We introduce WEECFP, a parameter-free 1024-dimensional continuous molecular fingerprint that scatters each Morgan substructure across roughly thirty-two signed positions of a single vector, and WEECFP-SuRGE, a transformer architecture whose self-attention applies SuRGE (Substructure Rotary Graph-distance Encoding) -- a RoPE-like rotation parameterized by molecular shortest-path graph distance -- to WEECFP substructure tokens. A 7-model blend of this architecture (the WEECFP-SuRGE Blend) achieves the lowest average regression rank on the TDC ADMET leaderboard; is #2 overall on the TDC ADMET leaderboard (behind only pretrained MapLight+GNN), and is #1 overall among methods that use no external pretraining; takes leaderboard #1 finishes on Pgp, Lipophilicity, CYP2D6 Substrate, Clearance Microsome, and LD50 (with the WEECFP-NoSuRGE Blend separately reaching #1 on HIA) across the full 22-benchmark suite -- without any external pretraining. On MoleculeNet, WEECFP-SuRGE beats every classical-fingerprint baseline on 3 of 4 regression tasks (ESOL, Lipophilicity, QM9). We further show that WEECFP tokenization is near-lossless: a greedy overlap reconstruction recovers the exact canonical SMILES of 99.9% of in-distribution molecules across 9 MoleculeNet datasets and 98.93% of molecules in a cross-dataset holdout (HIV->Lipophilicity), and that a three-reference farthest-first encoding of graph distance correlates at Pearson r = 0.901 with the true pairwise distance, enabling O(S) positional memory at matching accuracy.
We show that susceptibilities, an interpretability technique developed for neural networks, can identify the presence of algorithmic structure in Turing machines by probing the local loss landscape of a learning problem for noisy Turing machines introduced by Murfet and Troiani (arXiv:2504.08075). We prove that symmetries and path separation in the algorithm implemented by a Turing machine induce permutation symmetries and low-rank blocks in its susceptibility matrix. We study this empirically on a set of deterministic finite automata (DFAs) and demonstrate that algorithmic features can be recovered by principal component analysis and clustering methods in susceptibility space.
Billy Snikkers, Rumi Salazar, Daniel Murfet et al.· 0 citations
Symbolic regression (SR) discovers closed-form mathematical expressions from data, offering interpretability beyond black-box models. Existing methods suffer from slow convergence in combinatorial search spaces and lack mechanisms to exploit compositional structure in the data. We introduce SMILE (Sine, Multiplication, Identity, Logarithm, Exponential), a hybrid framework that unifies continuous gradient-based optimization with discrete symbolic recovery through three stages: structural analysis of the data to identify the compositional hierarchy of the target expression, continuous optimization to learn parameters of a network that encodes the target expression using interpretable activations, and symbolic recovery through structured pruning, coefficient optimization, and rounding. This final stage distills the learned network into a compact expression with exact symbolic constants. We evaluate SMILE on SRBench across ground-truth and black-box datasets, with ablation studies validating each component. SMILE achieves the highest symbolic solution rate at the largest noise levels, demonstrating strong robustness where competing methods degrade substantially. It consistently lies on the Pareto front of accuracy versus complexity, recovering significantly simpler expressions in a fraction of the time required by the competing methods.
Mansooreh Montazerin, Antonio Ortega, Ajitesh Srivastava· 0 citations
Neural ocean emulators are being proposed for regional forecasting in cyclone-exposed coastal seas, and a natural design choice is to hand the network the cyclone as a prescribed input. We test that choice in the Bay of Bengal and find it harmful. We withhold 15 whole cyclones spanning 65 to 150 kt from GLORYS12 reanalysis and compare two U-Nets that are identical except for four prescribed cyclone-track channels. Across three seeds the ocean-only model beats persistence in every run and the storm-conditioned model loses to it in every run, with the two skill ranges disjoint (p = 3.1e-5, paired across storms). The cause is exposure frequency rather than signal content: the channels are non-zero on only 7.9% of training days, so they are out of distribution the moment they activate. The extra error falls inside the prescribed storm footprint, and replacing the real cyclone map with a no-storm map at inference improves held-out storm forecasts by 7.5 to 16.4% in every seed. The conditioned network has learned a response to a rare signal that is confidently wrong.
Sumaiya Islam· 0 citations
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Graph coarsening reduces the large Quadratic Unconstrained Binary Optimization (QUBO) formulations arising when vehicle-routing problems are solved by quantum annealing. Nearby customers with compatible time windows are merged into super-nodes, the reduced problem is solved, and the solution is expanded to the original graph. For the Capacitated Vehicle Routing Problem with Time Windows (CVRPTW), existing coarsening heuristics require family-specific tuning and remain unreliable on random instances. We address these limitations on the Solomon benchmark using simulated annealing and a D-Wave Advantage2 processor.
We first introduce adaptive penalty calibration. Uniform penalty scaling has little effect, whereas controlling the internal coefficient range substantially improves raw samples. Removing non-binding constraints, normalising binding ones, and scaling the remaining penalties reduces mean raw constraint violations from 33.0 to 0.06 at the same solver budget (p=3.7e-11, n=56). A variable-count-preserving control attributes this gain to conditioning rather than problem size.
Second, we replace the hand-tuned merge score with a graph neural network (GNN) using one configuration across all families. At N=10, it achieves 100% feasibility across all Solomon families, including R-type (100% vs. 80% for the tuned heuristic). Across N=10,...,100, feasibility is 83% vs. 69%, with the GNN better or tied on 85/90 instance-size pairs. At N=80,100, the difference is significant (p=0.002; 25/25 pairs), while the QUBO remains approximately 5-6 times smaller.
Finally, hardware experiments reproduce the conditioning effect at fixed logical variable count: feasible samples increase from 0.02% to 39% across 13 instances. Classical repair with local search remains a reference bound for end-to-end solution cost.
The representation chosen for a mathematical operation can affect both its algebraic form and its empirical learning difficulty. We study this phenomenon for inversion over \(\mathbb F_{2^n}\), with field elements expressed in varying ordered \(\mathbb F_2\)-bases. We prove that two ordered bases induce the same coordinate inversion map if and only if they belong to the same Galois orbit. Since every orbit has size \(n\), the correspondence between ordered bases and distinct inversion maps is exactly \(n\)-to-one. We then analyze three Boolean formulations of inversion. The reference formulation has algebraic degree \(n-1\) and joint ANF leap \(1\), the mixed representation formulation has degree \(2(n-1)\) and joint ANF leap \(2\), and the complete raw formulation has degree at most \(3(n-1)\) and joint ANF leap at least \(n\). Exhaustive computations agree with the theoretical results and bounds in the cases considered. Controlled experiments with multilayer perceptrons show the same ordering in learning difficulty, while Galois orbit redundancy provides only a limited generalization benefit under the tested conditions. These results show that exact redundancy among representations can coexist with changes in Boolean structure and learning behavior when the representation is exposed as part of the input.
We investigate how optimizers scale across the overtraining axis and show that relative optimizer performance and optimal hyperparameters change substantially with training horizon. In particular, we study how matrix-preconditioned methods (Muon and SOAP) and a momentum-scheduled method (ADANA) scale relative to AdamW. We compare these four optimizers across models from 51M to 253M parameters and overtraining (OT) factors from 1x to 256x, sweeping the base learning rate at every setting. The preferred learning rate schedule can reverse across the overtraining axis, the best weight decay coefficient scales approximately as sqrt(OT), and longer horizons generally favor longer fixed memory. ADANA's scaling advantage over AdamW persists after tuning AdamW's fixed memory separately at each horizon. Log-time weight decay and momentum cooldown provide substantial gains for ADANA that compound as training increases. With this treatment, ADANA outscales AdamW with an exponent advantage close to that predicted by DANA theory on power-law random features. Muon and SOAP instead provide roughly constant token-efficiency advantages over AdamW across most of the measured range, although SOAP may gain further at the highest overtraining factors. ADANA begins behind both matrix-preconditioned optimizers but closes the gaps as training increases, surpassing Muon and becoming competitive with SOAP at our highest OT factors. These results establish training horizon as an essential axis for optimizer evaluation and design.
The FitzHugh-Nagumo (FHN) system serves as a simplified model of neuronal voltage dynamics, capturing the activator-inhibitor structure behind both isolated action potentials and the rhythmic spiking seen across the brain. Exploring its 5D physiological parameter space is important for neuromodulation and mapping voltage recordings back to biophysics, yet classical finite-difference solvers make rapid parameter sweeps expensive. We train parameter-conditioned Fourier Neural Operators (FNOs) as fast, differentiable surrogates for the FHN voltage and recovery fields on a one-dimensional spatial domain, conditioning each Fourier layer on the parameter vector $\lambda = (D_u, D_v, a, b, \tau)$ via feature-wise linear modulation (FiLM). We apply a single bifurcation analysis that delimits the two distinct regimes the model spans, oscillatory (tonic firing) and excitable (action-potential propagation), and we train one operator in each. In the oscillatory regime the surrogate attains sub-$0.1\%$ relative $L^2$ error on both fields, runs nearly three orders of magnitude faster than the finite-difference baseline, generalizes uniformly across the parameter space, and extrapolates to low single-digit percentage errors outside of the training bounds. In the excitable regime the same operator accurately reproduces the firing threshold and the $c \propto \sqrt{D_u}$ conduction-velocity law and replicates full traveling pulses, fully capturing the excitable bifurcation structure rather than just smoothly interpolating fields.
We introduce Mitra-v2, a tabular foundation model that delivers state-of-the-art performance on real-world classification and regression problems, from credit-risk scoring and clinical prediction to equipment-failure detection and house-price estimation. Mitra-v2 is trained only on synthetic data, with a pretraining distribution that is much larger and more diverse than Mitra-v1's. Built on a small 2D Transformer backbone, Mitra-v2 supports longer contexts and larger feature spaces. Improved optimization lets it learn from this larger task distribution. We evaluate Mitra-v2 on the TabArena and TALENT benchmarks, comprising more than 300 real-world datasets under two evaluation protocols. On the full TabArena benchmark, Mitra-v2 delivers state-of-the-art performance at the level of the industry-scale TabFM and EXAONE Tabular models, while surpassing TabPFN-3 by a wide margin in both classification and regression. Mitra-v2 matches the 1.6B-parameter TabFM with only 5% of its size (77M parameters), delivering frontier performance at a fraction of the cost. On TALENT, Mitra-v2 remains among the leading models, clearly outperforming TabPFN-3 and TabICLv2. It also ranks first on classification tasks with more than ten classes, even though it was pretrained only on tasks with at most ten classes. These results make Mitra-v2 one of the strongest and most broadly applicable open tabular foundation models released to date. We release the model weights, the inference and fine-tuning code, and our evaluation results under the Apache-2.0 license.
Yefan Tao (Bernie), Xiyuan Zhang (Bernie), Xinyi Liu (Bernie) et al.· 0 citations
Language generation is almost universally treated as a sequential process: autoregressive models emit one token at a time, while diffusion language models replace token-level seriality with a long trajectory of iterative refinement. In this work, we introduce PlaidQ, a 0.7B continuous diffusion language model for code generation, and show that its trajectory can be aggressively distilled into only a few denoising steps---or even one, enabling efficient code generation. PlaidQ repurposes a pretrained autoregressive model as a bidirectional denoiser over continuous token embeddings. We distill PlaidQ with distribution matching for few-step generation and paired-trajectory supervision for one-step generation. At matched model scale, PlaidQ is competitive with discrete diffusion language models on code generation. Distillation then shifts the quality--compute frontier: a 16-step student reaches 31.78 and 40.49 pass@10 on HumanEval and MBPP+, surpassing the same PlaidQ teacher sampled for 512 steps. At the extreme, paired-trajectory distillation achieves 7.07 pass@1 on HumanEval with a single denoising step, producing functionally correct programs. Together, these results establish continuous diffusion as a viable path to few-step and one-step code generation. Broadly, continuous diffusion is not merely another representation for language: it provides an interface through which language models can inherit the acceleration and distillation machinery of continuous diffusion modeling. Training and inference code and model checkpoints are available at https://github.com/pengzhangzhi/plaidq.
Fred Zhangzhi Peng, Kaiwen Zheng, Anru R. Zhang· 0 citations
We develop an energy-based reduced-order model for micromagnetic magnetization dynamics that couples a convolutional autoencoder to a structured latent neural ordinary differential equation. Motivated by the precessional-dissipative structure of the Landau-Lifshitz-Gilbert equation, the latent vector field is generated from the gradient of a learned scalar potential through an antisymmetric operator and a symmetric positive-semidefinite dissipative operator. This potential is learned in nonunique latent coordinates and is not identified with the Gibbs free energy, but decreases monotonically along autonomous continuous-time solutions, while the antisymmetric component permits motion along its level sets. The encoder, decoder, latent energy, and operators are trained jointly on short trajectory windows using latent and decoded-rollout losses alone, without time-derivative supervision, physical-energy labels, or dissipation penalties. At inference, an initial state is encoded once, evolved in latent space, and decoded only at the requested output times, enabling substantially cheaper trajectory prediction than the micromagnetic solver used to generate the training data. We compare quadratic, deep, and additive deep-quadratic latent energies on two datasets parameterized by field amplitude and generated for the two applied-field directions of the NIST $\mu$MAG Standard Problem 4. Dissipative-only and antisymmetric-dissipative models achieve comparable accuracy on short training-style windows but differ substantially on uninterrupted rollouts, for which the antisymmetric-dissipative models provide markedly more accurate trajectory predictions. The deep-quadratic energy gives the best overall accuracy for both field directions and exhibits slower error growth when rollouts are extended to twice the training horizon.
In Geometric Deep Learning, inductive biases serve two primary functions: enforcing manifold constraints and embedding relational priors. Currently, representation learning on SPD manifolds frequently relies on pullback Euclidean metrics, such as the Log-Euclidean Metric, to satisfy the former. While computationally efficient in avoiding domain boundary violations, these metrics induce a flat geometry that may fail to capture the intrinsic relational priors of datasets. While metrics such as the Poincar\'e metric are widely utilized to induce domain-aligned relational priors, generalizing them from standard vector representations to the SPD manifold has remained a challenge. To bridge this gap, we introduce a Nested Inductive Bias framework that utilizes a two-stage diffeomorphic composition to formally pull back non-Euclidean target geometries onto the SPD manifold. This framework enables the construction of curvature-aligned Riemannian classifiers that simultaneously respect matrix constraints and the latent relational geometry of the data. Empirical evaluations on kinematic and signal processing benchmarks, together with synthetic experiments, demonstrate that deep manifold networks experience degradation in class separability unless the metric curvature aligns with the intrinsic data distribution. Furthermore, for standard vectorized architectures, we propose the Rational Conformal Metric (RCM), designed to establish state-of-the-art geometric robustness against outliers by bounding the representation space.
A weeklong summer workshop brought higher education faculty to campus to explore how AI and machine learning materials can be adapted for their classrooms.
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
MIT News · Artificial Intelligence· news.mit.eduAug 24, 2026
A new method for surgically removing training examples from a model reveals that as datasets grow, the link between what a model learns and what it produces dissolves.
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