MAVISEG: Manifold Propagation and Visual Prototypes for Zero-Shot Open-Vocabulary Segmentation in Diffusion Transformers

Text-to-image diffusion transformers learn about objects and scenes by learning to generate them, making them strong candidates for training-free zero-shot open-vocabulary semantic segmentation. State-of-the-art attribution methods score each pixel independently, comparing its features against a fixed text-derived class representation, whether as an output-space similarity or as a cross-attention weight. This discards structured signals the model itself exposes: the temporal structure of the generative trajectory, the visual appearance statistics of each concept, and the image's own pairwise feature geometry. We present MAVISEG, a training-free refinement layer that recovers these signals. Because its operators consume only a pixel-by-concept score field and a pixel feature space, MAVISEG is capture-agnostic rather than tied to one attribution method. Across six benchmarks it achieves the strongest overall results among training-free methods, including the best mIoU on every benchmark. Interestingly, gains are largest where the initial capture is weakest, and individual operators contribute depending on the noise in the field they refine. Our results indicate that diffusion transformers carry more concept-level information than current attribution methods recover, and that much of it is lost on the way to the mask rather than absent from the model.

Abstention as an Action Can Kill Both the Reward Gradient and the KL Anchor: Collapse Law and Repair for Error-Penalized Reinforcement Learning

Error-penalized scoring rules ($+1$ for a correct answer, $-λ$ for a wrong one, $0$ for abstaining) are increasingly prescribed against hallucination: a rational agent facing such a rule answers exactly when its correctness probability exceeds Chow's threshold $t^\ast=λ/(1+λ)$. We prove that a KL-anchored gradient learner can do the opposite. When abstention is a discrete action, the reward gradient and the anchor's restoring force are throttled by the same gate-saturation factor and die together: under explicit conditions (among them, blanket answering loses score in expectation and prompts share a bounded readout) the model drifts toward refusing everything, its mean training reward rising to zero like $1/t$ in training time $t$, so the curve reads as improvement while coverage collapses. The advantage estimator compounds the failure: in its sparse-answer regime, group normalization silently replaces every designed penalty with an effective penalty of one, moving the learned threshold from $t^\ast$ to $1/2$. The repair is structural: train a mandatory confidence report with a strictly proper score plus a correctness reward, and abstain only at deployment by thresholding the report. The always-emitted report has no gate to saturate, so no shared factor can kill its reward gradient and its anchor together, and its calibrated optimum is attracting. Simulations confirm every prediction, and experiments on language models at two scales confirm the mechanism live: the rule silences questions the models demonstrably still solve within ten optimizer steps, an ablation isolates the cause, and report-level training raises coverage, accuracy, and calibration together.

StraightDP: Geometry-Aware Differential Privacy for Rectified-Flow Transformers

Differentially private (DP) training of text-conditioned generative models suffers a utility cliff at strong privacy. We revisit this problem through the geometry of rectified flows: along the straight interpolation between noise and data, the Bayes-optimal velocity is governed to leading order at the noise end by a few class-conditional moments, and increasingly sample-specific structure matters toward the data end. StraightDP exploits this heterogeneity end to end. A small budget share releases whitened class-conditional moments once, to be distilled into the weights or injected at sampling time. The rest is spent by pre-declared DP-SGD toward the data end, beyond the moments' reach. At $\varepsilon=1$ on MNIST, the released moments alone already attain $0.76$ downstream accuracy with prototype-like samples and an FID of $237$, and uniform DP-SGD attains $0.21$. The pipeline built on the release reaches $0.81$ accuracy at FID $56$ in a public latent space. Constraining per-token stream norms of the multimodal backbone leaves the pretraining loss unchanged yet improves downstream accuracy in the extreme-noise pixel-space regime, and its accuracy effect becomes monotonically more favorable as privacy strengthens. The released moments also port to frozen SD3-medium, where sampling-time injection beats DP-LoRA training at a fraction of the budget.

MARLIN: De Novo Molecular Structure Elucidation from Tandem Mass Spectra without a Ground-Truth Formula

Untargeted tandem mass spectrometry (MS/MS) detects thousands of small molecules per biological sample, yet most go unidentified because they are absent from spectral libraries. These uncharacterized metabolites and natural products are precisely the compounds that matter for drug discovery, biomarker research, and exposomics. Computational de novo structure elucidation could close this gap, but almost all state-of-the-art methods assume the ground-truth molecular formula is known, an oracle that does not exist for genuinely novel compounds and is itself predicted with substantial error. We present MARLIN, a de novo method that elucidates structures directly from a spectrum with no molecular formula at any stage. A self-supervised encoder predicts a molecular fingerprint from the raw peaks, and a block-diffusion language model generates candidate structures conditioned only on the fingerprint and the instrument-measured precursor mass. A provably safe mass-shell constraint keeps every candidate consistent with the measured mass without fixing the atom inventory, and candidates are accepted by exact parts-per-million mass agreement. A symmetric noise objective absorbs encoder error, and a candidate-diversity mechanism keeps the candidates from collapsing to a single structure. On the NPLIB1 benchmark, MARLIN is the strongest method evaluated without a ground-truth formula across exact-match accuracy, structural distance, and fingerprint similarity, and it recovers the correct molecular formula as a byproduct about as often as a dedicated predictor without ever using one. MARLIN enables reliable de novo structure elucidation in the realistic discovery regime where the molecular formula is unavailable.

Comparative Analysis of Formula and Structure Prediction from Tandem Mass Spectra

Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease mechanisms and provide information about environmental exposures and their effects on human health. Metabolomics and exposomics are made possible by the high resolving power of LC and high mass measurement accuracy of MS. However, a majority of the signals from such studies still cannot be identified or annotated using conventional library searching because existing spectral libraries are far from covering the vast chemical space captured by LC-MS/MS. To address this challenge and unleash the full potential of metabolomics and exposomics, a number of computational approaches have been developed to predict compounds based on tandem mass spectra. Published assessment of these approaches used different datasets and evaluation. To select prediction workflows for practical applications and identify areas for further improvements, we have carried out a systematic evaluation of the state-of-the-art prediction algorithms. Specifically, the accuracy of formula prediction and structure prediction was evaluated for different types of adducts. The resulting findings have established realistic performance baselines, identified critical bottlenecks, and provided guidance to further improve compound predictions based on MS.