affecting performance in the general domain. In this paper, we fine-tune LLaMA-series models using 52k diverse, machine-generated, medical instruction-following data, MedInstruct-52k, resulting in the model AlpaCare. Comprehensive experimental results on both general and medical-specific domain free-form instruction evaluations showcase AlpaCare's strong medical proficiency and generalizability compared to previous instruction-tuned models in both medical and general domains. We provide public access to our MedInstruct-52k dataset and a clinician-crafted free-form instruction test set, MedInstruct-test, along with our codebase, to foster further research and development. Our project page is available at https://github.com/XZhang97666/AlpaCare.

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

Recently, large-scale diffusion models have made impressive progress in text-to-image (T2I) generation. To further equip these T2I models with fine-grained spatial control, approaches like ControlNet introduce an extra network that learns to follow a condition image. However, for every single condition type, ControlNet requires independent training on millions of data pairs with hundreds of GPU hours, which is quite expensive and makes it challenging for ordinary users to explore and develop new types of conditions. To address this problem, we propose the CtrLoRA framework, which trains a Base ControlNet to learn the common knowledge of image-to-image generation from multiple base conditions, along with condition-specific LoRAs to capture distinct characteristics of each condition. Utilizing our pretrained Base ControlNet, users can easily adapt it to new conditions, requiring as few as 1,000 data pairs and less than one hour of single-GPU training to obtain satisfactory results in most scenarios. Moreover, our CtrLoRA reduces the learnable parameters by 90% compared to ControlNet, significantly lowering the threshold to distribute and deploy the model weights. Extensive experiments on various types of conditions demonstrate the efficiency and effectiveness of our method. Codes and model weights will be released at https://github.com/xyfJASON/ctrlora.

In this paper, we introduce EasyEdit2, a framework designed to enable plug-and-play adjustability for controlling Large Language Model (LLM) behaviors. EasyEdit2 supports a wide range of test-time interventions, including safety, sentiment, personality, reasoning patterns, factuality, and language features. Unlike its predecessor, EasyEdit2 features a new architecture specifically designed for seamless model steering. It comprises key modules such as the steering vector generator and the steering vector applier, which enable automatic generation and application of steering vectors to influence the model's behavior without modifying its parameters. One of the main advantages of EasyEdit2 is its ease of use-users do not need extensive technical knowledge. With just a single example, they can effectively guide and adjust the model's responses, making precise control both accessible and efficient. Empirically, we report model steering performance across different LLMs, demonstrating the effectiveness of these techniques. We have released the source code on GitHub at https://github.com/zjunlp/EasyEdit along with a demonstration notebook. In addition, we provide a demo video at https://zjunlp.github.io/project/EasyEdit2/video for a quick introduction.

Designing effective strategies for controlling epidemic spread by vaccination is an important question in epidemiology, especially in the early stages when vaccines are limited. This is a challenging question when the contact network is very heterogeneous, and strategies based on controlling network properties, such as the degree and spectral radius, have been shown to be effective. Implementation of such strategies requires detailed information on the contact structure, which might be sensitive in many applications. Our focus here is on choosing effective vaccination strategies when the edges are sensitive and differential privacy guarantees are needed. Our main contributions are (varepsilon,delta)-differentially private algorithms for designing vaccination strategies by reducing the maximum degree and spectral radius. Our key technique is a private algorithm for the multi-set multi-cover problem, which we use for controlling network properties. We evaluate privacy-utility tradeoffs of our algorithms on multiple synthetic and real-world networks, and show their effectiveness.

Controlling the format of outputs generated by large language models (LLMs) is a critical functionality in various applications. Current methods typically employ constrained decoding with rule-based automata or fine-tuning with manually crafted format instructions, both of which struggle with open-domain format requirements. To address this limitation, we introduce a novel framework for controlled generation in LLMs, leveraging user-provided, one-shot QA pairs. This study investigates LLMs' capabilities to follow open-domain, one-shot constraints and replicate the format of the example answers. We observe that this is a non-trivial problem for current LLMs. We also develop a dataset collection methodology for supervised fine-tuning that enhances the open-domain format control of LLMs without degrading output quality, as well as a benchmark on which we evaluate both the helpfulness and format correctness of LLM outputs. The resulting datasets, named OIFC-SFT, along with the related code, will be made publicly available at https://github.com/cofe-ai/OIFC.

How much private information do text embeddings reveal about the original text? We investigate the problem of embedding inversion, reconstructing the full text represented in dense text embeddings. We frame the problem as controlled generation: generating text that, when reembedded, is close to a fixed point in latent space. We find that although a na\"ive model conditioned on the embedding performs poorly, a multi-step method that iteratively corrects and re-embeds text is able to recover 92% of 32-token text inputs exactly. We train our model to decode text embeddings from two state-of-the-art embedding models, and also show that our model can recover important personal information (full names) from a dataset of clinical notes. Our code is available on Github: https://github.com/jxmorris12/vec2text{github.com/jxmorris12/vec2text}.

Large-scale language models show promising text generation capabilities, but users cannot easily control particular aspects of the generated text. We release CTRL, a 1.63 billion-parameter conditional transformer language model, trained to condition on control codes that govern style, content, and task-specific behavior. Control codes were derived from structure that naturally co-occurs with raw text, preserving the advantages of unsupervised learning while providing more explicit control over text generation. These codes also allow CTRL to predict which parts of the training data are most likely given a sequence. This provides a potential method for analyzing large amounts of data via model-based source attribution. We have released multiple full-sized, pretrained versions of CTRL at https://github.com/salesforce/ctrl.

Generative Behavior Cloning (GBC) is a simple yet effective framework for robot learning, particularly in multi-task settings. Recent GBC methods often employ diffusion policies with open-loop (OL) control, where actions are generated via a diffusion process and executed in multi-step chunks without replanning. While this approach has demonstrated strong success rates and generalization, its inherent stochasticity can result in erroneous action sampling, occasionally leading to unexpected task failures. Moreover, OL control suffers from delayed responses, which can degrade performance in noisy or dynamic environments. To address these limitations, we propose two novel techniques to enhance the consistency and reactivity of diffusion policies: (1) self-guidance, which improves action fidelity by leveraging past observations and implicitly promoting future-aware behavior; and (2) adaptive chunking, which selectively updates action sequences when the benefits of reactivity outweigh the need for temporal consistency. Extensive experiments show that our approach substantially improves GBC performance across a wide range of simulated and real-world robotic manipulation tasks. Our code is available at https://github.com/junhyukso/SGAC

Aligning large language models (LLMs) with human preferences is essential for safe and useful LLMs. Previous works mainly adopt reinforcement learning (RLHF) and direct preference optimization (DPO) with human feedback for alignment. Nevertheless, they have certain drawbacks. One such limitation is that they can only align models with one preference at the training time (e.g., they cannot learn to generate concise responses when the preference data prefers detailed responses), or have certain constraints for the data format (e.g., DPO only supports pairwise preference data). To this end, prior works incorporate controllable generations for alignment to make language models learn multiple preferences and provide outputs with different preferences during inference if asked. Controllable generation also offers more flexibility with regard to data format (e.g., it supports pointwise preference data). Specifically, it uses different control tokens for different preferences during training and inference, making LLMs behave differently when required. Current controllable generation methods either use a special token or hand-crafted prompts as control tokens, and optimize them together with LLMs. As control tokens are typically much lighter than LLMs, this optimization strategy may not effectively optimize control tokens. To this end, we first use parameter-efficient tuning (e.g., prompting tuning and low-rank adaptation) to optimize control tokens and then fine-tune models for controllable generations, similar to prior works. Our approach, alignMEnt with parameter-Efficient Tuning (MEET), improves the quality of control tokens, thus improving controllable generation quality consistently by an apparent margin on two well-recognized datasets compared with prior works.

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce \ourdataset, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. \ourdataset~ consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). \ourdataset~is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with \ourdataset~can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at https://huggingface.co/datasets/medexanon/Medex{huggingface.co/datasets/medexanon/Medex}, and will provide expanded versions as available literature grows.

We consider the task of evaluating policies of algorithmic resource allocation through randomized controlled trials (RCTs). Such policies are tasked with optimizing the utilization of limited intervention resources, with the goal of maximizing the benefits derived. Evaluation of such allocation policies through RCTs proves difficult, notwithstanding the scale of the trial, because the individuals' outcomes are inextricably interlinked through resource constraints controlling the policy decisions. Our key contribution is to present a new estimator leveraging our proposed novel concept, that involves retrospective reshuffling of participants across experimental arms at the end of an RCT. We identify conditions under which such reassignments are permissible and can be leveraged to construct counterfactual trials, whose outcomes can be accurately ascertained, for free. We prove theoretically that such an estimator is more accurate than common estimators based on sample means -- we show that it returns an unbiased estimate and simultaneously reduces variance. We demonstrate the value of our approach through empirical experiments on synthetic, semi-synthetic as well as real case study data and show improved estimation accuracy across the board.

Recently, multi-aspect controllable text generation that controls the generated text in multiple aspects (e.g., sentiment, topic, and keywords) has attracted increasing attention. Although methods based on parameter efficient tuning like prefix-tuning could achieve multi-aspect controlling in a plug-and-play way, the mutual interference of multiple prefixes leads to significant degeneration of constraints and limits their extensibility to training-time unseen aspect combinations. In this work, we provide a theoretical lower bound for the interference and empirically found that the interference grows with the number of layers where prefixes are inserted. Based on these analyses, we propose using trainable gates to normalize the intervention of prefixes to restrain the growing interference. As a result, controlling training-time unseen combinations of aspects can be realized by simply concatenating corresponding plugins such that new constraints can be extended at a lower cost. In addition, we propose a unified way to process both categorical and free-form constraints. Experiments on text generation and machine translation demonstrate the superiority of our approach over baselines on constraint accuracy, text quality, and extensibility.

Manipulation of facial images to meet specific controls such as pose, expression, and lighting, also known as face rigging, is a complex task in computer vision. Existing methods are limited by their reliance on image datasets, which necessitates individual-specific fine-tuning and limits their ability to retain fine-grained identity and semantic details, reducing practical usability. To overcome these limitations, we introduce ControlFace, a novel face rigging method conditioned on 3DMM renderings that enables flexible, high-fidelity control. We employ a dual-branch U-Nets: one, referred to as FaceNet, captures identity and fine details, while the other focuses on generation. To enhance control precision, the control mixer module encodes the correlated features between the target-aligned control and reference-aligned control, and a novel guidance method, reference control guidance, steers the generation process for better control adherence. By training on a facial video dataset, we fully utilize FaceNet's rich representations while ensuring control adherence. Extensive experiments demonstrate ControlFace's superior performance in identity preservation and control precision, highlighting its practicality. Please see the project website: https://cvlab-kaist.github.io/ControlFace/.

Large language models (LLMs) appear to bias their survey answers toward certain values. Nonetheless, some argue that LLMs are too inconsistent to simulate particular values. Are they? To answer, we first define value consistency as the similarity of answers across (1) paraphrases of one question, (2) related questions under one topic, (3) multiple-choice and open-ended use-cases of one question, and (4) multilingual translations of a question to English, Chinese, German, and Japanese. We apply these measures to a few large (>=34b), open LLMs including llama-3, as well as gpt-4o, using eight thousand questions spanning more than 300 topics. Unlike prior work, we find that models are relatively consistent across paraphrases, use-cases, translations, and within a topic. Still, some inconsistencies remain. Models are more consistent on uncontroversial topics (e.g., in the U.S., "Thanksgiving") than on controversial ones ("euthanasia"). Base models are both more consistent compared to fine-tuned models and are uniform in their consistency across topics, while fine-tuned models are more inconsistent about some topics ("euthanasia") than others ("women's rights") like our human subjects (n=165).

As the capabilities of Large Language Models (LLMs) in healthcare and medicine continue to advance, there is a growing need for competitive open-source models that can safeguard public interest. With the increasing availability of highly competitive open base models, the impact of continued pre-training is increasingly uncertain. In this work, we explore the role of instruct tuning, model merging, alignment, red teaming and advanced inference schemes, as means to improve current open models. To that end, we introduce the Aloe family, a set of open medical LLMs highly competitive within its scale range. Aloe models are trained on the current best base models (Mistral, LLaMA 3), using a new custom dataset which combines public data sources improved with synthetic Chain of Thought (CoT). Aloe models undergo an alignment phase, becoming one of the first few policy-aligned open healthcare LLM using Direct Preference Optimization, setting a new standard for ethical performance in healthcare LLMs. Model evaluation expands to include various bias and toxicity datasets, a dedicated red teaming effort, and a much-needed risk assessment for healthcare LLMs. Finally, to explore the limits of current LLMs in inference, we study several advanced prompt engineering strategies to boost performance across benchmarks, yielding state-of-the-art results for open healthcare 7B LLMs, unprecedented at this scale.

Existing methods for controlling language models, such as RLHF and Constitutional AI, involve determining which LLM behaviors are desirable and training them into a language model. However, in many cases, it is desirable for LLMs to be controllable at inference time, so that they can be used in multiple contexts with diverse needs. We illustrate this with the Pink Elephant Problem: instructing an LLM to avoid discussing a certain entity (a ``Pink Elephant''), and instead discuss a preferred entity (``Grey Elephant''). We apply a novel simplification of Constitutional AI, Direct Principle Feedback, which skips the ranking of responses and uses DPO directly on critiques and revisions. Our results show that after DPF fine-tuning on our synthetic Pink Elephants dataset, our 13B fine-tuned LLaMA 2 model significantly outperforms Llama-2-13B-Chat and a prompted baseline, and performs as well as GPT-4 in on our curated test set assessing the Pink Elephant Problem.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

In recent years, text-driven image editing has made significant progress. However, due to the inherent ambiguity and discreteness of natural language, color editing still faces challenges such as insufficient precision and difficulty in achieving continuous control. Although linearly interpolating the embedding vectors of different textual descriptions can guide the model to generate a sequence of images with varying colors, this approach lacks precise control over the range of color changes in the output images. Moreover, the relationship between the interpolation coefficient and the resulting image color is unknown and uncontrollable. To address these issues, we introduce a color mapping module that explicitly models the correspondence between the text embedding space and image RGB values. This module predicts the corresponding embedding vector based on a given RGB value, enabling precise color control of the generated images while maintaining semantic consistency. Users can specify a target RGB range to generate images with continuous color variations within the desired range, thereby achieving finer-grained, continuous, and controllable color editing. Experimental results demonstrate that our method performs well in terms of color continuity and controllability.

Diffusion models for continuous data gained widespread adoption owing to their high quality generation and control mechanisms. However, controllable diffusion on discrete data faces challenges given that continuous guidance methods do not directly apply to discrete diffusion. Here, we provide a straightforward derivation of classifier-free and classifier-based guidance for discrete diffusion, as well as a new class of diffusion models that leverage uniform noise and that are more guidable because they can continuously edit their outputs. We improve the quality of these models with a novel continuous-time variational lower bound that yields state-of-the-art performance, especially in settings involving guidance or fast generation. Empirically, we demonstrate that our guidance mechanisms combined with uniform noise diffusion improve controllable generation relative to autoregressive and diffusion baselines on several discrete data domains, including genomic sequences, small molecule design, and discretized image generation.

Recently, 3D generative models have shown promising performances in structure-based drug design by learning to generate ligands given target binding sites. However, only modeling the target-ligand distribution can hardly fulfill one of the main goals in drug discovery -- designing novel ligands with desired properties, e.g., high binding affinity, easily synthesizable, etc. This challenge becomes particularly pronounced when the target-ligand pairs used for training do not align with these desired properties. Moreover, most existing methods aim at solving de novo design task, while many generative scenarios requiring flexible controllability, such as R-group optimization and scaffold hopping, have received little attention. In this work, we propose DecompOpt, a structure-based molecular optimization method based on a controllable and decomposed diffusion model. DecompOpt presents a new generation paradigm which combines optimization with conditional diffusion models to achieve desired properties while adhering to the molecular grammar. Additionally, DecompOpt offers a unified framework covering both de novo design and controllable generation. To achieve so, ligands are decomposed into substructures which allows fine-grained control and local optimization. Experiments show that DecompOpt can efficiently generate molecules with improved properties than strong de novo baselines, and demonstrate great potential in controllable generation tasks.

With the rapid advancement of 2D generative models, preserving subject identity while enabling diverse editing has emerged as a critical research focus. Existing methods typically face inherent trade-offs between identity preservation and personalized manipulation. We introduce FlexIP, a novel framework that decouples these objectives through two dedicated components: a Personalization Adapter for stylistic manipulation and a Preservation Adapter for identity maintenance. By explicitly injecting both control mechanisms into the generative model, our framework enables flexible parameterized control during inference through dynamic tuning of the weight adapter. Experimental results demonstrate that our approach breaks through the performance limitations of conventional methods, achieving superior identity preservation while supporting more diverse personalized generation capabilities (Project Page: https://flexip-tech.github.io/flexip/).

Controllable text generation is a fundamental aspect of natural language generation, with numerous methods proposed for different constraint types. However, these approaches often require significant architectural or decoding modifications, making them challenging to apply to additional constraints or resolve different constraint combinations. To address this, our paper introduces Regular Expression Instruction (REI), which utilizes an instruction-based mechanism to fully exploit regular expressions' advantages to uniformly model diverse constraints. Specifically, our REI supports all popular fine-grained controllable generation constraints, i.e., lexical, positional, and length, as well as their complex combinations, via regular expression-style instructions. Our method only requires fine-tuning on medium-scale language models or few-shot, in-context learning on large language models, and requires no further adjustment when applied to various constraint combinations. Experiments demonstrate that our straightforward approach yields high success rates and adaptability to various constraints while maintaining competitiveness in automatic metrics and outperforming most previous baselines.

We propose affine concept editing (ACE) as an approach for steering language models' behavior by intervening directly in activations. We begin with an affine decomposition of model activation vectors and show that prior methods for steering model behavior correspond to subsets of terms of this decomposition. We then provide a derivation of ACE and use it to control refusal behavior on ten different models, including Llama 3 70B. ACE combines affine subspace projection and activation addition to reliably control the model's refusal responses across prompt types. We evaluate the results using LLM-based scoring on a collection of harmful and harmless prompts. Our experiments demonstrate that ACE consistently achieves more precise control over model behavior than existing methods and generalizes to models where directional ablation via affine subspace projection alone produces incoherent outputs. Code for reproducing our results is available at https://github.com/EleutherAI/steering-llama3 .

Diffusion models have achieved remarkable success in generating realistic images but suffer from generating accurate human hands, such as incorrect finger counts or irregular shapes. This difficulty arises from the complex task of learning the physical structure and pose of hands from training images, which involves extensive deformations and occlusions. For correct hand generation, our paper introduces a lightweight post-processing solution called HandRefiner. HandRefiner employs a conditional inpainting approach to rectify malformed hands while leaving other parts of the image untouched. We leverage the hand mesh reconstruction model that consistently adheres to the correct number of fingers and hand shape, while also being capable of fitting the desired hand pose in the generated image. Given a generated failed image due to malformed hands, we utilize ControlNet modules to re-inject such correct hand information. Additionally, we uncover a phase transition phenomenon within ControlNet as we vary the control strength. It enables us to take advantage of more readily available synthetic data without suffering from the domain gap between realistic and synthetic hands. Experiments demonstrate that HandRefiner can significantly improve the generation quality quantitatively and qualitatively. The code is available at https://github.com/wenquanlu/HandRefiner .

Controllable text generation is a growing field within natural language generation (NLG) that focuses on producing text that meets specific constraints in real-world applications. Previous approaches, such as plug-and-play controllers (PPCs), aimed to steer the properties of generated text in a flexible manner. However, these methods often compromised the integrity of the language model's decoding process, resulting in less smooth text generation. Alternatively, other techniques utilized multiple attribute prompts to align the generated text with desired attributes, but this approach required prompt design for each attribute and was dependent on the size of the language model. This paper introduces a novel method for flexible attribute control in text generation using pre-trained language models (PLMs). The proposed approach aims to enhance the fluency of generated text by guiding the generation process with PPCs. The key idea is to dynamically adjust the distribution of generated text by modifying prompts, effectively constraining the output space of the language model and influencing the desired attribute. To enable smooth cooperation between the PLM and the PPC, our work innovatively proposes a new model fine-tuning method: Reinforcement Learning with Dynamic Adjust Feedback (RLDAF).This fine-tuning process adapts a small subset of the language model's parameters based on the generating actions taken during the PPC control process. The resulting harmonious collaboration between the PLM and PPC leads to improved smoothness in text generation during inference. Extensive experiments were conducted on the SST2 dataset, and the proposed method outperformed previous approaches in various evaluation metrics, including text fluency and attribute consistency.

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

This paper reports on patterns exhibiting self-replication with spontaneous, inheritable mutations and exponential genetic drift in Neural Cellular Automata. Despite the models not being explicitly trained for mutation or inheritability, the descendant patterns exponentially drift away from ancestral patterns, even when the automaton is deterministic. While this is far from being the first instance of evolutionary dynamics in a cellular automaton, it is the first to do so by exploiting the power and convenience of Neural Cellular Automata, arguably increasing the space of variations and the opportunity for Open Ended Evolution.

In recent years, significant progress has been made in the development of text-to-image generation models. However, these models still face limitations when it comes to achieving full controllability during the generation process. Often, specific training or the use of limited models is required, and even then, they have certain restrictions. To address these challenges, A two-stage method that effectively combines controllability and high quality in the generation of images is proposed. This approach leverages the expertise of pre-trained models to achieve precise control over the generated images, while also harnessing the power of diffusion models to achieve state-of-the-art quality. By separating controllability from high quality, This method achieves outstanding results. It is compatible with both latent and image space diffusion models, ensuring versatility and flexibility. Moreover, This approach consistently produces comparable outcomes to the current state-of-the-art methods in the field. Overall, This proposed method represents a significant advancement in text-to-image generation, enabling improved controllability without compromising on the quality of the generated images.

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem. This introduces a new paradigm of multitask language models which seamlessly bridge sequence regression and conditional sequence generation. We thoroughly demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction tasks of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a highly competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by a novel, alternating training scheme that enables the model to decorate seed sequences by desired properties, e.g., to optimize reaction yield. In sum, the RT is the first report of a multitask model that concurrently excels at predictive and generative tasks in biochemistry. This finds particular application in property-driven, local exploration of the chemical or protein space and could pave the road toward foundation models in material design. The code to reproduce all experiments of the paper is available at: https://github.com/IBM/regression-transformer

Aligned instruction following models can better fulfill user requests than their unaligned counterparts. However, it has been shown that there is a length bias in evaluation of such models, and that training algorithms tend to exploit this bias by learning longer responses. In this work we show how to train models that can be controlled at inference time with instructions containing desired length constraints. Such models are superior in length instructed evaluations, outperforming standard instruction following models such as GPT4, Llama 3 and Mixtral.

The widespread adoption of synthetic data raises new questions about how models generating the data can influence other large language models (LLMs) via distilled data. To start, our work exhaustively characterizes the impact of passive inheritance of model properties by systematically studying the consequences of synthetic data integration. We provide one of the most comprehensive studies to-date of how the source of synthetic data shapes models' internal biases, calibration and generations' textual attributes and preferences. We find that models are surprisingly sensitive towards certain attributes even when the synthetic data prompts appear "neutral". which invites the question whether this sensitivity can be exploited for good. Our findings invite the question can we explicitly steer the models towards the properties we want at test time by exploiting the data generation process? This would have historically been considered infeasible due to the cost of collecting data with a specific characteristic or objective in mind. However, improvement in the quality of synthetic data, as well as a shift towards general-purpose models designed to follow a diverse way of instructions, means this question is timely. We propose active inheritance as a term to describe intentionally constraining synthetic data according to a non-differentiable objective. We demonstrate how active inheritance can steer the generation profiles of models towards desirable non-differentiable attributes, e.g. high lexical diversity or low toxicity.

Controlled text perturbation is useful for evaluating and improving model generalizability. However, current techniques rely on training a model for every target perturbation, which is expensive and hard to generalize. We present Tailor, a semantically-controlled text generation system. Tailor builds on a pretrained seq2seq model and produces textual outputs conditioned on control codes derived from semantic representations. We craft a set of operations to modify the control codes, which in turn steer generation towards targeted attributes. These operations can be further composed into higher-level ones, allowing for flexible perturbation strategies. We demonstrate the effectiveness of these perturbations in multiple applications. First, we use Tailor to automatically create high-quality contrast sets for four distinct natural language processing (NLP) tasks. These contrast sets contain fewer spurious artifacts and are complementary to manually annotated ones in their lexical diversity. Second, we show that Tailor perturbations can improve model generalization through data augmentation. Perturbing just 2% of training data leads to a 5.8-point gain on an NLI challenge set measuring reliance on syntactic heuristics.

Randomized controlled trials (RCTs) are considered the gold standard for estimating the average treatment effect (ATE) of interventions. One use of RCTs is to study the causes of global poverty -- a subject explicitly cited in the 2019 Nobel Memorial Prize awarded to Duflo, Banerjee, and Kremer "for their experimental approach to alleviating global poverty." Because the ATE is a population summary, anti-poverty experiments often seek to unpack the effect variation around the ATE by conditioning (CATE) on tabular variables such as age and ethnicity that were measured during the RCT data collection. Although such variables are key to unpacking CATE, using only such variables may fail to capture historical, geographical, or neighborhood-specific contributors to effect variation, as tabular RCT data are often only observed near the time of the experiment. In global poverty research, when the location of the experiment units is approximately known, satellite imagery can provide a window into such factors important for understanding heterogeneity. However, there is no method that specifically enables applied researchers to analyze CATE from images. In this paper, using a deep probabilistic modeling framework, we develop such a method that estimates latent clusters of images by identifying images with similar treatment effects distributions. Our interpretable image CATE model also includes a sensitivity factor that quantifies the importance of image segments contributing to the effect cluster prediction. We compare the proposed methods against alternatives in simulation; also, we show how the model works in an actual RCT, estimating the effects of an anti-poverty intervention in northern Uganda and obtaining a posterior predictive distribution over effects for the rest of the country where no experimental data was collected. We make all models available in open-source software.

As the text generation capabilities of large language models become increasingly prominent, recent studies have focused on controlling particular aspects of the generated text to make it more personalized. However, most research on controllable text generation focuses on controlling the content or modeling specific high-level/coarse-grained attributes that reflect authors' writing styles, such as formality, domain, or sentiment. In this paper, we focus on controlling fine-grained attributes spanning multiple linguistic dimensions, such as lexical and syntactic attributes. We introduce a novel benchmark to train generative models and evaluate their ability to generate personalized text based on multiple fine-grained linguistic attributes. We systematically investigate the performance of various large language models on our benchmark and draw insights from the factors that impact their performance. We make our code, data, and pretrained models publicly available.

We propose controlled decoding (CD), a novel off-policy reinforcement learning method to control the autoregressive generation from language models towards high reward outcomes. CD solves an off-policy reinforcement learning problem through a value function for the reward, which we call a prefix scorer. The prefix scorer is used at inference time to steer the generation towards higher reward outcomes. We show that the prefix scorer may be trained on (possibly) off-policy data to predict the expected reward when decoding is continued from a partially decoded response. We empirically demonstrate that CD is effective as a control mechanism on Reddit conversations corpus. We also show that the modularity of the design of CD makes it possible to control for multiple rewards, effectively solving a multi-objective reinforcement learning problem with no additional complexity. Finally, we show that CD can be applied in a novel blockwise fashion at inference-time, again without the need for any training-time changes, essentially bridging the gap between the popular best-of-K strategy and token-level reinforcement learning. This makes CD a promising approach for alignment of language models.

Fine-tuning large pre-trained models has become the de facto strategy for developing both task-specific and general-purpose machine learning systems, including developing models that are safe to deploy. Despite its clear importance, there has been minimal work that explains how fine-tuning alters the underlying capabilities learned by a model during pretraining: does fine-tuning yield entirely novel capabilities or does it just modulate existing ones? We address this question empirically in synthetic, controlled settings where we can use mechanistic interpretability tools (e.g., network pruning and probing) to understand how the model's underlying capabilities are changing. We perform an extensive analysis of the effects of fine-tuning in these settings, and show that: (i) fine-tuning rarely alters the underlying model capabilities; (ii) a minimal transformation, which we call a 'wrapper', is typically learned on top of the underlying model capabilities, creating the illusion that they have been modified; and (iii) further fine-tuning on a task where such hidden capabilities are relevant leads to sample-efficient 'revival' of the capability, i.e., the model begins reusing these capability after only a few gradient steps. This indicates that practitioners can unintentionally remove a model's safety wrapper merely by fine-tuning it on a, e.g., superficially unrelated, downstream task. We additionally perform analysis on language models trained on the TinyStories dataset to support our claims in a more realistic setup.

We propose a novel machine learning approach for inferring causal variables of a target variable from observations. Our focus is on directly inferring a set of causal factors without requiring full causal graph reconstruction, which is computationally challenging in large-scale systems. The identified causal set consists of all potential regulators of the target variable under experimental settings, enabling efficient regulation when intervention costs and feasibility vary across variables. To achieve this, we train a neural network using supervised learning on simulated data to infer causality. By employing a local-inference strategy, our approach scales with linear complexity in the number of variables, efficiently scaling up to thousands of variables. Empirical results demonstrate superior performance in identifying causal relationships within large-scale gene regulatory networks, outperforming existing methods that emphasize full-graph discovery. We validate our model's generalization capability across out-of-distribution graph structures and generating mechanisms, including gene regulatory networks of E. coli and the human K562 cell line. Implementation codes are available at https://github.com/snu-mllab/Targeted-Cause-Discovery.

We study the problem of adaptively identifying patient subpopulations that benefit from a given treatment during a confirmatory clinical trial. This type of adaptive clinical trial has been thoroughly studied in biostatistics, but has been allowed only limited adaptivity so far. Here, we aim to relax classical restrictions on such designs and investigate how to incorporate ideas from the recent machine learning literature on adaptive and online experimentation to make trials more flexible and efficient. We find that the unique characteristics of the subpopulation selection problem -- most importantly that (i) one is usually interested in finding subpopulations with any treatment benefit (and not necessarily the single subgroup with largest effect) given a limited budget and that (ii) effectiveness only has to be demonstrated across the subpopulation on average -- give rise to interesting challenges and new desiderata when designing algorithmic solutions. Building on these findings, we propose AdaGGI and AdaGCPI, two meta-algorithms for subpopulation construction. We empirically investigate their performance across a range of simulation scenarios and derive insights into their (dis)advantages across different settings.

Jailbreaks on large language models (LLMs) have recently received increasing attention. For a comprehensive assessment of LLM safety, it is essential to consider jailbreaks with diverse attributes, such as contextual coherence and sentiment/stylistic variations, and hence it is beneficial to study controllable jailbreaking, i.e. how to enforce control on LLM attacks. In this paper, we formally formulate the controllable attack generation problem, and build a novel connection between this problem and controllable text generation, a well-explored topic of natural language processing. Based on this connection, we adapt the Energy-based Constrained Decoding with Langevin Dynamics (COLD), a state-of-the-art, highly efficient algorithm in controllable text generation, and introduce the COLD-Attack framework which unifies and automates the search of adversarial LLM attacks under a variety of control requirements such as fluency, stealthiness, sentiment, and left-right-coherence. The controllability enabled by COLD-Attack leads to diverse new jailbreak scenarios which not only cover the standard setting of generating fluent (suffix) attack with continuation constraint, but also allow us to address new controllable attack settings such as revising a user query adversarially with paraphrasing constraint, and inserting stealthy attacks in context with position constraint. Our extensive experiments on various LLMs (Llama-2, Mistral, Vicuna, Guanaco, GPT-3.5, and GPT-4) show COLD-Attack's broad applicability, strong controllability, high success rate, and attack transferability. Our code is available at https://github.com/Yu-Fangxu/COLD-Attack.

Designing sequences that satisfy multiple, often conflicting, objectives is a central challenge in therapeutic and biomolecular engineering. Existing generative frameworks largely operate in continuous spaces with single-objective guidance, while discrete approaches lack guarantees for multi-objective Pareto optimality. We introduce AReUReDi (Annealed Rectified Updates for Refining Discrete Flows), a discrete optimization algorithm with theoretical guarantees of convergence to the Pareto front. Building on Rectified Discrete Flows (ReDi), AReUReDi combines Tchebycheff scalarization, locally balanced proposals, and annealed Metropolis-Hastings updates to bias sampling toward Pareto-optimal states while preserving distributional invariance. Applied to peptide and SMILES sequence design, AReUReDi simultaneously optimizes up to five therapeutic properties (including affinity, solubility, hemolysis, half-life, and non-fouling) and outperforms both evolutionary and diffusion-based baselines. These results establish AReUReDi as a powerful, sequence-based framework for multi-property biomolecule generation.

The development of robust safety benchmarks for large language models requires open, reproducible datasets that can measure both appropriate refusal of harmful content and potential over-restriction of legitimate scientific discourse. We present an open-source dataset and testing framework for evaluating LLM safety mechanisms across mainly controlled substance queries, analyzing four major models' responses to systematically varied prompts. Our results reveal distinct safety profiles: Claude-3.5-sonnet demonstrated the most conservative approach with 73% refusals and 27% allowances, while Mistral attempted to answer 100% of queries. GPT-3.5-turbo showed moderate restriction with 10% refusals and 90% allowances, and Grok-2 registered 20% refusals and 80% allowances. Testing prompt variation strategies revealed decreasing response consistency, from 85% with single prompts to 65% with five variations. This publicly available benchmark enables systematic evaluation of the critical balance between necessary safety restrictions and potential over-censorship of legitimate scientific inquiry, while providing a foundation for measuring progress in AI safety implementation. Chain-of-thought analysis reveals potential vulnerabilities in safety mechanisms, highlighting the complexity of implementing robust safeguards without unduly restricting desirable and valid scientific discourse.

We present MixtureVitae, an open-access pretraining corpus built to minimize legal risk while providing strong model performance. MixtureVitae follows a risk-mitigated sourcing strategy that combines public-domain and permissively licensed text (e.g., CC-BY/Apache) with carefully justified low-risk additions (e.g., government works and EU TDM-eligible sources), alongside targeted instruction, reasoning and synthetic data with documented provenance. We detail a transparent, multi-stage pipeline for license-aware filtering, safety and quality screening, and domain-aware mixing, and we release the dataset and curation recipes to support reproducible research. In controlled experiments using the open-sci-ref training protocol (fixed architectures at 130M/400M/1.3B/1.7B parameters; training budgets of 50B and 300B tokens), models trained on MixtureVitae consistently outperform other permissive datasets across a suite of standard benchmarks, and at the 1.7B/300B setting they surpass FineWeb-Edu and approach DCLM in the later stages of training. Performance is particularly strong on math/code and competitive on QA tasks. These results demonstrate that permissive-first, risk-mitigated data provides a practical and legally mitigated foundation for training capable LLMs, reducing reliance on indiscriminate web scraping without sacrificing competitiveness. Code: https://github.com/ontocord/mixturevitae

It has always been an important yet challenging problem to control language models to avoid generating texts with undesirable attributes, such as toxic language and unnatural repetition. We introduce Click for controllable text generation, which needs no modification to the model architecture and facilitates out-of-the-box use of trained models. It employs a contrastive loss on sequence likelihood, which fundamentally decreases the generation probability of negative samples (i.e., generations with undesirable attributes). It also adopts a novel likelihood ranking-based strategy to construct contrastive samples from model generations. On the tasks of language detoxification, sentiment steering, and repetition reduction, we show that Click outperforms strong baselines of controllable text generation and demonstrate the superiority of Click's sample construction strategy.

Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experimental or interventional conditions. BaCaDI is fully differentiable, which allows us to infer the complex joint posterior over the intervention targets and the causal structure via efficient gradient-based variational inference. In experiments on synthetic causal discovery tasks and simulated gene-expression data, BaCaDI outperforms related methods in identifying causal structures and intervention targets.

Testing and evaluation is a critical step in the development and deployment of connected and automated vehicles (CAVs). Due to the black-box property and various types of CAVs, how to test and evaluate CAVs adaptively remains a major challenge. Many approaches have been proposed to adaptively generate testing scenarios during the testing process. However, most existing approaches cannot be applied to complex scenarios, where the variables needed to define such scenarios are high dimensional. Towards filling this gap, the adaptive testing with sparse control variates method is proposed in this paper. Instead of adaptively generating testing scenarios, our approach evaluates CAVs' performances by adaptively utilizing the testing results. Specifically, each testing result is adjusted using multiple linear regression techniques based on control variates. As the regression coefficients can be adaptively optimized for the CAV under test, using the adjusted results can reduce the estimation variance, compared with using the testing results directly. To overcome the high dimensionality challenge, sparse control variates are utilized only for the critical variables of testing scenarios. To validate the proposed method, the high-dimensional overtaking scenarios are investigated, and the results demonstrate that our approach can further accelerate the evaluation process by about 30 times.

In the field of portrait video generation, the use of single images to generate portrait videos has become increasingly prevalent. A common approach involves leveraging generative models to enhance adapters for controlled generation. However, control signals (e.g., text, audio, reference image, pose, depth map, etc.) can vary in strength. Among these, weaker conditions often struggle to be effective due to interference from stronger conditions, posing a challenge in balancing these conditions. In our work on portrait video generation, we identified audio signals as particularly weak, often overshadowed by stronger signals such as facial pose and reference image. However, direct training with weak signals often leads to difficulties in convergence. To address this, we propose V-Express, a simple method that balances different control signals through the progressive training and the conditional dropout operation. Our method gradually enables effective control by weak conditions, thereby achieving generation capabilities that simultaneously take into account the facial pose, reference image, and audio. The experimental results demonstrate that our method can effectively generate portrait videos controlled by audio. Furthermore, a potential solution is provided for the simultaneous and effective use of conditions of varying strengths.

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

With COVID-19 having emerged as the most widespread human pandemic disease in a century, the need to control its spread to avoid massive loss of life became more than necessary, and extremely fast. Several vaccines were developed and the task of policy makers was suddenly to convince the reluctant population to be vaccinated by various means. While some countries have chosen a policy of mandatory vaccination or punitive incentives, many states in the United States have adopted various incentives to try to increase vaccination coverage. A study we conducted in recent months quantified the effect of these measures on the proportion of the population vaccinated, using the synthetic control method, by simulating what would have happened without these measures. The aim now is to generalize this study to smaller scales, to improve the results of our previous study, to quantify their robustness and to provide a tool that can be used by policy makers to adapt their behavior in light of the results obtained.

The field of text-to-image (T2I) generation has made significant progress in recent years, largely driven by advancements in diffusion models. Linguistic control enables effective content creation, but struggles with fine-grained control over image generation. This challenge has been explored, to a great extent, by incorporating additional user-supplied spatial conditions, such as depth maps and edge maps, into pre-trained T2I models through extra encoding. However, multi-control image synthesis still faces several challenges. Specifically, current approaches are limited in handling free combinations of diverse input control signals, overlook the complex relationships among multiple spatial conditions, and often fail to maintain semantic alignment with provided textual prompts. This can lead to suboptimal user experiences. To address these challenges, we propose AnyControl, a multi-control image synthesis framework that supports arbitrary combinations of diverse control signals. AnyControl develops a novel Multi-Control Encoder that extracts a unified multi-modal embedding to guide the generation process. This approach enables a holistic understanding of user inputs, and produces high-quality, faithful results under versatile control signals, as demonstrated by extensive quantitative and qualitative evaluations. Our project page is available in https://any-control.github.io.

Instruction tuning is instrumental in enabling Large Language Models~(LLMs) to follow user instructions to complete various open-domain tasks. The success of instruction tuning depends on the availability of high-quality instruction data. Owing to the exorbitant cost and substandard quality of human annotation, recent works have been deeply engaged in the exploration of the utilization of powerful closed-source models to generate instruction data automatically. However, these methods carry potential risks arising from the usage requirements of powerful closed-source models, which strictly forbid the utilization of their outputs to develop machine learning models. To deal with this problem, in this work, we explore alternative approaches to generate high-quality instruction data that do not rely on closed-source models. Our exploration includes an investigation of various existing instruction generation methods, culminating in the integration of the most efficient variant with two novel strategies to enhance the quality further. Evaluation results from two benchmarks and the GPT-4 model demonstrate the effectiveness of our generated instruction data, which can outperform Alpaca, a method reliant on closed-source models. We hope that more progress can be achieved in generating high-quality instruction data without using closed-source models.

Spatial conditioning in pretrained text-to-image diffusion models has significantly improved fine-grained control over the structure of generated images. However, existing control adapters exhibit limited adaptability and incur high training costs when encountering novel spatial control conditions that differ substantially from the training tasks. To address this limitation, we propose Universal Few-Shot Control (UFC), a versatile few-shot control adapter capable of generalizing to novel spatial conditions. Given a few image-condition pairs of an unseen task and a query condition, UFC leverages the analogy between query and support conditions to construct task-specific control features, instantiated by a matching mechanism and an update on a small set of task-specific parameters. Experiments on six novel spatial control tasks show that UFC, fine-tuned with only 30 annotated examples of novel tasks, achieves fine-grained control consistent with the spatial conditions. Notably, when fine-tuned with 0.1% of the full training data, UFC achieves competitive performance with the fully supervised baselines in various control tasks. We also show that UFC is applicable agnostically to various diffusion backbones and demonstrate its effectiveness on both UNet and DiT architectures. Code is available at https://github.com/kietngt00/UFC.

ControlNets are widely used for adding spatial control in image generation with different conditions, such as depth maps, canny edges, and human poses. However, there are several challenges when leveraging the pretrained image ControlNets for controlled video generation. First, pretrained ControlNet cannot be directly plugged into new backbone models due to the mismatch of feature spaces, and the cost of training ControlNets for new backbones is a big burden. Second, ControlNet features for different frames might not effectively handle the temporal consistency. To address these challenges, we introduce Ctrl-Adapter, an efficient and versatile framework that adds diverse controls to any image/video diffusion models, by adapting pretrained ControlNets (and improving temporal alignment for videos). Ctrl-Adapter provides diverse capabilities including image control, video control, video control with sparse frames, multi-condition control, compatibility with different backbones, adaptation to unseen control conditions, and video editing. In Ctrl-Adapter, we train adapter layers that fuse pretrained ControlNet features to different image/video diffusion models, while keeping the parameters of the ControlNets and the diffusion models frozen. Ctrl-Adapter consists of temporal and spatial modules so that it can effectively handle the temporal consistency of videos. We also propose latent skipping and inverse timestep sampling for robust adaptation and sparse control. Moreover, Ctrl-Adapter enables control from multiple conditions by simply taking the (weighted) average of ControlNet outputs. With diverse image/video diffusion backbones (SDXL, Hotshot-XL, I2VGen-XL, and SVD), Ctrl-Adapter matches ControlNet for image control and outperforms all baselines for video control (achieving the SOTA accuracy on the DAVIS 2017 dataset) with significantly lower computational costs (less than 10 GPU hours).

For industrial control, developing high-performance controllers with few samples and low technical debt is appealing. Foundation models, possessing rich prior knowledge obtained from pre-training with Internet-scale corpus, have the potential to be a good controller with proper prompts. In this paper, we take HVAC (Heating, Ventilation, and Air Conditioning) building control as an example to examine the ability of GPT-4 (one of the first-tier foundation models) as the controller. To control HVAC, we wrap the task as a language game by providing text including a short description for the task, several selected demonstrations, and the current observation to GPT-4 on each step and execute the actions responded by GPT-4. We conduct series of experiments to answer the following questions: 1)~How well can GPT-4 control HVAC? 2)~How well can GPT-4 generalize to different scenarios for HVAC control? 3) How different parts of the text context affect the performance? In general, we found GPT-4 achieves the performance comparable to RL methods with few samples and low technical debt, indicating the potential of directly applying foundation models to industrial control tasks.

Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the nucleotide sequences, especially specific motifs known as transcription factor binding sites (TFBSs). Designing high-fitness CREs is crucial for therapeutic and bioengineering applications. Current CRE design methods are limited by two major drawbacks: (1) they typically rely on iterative optimization strategies that modify existing sequences and are prone to local optima, and (2) they lack the guidance of biological prior knowledge in sequence optimization. In this paper, we address these limitations by proposing a generative approach that leverages reinforcement learning (RL) to fine-tune a pre-trained autoregressive (AR) model. Our method incorporates data-driven biological priors by deriving computational inference-based rewards that simulate the addition of activator TFBSs and removal of repressor TFBSs, which are then integrated into the RL process. We evaluate our method on promoter design tasks in two yeast media conditions and enhancer design tasks for three human cell types, demonstrating its ability to generate high-fitness CREs while maintaining sequence diversity. The code is available at https://github.com/yangzhao1230/TACO.

Large-scale Causal Language Models (CLMs), e.g., GPT3 and ChatGPT, have brought great success in text generation. However, it is still an open challenge to control the generation process of CLM while balancing flexibility, control granularity, and generation efficiency. In this paper, we provide a new alternative for controllable text generation (CTG), by designing a non-intrusive, lightweight control plugin to accompany the generation of CLM at arbitrary time steps. The proposed control plugin, namely Residual Memory Transformer (RMT), has an encoder-decoder setup, which can accept any types of control conditions and cooperate with CLM through a residual learning paradigm, to achieve a more flexible, general, and efficient CTG. Extensive experiments are carried out on various control tasks, in the form of both automatic and human evaluations. The results show the superiority of RMT over a range of state-of-the-art approaches, proving the effectiveness and versatility of our approach.

Many real-world multi-label prediction problems involve set-valued predictions that must satisfy specific requirements dictated by downstream usage. We focus on a typical scenario where such requirements, separately encoding value and cost, compete with each other. For instance, a hospital might expect a smart diagnosis system to capture as many severe, often co-morbid, diseases as possible (the value), while maintaining strict control over incorrect predictions (the cost). We present a general pipeline, dubbed as FavMac, to maximize the value while controlling the cost in such scenarios. FavMac can be combined with almost any multi-label classifier, affording distribution-free theoretical guarantees on cost control. Moreover, unlike prior works, it can handle real-world large-scale applications via a carefully designed online update mechanism, which is of independent interest. Our methodological and theoretical contributions are supported by experiments on several healthcare tasks and synthetic datasets - FavMac furnishes higher value compared with several variants and baselines while maintaining strict cost control. Our code is available at https://github.com/zlin7/FavMac

Controlled Text Generation (CTG) aims to produce texts that exhibit specific desired attributes. In this study, we introduce a pluggable CTG framework for Large Language Models (LLMs) named Dynamic Attribute Graphs-based controlled text generation (DATG). This framework utilizes an attribute scorer to evaluate the attributes of sentences generated by LLMs and constructs dynamic attribute graphs. DATG modulates the occurrence of key attribute words and key anti-attribute words, achieving effective attribute control without compromising the original capabilities of the model. We conduct experiments across four datasets in two tasks: toxicity mitigation and sentiment transformation, employing five LLMs as foundational models. Our findings highlight a remarkable enhancement in control accuracy, achieving a peak improvement of 19.29% over baseline methods in the most favorable task across four datasets. Additionally, we observe a significant decrease in perplexity, markedly improving text fluency.

Text-based image editing has advanced significantly in recent years. With the rise of diffusion models, image editing via textual instructions has become ubiquitous. Unfortunately, current models lack the ability to customize the quantity of the change per pixel or per image fragment, resorting to changing the entire image in an equal amount, or editing a specific region using a binary mask. In this paper, we suggest a new framework which enables the user to customize the quantity of change for each image fragment, thereby enhancing the flexibility and verbosity of modern diffusion models. Our framework does not require model training or fine-tuning, but instead performs everything at inference time, making it easily applicable to an existing model. We show both qualitatively and quantitatively that our method allows better controllability and can produce results which are unattainable by existing models. Our code is available at: https://github.com/exx8/differential-diffusion

The increasing use of foundation models highlights the urgent need to address and eliminate implicit biases present in them that arise during pretraining. In this paper, we introduce PEFTDebias, a novel approach that employs parameter-efficient fine-tuning (PEFT) to mitigate the biases within foundation models. PEFTDebias consists of two main phases: an upstream phase for acquiring debiasing parameters along a specific bias axis, and a downstream phase where these parameters are incorporated into the model and frozen during the fine-tuning process. By evaluating on four datasets across two bias axes namely gender and race, we find that downstream biases can be effectively reduced with PEFTs. In addition, we show that these parameters possess axis-specific debiasing characteristics, enabling their effective transferability in mitigating biases in various downstream tasks. To ensure reproducibility, we release the code to do our experiments.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

To enhance controllability in text-to-image generation, ControlNet introduces image-based control signals, while ControlNet++ improves pixel-level cycle consistency between generated images and the input control signal. To avoid the prohibitive cost of back-propagating through the sampling process, ControlNet++ optimizes only low-noise timesteps (e.g., t < 200) using a single-step approximation, which not only ignores the contribution of high-noise timesteps but also introduces additional approximation errors. A straightforward alternative for optimizing controllability across all timesteps is Direct Preference Optimization (DPO), a fine-tuning method that increases model preference for more controllable images (I^{w}) over less controllable ones (I^{l}). However, due to uncertainty in generative models, it is difficult to ensure that win--lose image pairs differ only in controllability while keeping other factors, such as image quality, fixed. To address this, we propose performing preference learning over control conditions rather than generated images. Specifically, we construct winning and losing control signals, c^{w} and c^{l}, and train the model to prefer c^{w}. This method, which we term Condition Preference Optimization (CPO), eliminates confounding factors and yields a low-variance training objective. Our approach theoretically exhibits lower contrastive loss variance than DPO and empirically achieves superior results. Moreover, CPO requires less computation and storage for dataset curation. Extensive experiments show that CPO significantly improves controllability over the state-of-the-art ControlNet++ across multiple control types: over 10% error rate reduction in segmentation, 70--80% in human pose, and consistent 2--5% reductions in edge and depth maps.

Radiology report generation requires advanced medical image analysis, effective temporal reasoning, and accurate text generation. Although recent innovations, particularly multimodal large language models (MLLMs), have shown improved performance, their supervised fine-tuning (SFT) objective is not explicitly aligned with clinical efficacy. In this work, we introduce EditGRPO, a mixed-policy reinforcement learning (RL) algorithm designed specifically to optimize the generation through clinically motivated rewards. EditGRPO integrates on-policy exploration with off-policy guidance by injecting sentence-level detailed corrections during training rollouts. This mixed-policy approach addresses the exploration dilemma and sampling efficiency issues typically encountered in RL. Applied to a Qwen2.5-VL-3B MLLM initialized with supervised fine-tuning (SFT), EditGRPO outperforms both SFT and vanilla GRPO baselines, achieving an average improvement of 3.4% in CheXbert, GREEN, Radgraph, and RATEScore metrics across four major chest X-ray report generation datasets. Notably, EditGRPO also demonstrates superior out-of-domain generalization, with an average performance gain of 5.9% on unseen datasets.

Purpose: With advancements in Large Language Models (LLMs) for healthcare, the need arises for competitive open-source models to protect the public interest. This work contributes to the field of open medical LLMs by optimizing key stages of data preprocessing and training, while showing how to improve model safety (through DPO) and efficacy (through RAG). The evaluation methodology used, which includes four different types of tests, defines a new standard for the field. The resultant models, shown to be competitive with the best private alternatives, are released with a permisive license. Methods: Building on top of strong base models like Llama 3.1 and Qwen 2.5, Aloe Beta uses a custom dataset to enhance public data with synthetic Chain of Thought examples. The models undergo alignment with Direct Preference Optimization, emphasizing ethical and policy-aligned performance in the presence of jailbreaking attacks. Evaluation includes close-ended, open-ended, safety and human assessments, to maximize the reliability of results. Results: Recommendations are made across the entire pipeline, backed by the solid performance of the Aloe Family. These models deliver competitive performance across healthcare benchmarks and medical fields, and are often preferred by healthcare professionals. On bias and toxicity, the Aloe Beta models significantly improve safety, showing resilience to unseen jailbreaking attacks. For a responsible release, a detailed risk assessment specific to healthcare is attached to the Aloe Family models. Conclusion: The Aloe Beta models, and the recipe that leads to them, are a significant contribution to the open-source medical LLM field, offering top-of-the-line performance while maintaining high ethical requirements. This work sets a new standard for developing and reporting aligned LLMs in healthcare.

Prefix-tuning is a powerful lightweight technique for adapting a large pre-trained language model to a downstream application. However, it uses the same dataset-level tuned prompt for all examples in the dataset. We extend this idea and propose a dynamic method, Control Prefixes, which allows for the inclusion of conditional input-dependent information, combining the benefits of prompt tuning and controlled generation. The method incorporates attribute-level learnable representations into different layers of a pre-trained transformer, allowing for the generated text to be guided in a particular direction. We provide a systematic evaluation of the technique and apply it to five datasets from the GEM benchmark for natural language generation (NLG). Although the aim is to develop a parameter-efficient model, we show Control Prefixes can even outperform full fine-tuning methods. We present state-of-the-art results on several data-to-text datasets, including WebNLG.

Seismic advances in generative AI algorithms for imagery, text, and other data types has led to the temptation to use synthetic data to train next-generation models. Repeating this process creates an autophagous (self-consuming) loop whose properties are poorly understood. We conduct a thorough analytical and empirical analysis using state-of-the-art generative image models of three families of autophagous loops that differ in how fixed or fresh real training data is available through the generations of training and in whether the samples from previous generation models have been biased to trade off data quality versus diversity. Our primary conclusion across all scenarios is that without enough fresh real data in each generation of an autophagous loop, future generative models are doomed to have their quality (precision) or diversity (recall) progressively decrease. We term this condition Model Autophagy Disorder (MAD), making analogy to mad cow disease.

Generating realistic simulations is critical for autonomous system applications such as self-driving and human-robot interactions. However, driving simulators nowadays still have difficulty in generating controllable, diverse, and rule-compliant behaviors for road participants: Rule-based models cannot produce diverse behaviors and require careful tuning, whereas learning-based methods imitate the policy from data but are not designed to follow the rules explicitly. Besides, the real-world datasets are by nature "single-outcome", making the learning method hard to generate diverse behaviors. In this paper, we leverage Signal Temporal Logic (STL) and Diffusion Models to learn controllable, diverse, and rule-aware policy. We first calibrate the STL on the real-world data, then generate diverse synthetic data using trajectory optimization, and finally learn the rectified diffusion policy on the augmented dataset. We test on the NuScenes dataset and our approach can achieve the most diverse rule-compliant trajectories compared to other baselines, with a runtime 1/17X to the second-best approach. In the closed-loop testing, our approach reaches the highest diversity, rule satisfaction rate, and the least collision rate. Our method can generate varied characteristics conditional on different STL parameters in testing. A case study on human-robot encounter scenarios shows our approach can generate diverse and closed-to-oracle trajectories. The annotation tool, augmented dataset, and code are available at https://github.com/mengyuest/pSTL-diffusion-policy.