Latent Space Optimization

Conditional neural fields represent signals continuously, but their effectiveness depends on how the conditional latent representations are inferred from observed data. In meta-learning, this encoding occurs through gradient updates induced by the decoder, tying representation learning directly to decoder design. We formalize this connection by interpreting latent optimization as an optimization encoder, unifying the roles of second-order differentiation, latent parameterization, and task supervision. This concept enables second-order meta-learning for end-to-end training of the encoding procedure alongside the decoder, and clarifies which learning pathway first-order approximations discard. Guided by this view, we introduce Attentive Latent Fields (MetaLF), an equivariant transformer-based neural field that contextualizes a latent pointcloud through self-attention. These interactions shape both field predictions and the updates that construct their representation, allowing local observations to inform coherent non-local structure. Disentangling the inner encoding objective from outer task supervision unifies reconstruction, classification, and segmentation within an end-to-end meta-learning framework, using reconstruction-only latent adaptation at test time. Controlled experiments on polynomial fields link latent coordination to lower effective rank and stronger alignment with the underlying function space. Across image and 3D shape reconstruction, MetaLF improves fidelity within three to five gradient updates, while supporting semantic prediction across images, shapes, and volumes. Together, these findings position the optimization encoder perspective as a unified basis for designing neural fields around how representations are constructed, coordinated, and used.

Model-guided directed evolution seeks to identify high-fitness protein variants under limited oracle budgets. Protein language models (PLMs) provide rich representations for this task, but task-agnostic zero-shot scores can be misaligned with a target assay, while supervised search in high-dimensional embedding spaces can make surrogate modeling and uncertainty estimation sample-inefficient. We propose the Linear Fitness Subspace (LFS) hypothesis: within mutation-induced residue-level representation changes, a compact, assay-specific set of directions makes fitness variation linearly accessible from few labeled variants. This is a local, supervision-recoverable statement rather than a claim that protein fitness landscapes or global PLM geometry are universally linear. Building on this observation, we introduce Subspace-Guided Evolutionary Search (SGES), which estimates an LFS from a small initial sample and performs surrogate modeling, uncertainty estimation, and acquisition in the learned subspace. Across 10 core ProteinGym assays, 87 extended static-validation assays, and an 18-assay budgeted-search evaluation, SGES improves fitness prediction and search efficiency over zero-shot PLMs and recent ML-guided protein optimization baselines. Controlled comparisons with PCA, random projections, label-shuffled PLS, classical mutation features, and acquisition ablations further isolate the benefit of a fitness-aligned site-delta coordinate.

Zero-shot Neural Architecture Search removes the prohibitive cost of traditional NAS, but its search process is typically based on the evolutionary algorithm (EA); lacking an explicit model of the objective, it often resorts to a near-random search through mutation. Bayesian Optimization offers a principled alternative by modeling the objective and aggregating information across iterations, but scales poorly to the high-dimensional, discrete, graph-structured spaces of modern NAS, restricting its use to only small networks. In this paper, we bring Bayesian Optimization to zero-shot NAS for large-scale architectures by learning a latent space via a Variational Autoencoder trained to reconstruct a novel prefix encoding of architectures and propose a proxy scalarization that combines several zero-shot proxies into a single Bayesian Optimization objective. After only 10,000 iterations of the proposed search algorithm (8 hours on a single GPU), our method found a network architecture which under the given model parameter count constraints achieves state-of-the-art results on three separate tasks -- image classification, object detection and semantic segmentation.

Inverse design of physical systems (molecules, devices, microstructures) often reduces to optimizing a high-dimensional structure against an expensive black-box simulator. Direct search is difficult because the space is non-Euclidean, feasibility is hard to encode, and each evaluation is expensive. We present Co-PiLOT, a latent optimization approach that maps candidates through a generative encoder-decoder, uses the decoder as a learned validity prior, and searches the latent space with physics-informed black-box optimization. The framework is applied on the inverse design of magnesium alloy microstructure/texture. We develop a vision transformer based-encoder; paired with latent diffusion, diffusion transformer and rectified-flow transformer-based decoders on $\sim80{,}000$ EBSD-derived microstructure dataset to learn a minimal bottleneck, $z$. The ViT-FMDiT model ($z$=$768$) reconstructs high-fidelity microstructure images (FID $27.86$, MS-SSIM $0.178$), which our self-segmenting orientation codec converts into input grids for crystal plasticity solver. Finally, we introduce MERIDIAN, an active latent optimizer driven by deep-kernel Gaussian-process uncertainty, failure-aware feasibility prediction, manifold-aware trust regions, and target-aware acquisition. Within a budget of $160$ simulations, the ViT-FMDiT and MERIDIAN combination yields the best target-driven objective score, reducing the relative target error by $3$--$22\%$ against seven baselines (DANTE, TuRBO, BAxUS, CMA-ES, DDOM, SEIKO, DDPO) on the same decoder.

Large Reasoning Models (LRMs) have shown remarkable reasoning capabilities, yet they still suffer from overthinking, generating redundant reasoning steps which incur substantial token consumption. Existing methods, such as suppressing reflective keywords or forcing shorter reasoning lengths, attempt to mitigate this issue but inevitably truncate necessary steps and induce underthinking, thereby compromising performance. To address this dilemma, we investigate the latent representations and observe that efficient reasoning steps naturally cluster into a concentrated region in latent space, while those deviating from this region tend to produce verbose sequences. To leverage this, we keep reasoning focused within this region via a quadratic program which projects deviating hidden states back into the region. Then we propose a novel training-free framework to achieve efficient reasoning that reduces token generation costs without sacrificing performance. Extensive experiments conducted on four models ranging from 1.5B to 14B, and across six benchmarks in math reasoning, coding, and scientific QA, validate the effectiveness of our method, up to a 12.1% improvement in accuracy while reducing generated tokens by 11.8% to 52.8%. Codes are available at https://github.com/hzn18/Opt4Reasoning.

Language models are increasingly used as proposal models for black-box search, from program optimization to molecular design. Existing approaches typically improve proposals through iterative prompting or parameter updates, offering limited control over how completely and efficiently the model's search space is explored. Continuous optimization methods, such as Bayesian optimization, provide a principled way to search but require a suitable domain to operate over. To address this, we introduce BOReFT, which learns a compact, low-dimensional space of hidden-state interventions in a frozen language model, and uses this space as the search domain for Bayesian optimization with an external scoring function. Empirically, we find that the learned domain spans semantic regions and exhibits smoothness properties that support search. Theoretically, we show that semantic coverage and interpolation control the best score available in the learned space, and that decoding from this space yields a standard stochastic-bandit observation model for adaptive search. We evaluate BOReFT on the interpretable word search task "Semantle" and on three more real-world discovery tasks in de novo molecule property optimization. Compared to strong LLM baselines, BOReFT finds in Semantle a higher number of hidden targets and, on two out of three molecular objectives, achieves higher property scores. Consequently, our method provides a principled new bridge between discrete proposal spaces of LLM-based search and continuous black-box optimization.

Generative models are increasingly central to many de novo discovery pipelines, in which designs are generated at scale and filtered through virtual screens to determine a set of candidates to experimentally validate. While Bayesian optimization (BO) is a natural fit for this setting, as it uses past evaluations to guide future proposals, the computational overhead required for its sequential decision-making becomes a bottleneck when virtual screens are relatively cheap. We make BO practical in this regime by exploiting the unique combination of a linear model constrained to a spherical domain where high-dimensional latents concentrate. We build off recent work justifying the use of linear surrogates, while deriving nearly closed-form solutions to the surrogate modelling and acquisition problems that exploit spherical symmetry. The result is at least a 100x speedup over state-of-the art baselines, with matching or improved performance across molecular and image generation benchmarks. Altogether, our method makes BO a practical drop-in for de novo pipelines where it was previously too slow to consider.

Digital watermarking has emerged as a critical technique for provenance and copyright attribution in AI-generated imagery, yet its robustness against realistic, model-agnostic removal attacks remains poorly explored. Existing attacks either succeed only against specific generative models or achieve removal at the cost of severe visual degradation. In this paper, we propose MarkNull, a model-agnostic watermark removal attack via on-manifold latent manipulation. MarkNull is grounded in a key observation: watermarked images exhibit a strong statistical dependency between the generated latent representation and the embedded initial noise. To quantify this dependency, we introduce the Noise-Latent Alignment Score (NLAS) and formulate an optimization objective that selectively decorrelates the latent representation from the embedded watermark while preserving semantic fidelity. Extensive evaluations across different categories of watermarking paradigms, including post-hoc, fine-tuning-based, and initial-noise-based schemes, demonstrate that MarkNull reduces average bit accuracy to 53.14%, approaching random-guessing (50%), without perceptible image degradation. To further improve scalability, we propose MarkNull-A, an amortized, optimization-free variant that distills the attack into a single forward pass, achieving 0.50 s/image with modest computational overhead. Notably, our attacks successfully compromise Google's SynthID-Image system while preserving high visual quality and transfer effectively to video watermarking. Finally, we present an attack detection mechanism as a defensive counterpart to MarkNull and MarkNull-A, highlighting the necessity of developing watermark designs resilient to model-agnostic latent-space attacks.

The usefulness of a variational autoencoder (VAE) depends on two properties of its latent space that are hard to obtain together: high encoding capacity in the individual latent variables, and a low-dimensional, disentangled organization of those variables. Weakening the Kullback-Leibler regularization raises capacity but degrades disentanglement, while strengthening it prunes latent variables away entirely. We formulate VAE training as a soft-constrained optimization problem that addresses both. First, we impose an entropy-based constraint (EC) on individual latent variables, showing that the entropy of a latent code upper-bounds the mutual information it carries about the generative factors of the data. Second, we propose a weight-filter method that exploits the slack of the soft constraint to prune low-entropy dimensions during downstream training. On dSprites, the EC raises the aggregate latent-variable activation score by 43-62% over a vanilla VAE, attains the highest FactorVAE score among the \b{eta} \b{eta}-VAE variants (0.891 vs 0.847), and lowers reconstruction error by up to 38%. On MNIST, the weight filter reduces the latent dimensionality supplied to a downstream classifier from ten to two while holding accuracy above 90%, converging in 37% fewer epochs than the same procedure without the EC. We also find that low-entropy discrete factors tend to merge into a single latent variable, whereas high-entropy continuous factors are distributed across several.

Variational autoencoders (VAEs) transform high-dimensional, often noisy data into a compact latent representation, making downstream optimization more tractable. Three challenges persist in VAE-based constrained optimization: (i) sampling effectively within the latent space, (ii) identifying the active decision variables that actually influence the objective and constraints, and (iii) enforcing constraints without destabilizing training. We propose a Multi-stage Constrained Optimization Framework (MCOF). First, an entropy-constrained VAE (EC-VAE) coupled with a feature selector embeds objective and constraint information into a designated subset of latent variables, so that optimization proceeds over a low-dimensional subspace while the remaining coordinates supply solution diversity. Second, a Uniform Transformation (UT) module applies a per-dimension probability integral transform, replacing the irregular aggregate posterior with a uniform distribution over a bounded box and mitigating posterior collapse and Gaussian mixture bias. Third, a constraint-priority filter method (CPFM) solves the resulting surrogate problem by alternating violation-reduction and objective-reduction steps under a filter acceptance test, returning solutions that are feasible for the learned surrogate to a specified tolerance without requiring multiplier estimation. Finally, unselected latent coordinates are resampled to generate diverse decodings of a single optimized solution. We validate MCOF on a synthetic problem, where we ablate each stage and recover the analytic optimum, and on a ZINC250k drug design task, where the generated molecules satisfy the imposed constraints and are entirely novel relative to the training set.

In real-world machine learning applications, incomplete observations create a fundamental challenge. Researchers have come up with several ideas to address this crucial problem. However, current models still face challenges in balancing scalability and structural consistency. This study proposes a feature imputation method, called FILLER, that deliberately searches the two-dimensional latent space produced by a generative model and fills the missing values with appropriate entries. The generative model is trained on fully observed data to generate samples from the latent space, and FILLER uses this trained model to impute the values missing in the corrupted test samples. In this study, G-NeuroDAVIS serves the purpose of the generative model. This work also presents a mathematical proof on the convergence of the iterative search. Finally, FILLER has been evaluated on several image datasets under random and structured missingness patterns with varying levels of imputation complexities. In order to justify the efficacy of FILLER, it has been compared against existing state-of-the-art solution strategies in terms of RMSE, PSNR, and SSIM. In addition, Wilcoxon signed-rank test has been carried out to validate statistical significance. Moreover, downstream analyses (classification and clustering) have also established the quality of imputation in terms of standard metrics.

Principal Component Analysis or PCA-like properties (orthogonality, variance ranking) are seldom realized in deep autoencoder architectures. In this work, we present ODIN (Orthogonal Dendritic Intrinsic Network), a novel autoencoder architecture that recovers PCA-like latent structure in a fully non-linear regime. By incorporating a set of geometric constraints directly into the training objective, ODIN encourages latent dimensions to be mutually orthogonal and ordered by explained variance, mirroring the interpretable decomposition of PCA while retaining the expressive power of deep networks. We provide theoretical grounding for these constraints and demonstrate their compatibility with standard encoder-decoder frameworks. We also establish empirical results for both synthetic and real world datasets, establishing a principled path toward interpretable, structured feature learning and dimensionality reduction.

Therapeutic peptides are a promising drug modality, but their generation must satisfy multiple therapeutic constraints. We introduce BindSafe-PepBench, a fixed-budget benchmark that jointly evaluates target binding and four major safety metrics on the same generated candidates. We reveal that peptide length is a major confounder of joint binding-safety evaluation: longer peptides tend toward stronger predicted binding but less favorable predicted safety. This creates an apparent trade-off and can bias comparisons among models with different output-length distributions. We report absolute Safe-Active yield and exact-length-matched gains to distinguish generative improvements from output-length effects. High Safe-Active yield remains challenging, while the strongest multi-property methods rely on costly inference-time guidance. We therefore introduce Pepti-drift, a one-step generation framework that incorporates attraction toward target-specific binders and repulsion from liability-associated regions, requiring a single latent refinement followed by parallel decoding without inference-time guidance. Across 88 held-out targets, Pepti-drift achieves an 18.37% predicted Safe-Active yield while retaining positive exact-length-matched gains. The resulting gains are competitive with multi-property-guided baselines while requiring 468 times lower generation cost, enabling scalable and fair high-throughput peptide design.

Bayesian optimization (BO) is a central tool for sample-efficient design, and latent-space Bayesian optimization (LSBO) extends it to structured objects such as molecules and proteins. In parallel, tabular foundation models such as TabPFN and TabICL now achieve state-of-the-art regression performance and are increasingly used as BO surrogates. Because their Bayesian behavior is induced by large synthetic pretraining collections, the composition of this pretraining distribution is crucial. LSBO creates a distinctive mismatch: the induced map from latent code to objective value differs markedly from the regression tasks used to train current in-context models. We address this mismatch by complementing the pretraining stage of tabular foundation model surrogates with synthetic optimization tasks defined on the latent space of a molecular VAE. The continued-pretraining objective features a regularizer that anchors the model to the original checkpoint, preserving its broad regression prior while avoiding overspecialization to the adaptation tasks. On held-out molecular optimization benchmarks, the resulting model achieves strong performance, supporting the relevance of LSBO-specific adaptation for in-context surrogates.

With the growing concerns over copyright infringement in diffusion-based customization, adversarial attacks have emerged as a prominent defense strategy to prevent malicious content forgery in personalized image generation. However, current defenses typically introduce persistent perturbations in the latent space of Latent Diffusion Models (LDMs), which remain susceptible to adaptive bypasses by adversaries. In this paper, we introduce Two-Stage Latent Feature Optimization (TS-LFO), an efficient and effective copyright-stealing attack against protected diffusion-based customization. We begin by observing that existing defenses primarily disrupt the mapping between input images and their latent representations, thereby degrading the model's ability to produce personalized outputs. To counteract this, TS-LFO restores the broken mapping through a two-stage optimization process. In the Latent Denoising Stage, we enhance semantic consistency between latent codes and input images by jointly minimizing a Latent-Image Alignment Loss and a Latent Diffusion Loss with timestep-dependent weights, effectively suppressing the high-frequency noise introduced by defenses. In the Latent Reconstruction Stage, we recover low-frequency semantic information using pixel-level constraints to refine the latent features. Extensive experiments show that TS-LFO consistently bypasses state-of-the-art (SOTA) copyright defenses and outperforms SOTA copyright attacks such as DiffPure, GrIDPure and IMPRESS across diverse settings.

The integration of Large Language Models (LLMs) into evolutionary frameworks has established a new paradigm for automated heuristic discovery. Despite their promise, these methods typically search in the discrete space of program syntax, relying on stochastic sampling to navigate a highly non-convex optimization landscape. This work proposes a continuous heuristic discovery framework that shifts optimization to a learned latent manifold. We employ an encoder to map discrete programs into continuous embeddings and train a differentiable surrogate model to predict performance, enabling gradient-based search. To regularize the optimization trajectory, an invertible normalizing flow maps these embeddings to a structured Gaussian prior, where we perform gradient ascent. The resulting optimized latent vectors are projected through a learned mapper into soft prompts, which condition a frozen LLM to synthesize novel executable heuristics. We evaluate the proposed method on the Traveling Salesman Problem (TSP), the Capacitated Vehicle Routing Problem (CVRP), the Knapsack Problem (KSP), and Online Bin Packing (OBP). Empirical results demonstrate that continuous latent-space optimization achieves performance competitive with state-of-the-art discrete evolutionary baselines while offering a complementary methodological alternative for automated algorithm design. The implementation code is available at https://github.com/cheikh025/LHS.

Continuous latent-space reasoning offers a compact alternative to textual chain-of-thought for multimodal models, enabling high-dimensional visual evidence to be integrated without explicit reasoning tokens. However, we identify a previously overlooked optimization pathology in existing latent visual reasoning methods: although visual latents become semantically enriched during training, their contribution to final answer prediction is systematically suppressed. Within the shared parameter space, the autoregressive objective favors shortcut reliance on direct visual input, driving latent tokens toward transition-like states rather than informative reasoning content. We term this phenomenon Silenced Visual Latents. To address it, we disentangle the two conflicting objectives by directly optimizing the latent reasoning at inference time, keeping backbone parameters frozen. In Stage I, visual latents are warmed up via query-guided contrastive latent--visual alignment, improving semantic quality while preventing latent collapse. In Stage II, the latent reasoning is further optimized via a confidence-progression reward, which incentivizes predicted token distributions along the latent span to become progressively more concentrated, routing predictions through the latent reasoning rather than bypassing it. Experiments across eight benchmarks and four model backbones show that inference-time latent optimization, without any parameter updates, effectively unleashes the suppressed reasoning capacity of visual latents.

Adaptation of blackbox generative models has been widely studied recently through the exploration of several methods including generator fine-tuning, latent space searches, leveraging singular value decomposition, and so on. However, adapting large-scale generative AI tools to specific use cases continues to be challenging, as many of these industry-grade models are not made widely available. The traditional approach of fine-tuning certain layers of a generative network is not feasible due to the expense of storing and fine-tuning generative models, as well as the restricted access to weights and gradients. Recognizing these challenges, we propose a novel end-to-end pipeline aimed at domain adaptation by leveraging geometry-preserving loss functions in conjunction to pre-trained generative adversarial networks (GANs). Our method rethinks the problem of adaptation by re-contextualizing the role of GAN inversion in obtaining accurate latent space representations. Extending the ability of existing state-of-the-art inverters, we preserve pair-wise distances between tangent spaces to successfully train a latent generative model to produce samples from the target distribution. We evaluate our proposed pipeline on StyleGANs with real distribution shifts and demonstrate that the introduction of the geometry preserving loss function lends to improved adaptation of generative models compared to other traditional loss functions.

Bayesian optimisation (BO) enables sample-efficient global optimisation of expensive black-box functions but remains challenging in high dimensions. We investigate nonlinear dimensionality reduction to a sequence of low-dimensional latent-space BO (LSBO) problems. Early LSBO used linear random and supervised embeddings; building on Grosnit et al., we employ variational autoencoders (VAEs), deep metric loss for structured latent manifolds, and retraining to adapt the encoder-decoder pair to newly sampled regions. We couple LSBO with sequential domain reduction (SDR) directly in latent space (SDR-LSBO), narrowing search domains as evidence accumulates. Implemented in GPU-accelerated BoTorch with Mat'ern-5/2 Gaussian-process surrogates, our methods improve benchmark optimisation quality, and retraining can enhance BO performance. Comparisons with adaptive supervised linear random embeddings demonstrate the effectiveness of VAE-based BO for nonlinear low-dimensional structures. We analyse BO-VAE with a fixed pretrained representation, decomposing ambient-space simple regret into latent BO error and a fixed VAE-induced representation gap. Under a PAC-Bayes-certified reconstruction condition and standard fixed-prior assumptions for expected improvement with a Mat'ern-5/2 kernel, latent BO error vanishes as the evaluation budget increases, whereas the representation gap remains fixed and may impose a non-vanishing error floor. Visualisations empirically assess accessibility of the ambient optimum through the learned decoder. To our knowledge, this is the first study combining SDR with VAE-based LSBO. Our analysis clarifies metric shaping and retraining choices critical for scalable latent-space BO. For reproducibility, source code is available at https://github.com/L-Lok/Nonlinear-Dimensionality-Reduction-Techniques-for-Bayesian-Optimization.git.