Daily Papers

Humans easily determine which color belongs to which shape in multi-object scenes, an ability known as concept binding. Vision-language embedding models such as CLIP struggle with binding: they recognize individual concepts but fail to represent which concepts form which objects. Although CLIP behaves like a bag-of-concepts model in cross-modal retrieval, object information is recoverable from its image and text embeddings separately. We study this tension through the binding function, which maps concepts to scene embeddings. We find that scene embeddings decompose additively into object representations, explaining why uni-modal probes can recover object information. However, CLIP's binding function is high-complexity, which likely prevents the image and text encoders from learning a shared binding mechanism that generalizes to unseen concept combinations. We then ask whether this limitation is fundamental. We show that it is not. In controlled transformer models trained from scratch, binding generalization emerges with sufficient data coverage. These models learn low-complexity binding functions characterized by multiplicative interactions between concepts, enabling systematic generalization. Code is publicly available at https://github.com/oshapio/binding-concepts-complexity.

Protein-ligand binding affinity prediction is essential for drug discovery and toxicity assessment. While machine learning (ML) promises fast and accurate predictions, its progress is constrained by the availability of reliable data. In contrast, physics-based methods such as absolute binding free energy perturbation (AB-FEP) deliver high accuracy but are computationally prohibitive for high-throughput applications. To bridge this gap, we introduce ToxBench, the first large-scale AB-FEP dataset designed for ML development and focused on a single pharmaceutically critical target, Human Estrogen Receptor Alpha (ERalpha). ToxBench contains 8,770 ERalpha-ligand complex structures with binding free energies computed via AB-FEP with a subset validated against experimental affinities at 1.75 kcal/mol RMSE, along with non-overlapping ligand splits to assess model generalizability. Using ToxBench, we further benchmark state-of-the-art ML methods, and notably, our proposed DualBind model, which employs a dual-loss framework to effectively learn the binding energy function. The benchmark results demonstrate the superior performance of DualBind and the potential of ML to approximate AB-FEP at a fraction of the computational cost.

Stimulated by the renewed interest and recent developments in semi-empirical quantum chemical (SQC) methods for noncovalent interactions, we examine the properties of liquid water at ambient conditions by means of molecular dynamics (MD) simulations, both with the conventional NDDO-type (neglect of diatomic differential overlap) methods, e.g. AM1 and PM6, and with DFTB-type (density-functional tight-binding) methods, e.g. DFTB2 and GFN-xTB. Besides the original parameter sets, some specifically reparametrized SQC methods (denoted as AM1-W, PM6-fm, and DFTB2-iBi) targeting various smaller water systems ranging from molecular clusters to bulk are considered as well. The quality of these different SQC methods for describing liquid water properties at ambient conditions are assessed by comparison to well-established experimental data and also to BLYP-D3 density functional theory-based ab initio MD simulations. Our analyses reveal that static and dynamics properties of bulk water are poorly described by all considered SQC methods with the original parameters, regardless of the underlying theoretical models, with most of the methods suffering from too weak hydrogen bonds and hence predicting a far too fluid water with highly distorted hydrogen bond kinetics. On the other hand, the reparametrized force-matchcd PM6-fm method is shown to be able to quantitatively reproduce the static and dynamic features of liquid water, and thus can be used as a computationally efficient alternative to electronic structure-based MD simulations for liquid water that requires extended length and time scales. DFTB2-iBi predicts a slightly overstructured water with reduced fluidity, whereas AM1-W gives an amorphous ice-like structure for water at ambient conditions.

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.

Though end-to-end neural approaches have recently been dominating NLP tasks in both performance and ease-of-use, they lack interpretability and robustness. We propose Binder, a training-free neural-symbolic framework that maps the task input to a program, which (1) allows binding a unified API of language model (LM) functionalities to a programming language (e.g., SQL, Python) to extend its grammar coverage and thus tackle more diverse questions, (2) adopts an LM as both the program parser and the underlying model called by the API during execution, and (3) requires only a few in-context exemplar annotations. Specifically, we employ GPT-3 Codex as the LM. In the parsing stage, with only a few in-context exemplars, Codex is able to identify the part of the task input that cannot be answerable by the original programming language, correctly generate API calls to prompt Codex to solve the unanswerable part, and identify where to place the API calls while being compatible with the original grammar. In the execution stage, Codex can perform versatile functionalities (e.g., commonsense QA, information extraction) given proper prompts in the API calls. Binder achieves state-of-the-art results on WikiTableQuestions and TabFact datasets, with explicit output programs that benefit human debugging. Note that previous best systems are all finetuned on tens of thousands of task-specific samples, while Binder only uses dozens of annotations as in-context exemplars without any training. Our code is available at https://github.com/HKUNLP/Binder .

Parameterized tight-binding models fit to first principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, most previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly one million materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low energy crystal structures and then add them to the fitting dataset, iterating until predictions improve. We distribute the materials database and tools developed in this work publicly.

Predicting peptide--major histocompatibility complex I (pMHC-I) binding affinity remains challenging due to extreme allelic diversity (sim30,000 HLA alleles), severe data scarcity for most alleles, and noisy experimental measurements. Current methods particularly struggle with underrepresented alleles and quantitative binding prediction. We test whether domain-specific continued pre-training of protein language models is beneficial for their application to pMHC-I binding affinity prediction. Starting from ESM Cambrian (300M parameters), we perform masked-language modeling (MLM)-based continued pre-training on HLA-associated peptides (epitopes), testing two input formats: epitope sequences alone versus epitopes concatenated with HLA heavy chain sequences. We then fine-tune for functional IC_{50} binding affinity prediction using only high-quality quantitative data, avoiding mass spectrometry biases that are inherited by existing methods.

Text-conditioned image generation models often generate incorrect associations between entities and their visual attributes. This reflects an impaired mapping between linguistic binding of entities and modifiers in the prompt and visual binding of the corresponding elements in the generated image. As one notable example, a query like ``a pink sunflower and a yellow flamingo'' may incorrectly produce an image of a yellow sunflower and a pink flamingo. To remedy this issue, we propose SynGen, an approach which first syntactically analyses the prompt to identify entities and their modifiers, and then uses a novel loss function that encourages the cross-attention maps to agree with the linguistic binding reflected by the syntax. Specifically, we encourage large overlap between attention maps of entities and their modifiers, and small overlap with other entities and modifier words. The loss is optimized during inference, without retraining or fine-tuning the model. Human evaluation on three datasets, including one new and challenging set, demonstrate significant improvements of SynGen compared with current state of the art methods. This work highlights how making use of sentence structure during inference can efficiently and substantially improve the faithfulness of text-to-image generation.

Whole-genome sequencing (WGS) has revealed numerous non-coding short variants whose functional impacts remain poorly understood. Despite recent advances in deep-learning genomic approaches, accurately predicting and prioritizing clinically relevant mutations in gene regulatory regions remains a major challenge. Here we introduce Deep VRegulome, a deep-learning method for prediction and interpretation of functionally disruptive variants in the human regulome, which combines 700 DNABERT fine-tuned models, trained on vast amounts of ENCODE gene regulatory regions, with variant scoring, motif analysis, attention-based visualization, and survival analysis. We showcase its application on TCGA glioblastoma WGS dataset in prioritizing survival-associated mutations and regulatory regions. The analysis identified 572 splice-disrupting and 9,837 transcription-factor binding site altering mutations occurring in greater than 10% of glioblastoma samples. Survival analysis linked 1352 mutations and 563 disrupted regulatory regions to patient outcomes, enabling stratification via non-coding mutation signatures. All the code, fine-tuned models, and an interactive data portal are publicly available.

Region-instructed layout control in text-to-image generation is highly practical, yet existing methods suffer from limitations: (i) training-based approaches inherit data bias and often degrade image quality, and (ii) current techniques struggle with occlusion order, limiting real-world usability. To address these issues, we propose LayerBind. By modeling regional generation as distinct layers and binding them during the generation, our method enables precise regional and occlusion controllability. Our motivation stems from the observation that spatial layout and occlusion are established at a very early denoising stage, suggesting that rearranging the early latent structure is sufficient to modify the final output. Building on this, we structure the scheme into two phases: instance initialization and subsequent semantic nursing. (1) First, leveraging the contextual sharing mechanism in multimodal joint attention, Layer-wise Instance Initialization creates per-instance branches that attend to their own regions while anchoring to the shared background. At a designated early step, these branches are fused according to the layer order to form a unified latent with a pre-established layout. (2) Then, Layer-wise Semantic Nursing reinforces regional details and maintains the occlusion order via a layer-wise attention enhancement. Specifically, a sequential layered attention path operates alongside the standard global path, with updates composited under a layer-transparency scheduler. LayerBind is training-free and plug-and-play, serving as a regional and occlusion controller across Diffusion Transformers. Beyond generation, it natively supports editable workflows, allowing for flexible modifications like changing instances or rearranging visible orders. Both qualitative and quantitative results demonstrate LayerBind's effectiveness, highlighting its strong potential for creative applications.

Deep learning models have driven significant progress in predicting protein function and interactions at the protein level. While these advancements have been invaluable for many biological applications such as enzyme engineering and function annotation, a more detailed perspective is essential for understanding protein functional mechanisms and evaluating the biological knowledge captured by models. To address this demand, we introduce VenusX, the first large-scale benchmark for fine-grained functional annotation and function-based protein pairing at the residue, fragment, and domain levels. VenusX comprises three major task categories across six types of annotations, including residue-level binary classification, fragment-level multi-class classification, and pairwise functional similarity scoring for identifying critical active sites, binding sites, conserved sites, motifs, domains, and epitopes. The benchmark features over 878,000 samples curated from major open-source databases such as InterPro, BioLiP, and SAbDab. By providing mixed-family and cross-family splits at three sequence identity thresholds, our benchmark enables a comprehensive assessment of model performance on both in-distribution and out-of-distribution scenarios. For baseline evaluation, we assess a diverse set of popular and open-source models, including pre-trained protein language models, sequence-structure hybrids, structure-based methods, and alignment-based techniques. Their performance is reported across all benchmark datasets and evaluation settings using multiple metrics, offering a thorough comparison and a strong foundation for future research. Code and data are publicly available at https://github.com/ai4protein/VenusX.

We introduce AbBiBench (Antibody Binding Benchmarking), a benchmarking framework for antibody binding affinity maturation and design. Unlike previous strategies that evaluate antibodies in isolation, typically by comparing them to natural sequences with metrics such as amino acid recovery rate or structural RMSD, AbBiBench instead treats the antibody-antigen (Ab-Ag) complex as the fundamental unit. It evaluates an antibody design's binding potential by measuring how well a protein model scores the full Ab-Ag complex. We first curate, standardize, and share more than 184,500 experimental measurements of antibody mutants across 14 antibodies and 9 antigens-including influenza, lysozyme, HER2, VEGF, integrin, Ang2, and SARS-CoV-2-covering both heavy-chain and light-chain mutations. Using these datasets, we systematically compare 15 protein models including masked language models, autoregressive language models, inverse folding models, diffusion-based generative models, and geometric graph models by comparing the correlation between model likelihood and experimental affinity values. Additionally, to demonstrate AbBiBench's generative utility, we apply it to antibody F045-092 in order to introduce binding to influenza H1N1. We sample new antibody variants with the top-performing models, rank them by the structural integrity and biophysical properties of the Ab-Ag complex, and assess them with in vitro ELISA binding assays. Our findings show that structure-conditioned inverse folding models outperform others in both affinity correlation and generation tasks. Overall, AbBiBench provides a unified, biologically grounded evaluation framework to facilitate the development of more effective, function-aware antibody design models.

Text-to-image diffusion models particularly Stable Diffusion, have revolutionized the field of computer vision. However, the synthesis quality often deteriorates when asked to generate images that faithfully represent complex prompts involving multiple attributes and objects. While previous studies suggest that blended text embeddings lead to improper attribute binding, few have explored this in depth. In this work, we critically examine the limitations of the CLIP text encoder in understanding attributes and investigate how this affects diffusion models. We discern a phenomenon of attribute bias in the text space and highlight a contextual issue in padding embeddings that entangle different concepts. We propose Magnet, a novel training-free approach to tackle the attribute binding problem. We introduce positive and negative binding vectors to enhance disentanglement, further with a neighbor strategy to increase accuracy. Extensive experiments show that Magnet significantly improves synthesis quality and binding accuracy with negligible computational cost, enabling the generation of unconventional and unnatural concepts.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose FABind, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. FABind incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed FABind demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

Deep learning promises to dramatically improve scoring functions for molecular docking, leading to substantial advances in binding pose prediction and virtual screening. To train scoring functions-and to perform molecular docking-one must generate a set of candidate ligand binding poses. Unfortunately, the sampling protocols currently used to generate candidate poses frequently fail to produce any poses close to the correct, experimentally determined pose, unless information about the correct pose is provided. This limits the accuracy of learned scoring functions and molecular docking. Here, we describe two improved protocols for pose sampling: GLOW (auGmented sampLing with sOftened vdW potential) and a novel technique named IVES (IteratiVe Ensemble Sampling). Our benchmarking results demonstrate the effectiveness of our methods in improving the likelihood of sampling accurate poses, especially for binding pockets whose shape changes substantially when different ligands bind. This improvement is observed across both experimentally determined and AlphaFold-generated protein structures. Additionally, we present datasets of candidate ligand poses generated using our methods for each of around 5,000 protein-ligand cross-docking pairs, for training and testing scoring functions. To benefit the research community, we provide these cross-docking datasets and an open-source Python implementation of GLOW and IVES at https://github.com/drorlab/GLOW_IVES .

We report an accurate study of interactions between Benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory (DFT) using different van der Waals (vdW) functionals. In our QMC calculations, we use accurate correlated trial wave functions including three-body Jastrow factors, and backflow transformations. We consider two benzene molecules in the parallel displaced (PD) geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of -2.3(4) and -2.7(3) kcal/mol, respectively. The best estimate of the CCSD(T)/CBS limit is -2.65(2) kcal/mol [E. Miliordos et al, J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.

We present Universal Conditional Logic (UCL), a mathematical framework for prompt optimization that transforms prompt engineering from heuristic practice into systematic optimization. Through systematic evaluation (N=305, 11 models, 4 iterations), we demonstrate significant token reduction (29.8%, t(10)=6.36, p < 0.001, Cohen's d = 2.01) with corresponding cost savings. UCL's structural overhead function O_s(A) explains version-specific performance differences through the Over-Specification Paradox: beyond threshold S* = 0.509, additional specification degrades performance quadratically. Core mechanisms -- indicator functions (I_i in {0,1}), structural overhead (O_s = gamma * sum(ln C_k)), early binding -- are validated. Notably, optimal UCL configuration varies by model architecture -- certain models (e.g., Llama 4 Scout) require version-specific adaptations (V4.1). This work establishes UCL as a calibratable framework for efficient LLM interaction, with model-family-specific optimization as a key research direction.

The independent atom ansatz of density functional theory yields an accurate analytical expression for dynamic correlation energy in the H_{2} molecule: E_{c} = 0.5(1 - 2)(ab|ba) for the atom-additive self-consistent density rho = |a|^{2} + |b|^{2}. Combined with exact atomic self-exchange, it recovers more than 99.5 % of nearly exact SCAN exchange-correlation energy at R > 0.5 A, differing by less than 0.12 eV. The total energy functional correctly dissociates the H-H bond and yields absolute errors of 0.002 A, 0.19 eV, and 13 cm^{-1} relative to experiment at the tight binding computational cost. The chemical bond formation is attributed to the asymptotic Heitler-London resonance of quasi-orthogonal atomic states (- (ab|ba)) with no contributions from kinetic energy or charge accumulation in the bond.

Large language models (LLMs) generalize smoothly across continuous semantic spaces, yet strict logical reasoning demands the formation of discrete decision boundaries. Prevailing theories relying on linear isometric projections fail to resolve this fundamental tension. In this work, we argue that task context operates as a non-isometric dynamical operator that enforces a necessary "topological distortion." By applying Gram-Schmidt decomposition to residual-stream activations , we reveal a dual-modulation mechanism driving this process: a class-agnostic topological preservation that anchors global structure to prevent semantic collapse, and a specific algebraic divergence that directionally tears apart cross-class concepts to forge logical boundaries. We validate this geometric evolution across a gradient of tasks, from simple mapping to complex primality testing. Crucially, targeted specific vector ablation establishes a strict causal binding between this topology and model function: algebraically erasing the divergence component collapses parity classification accuracy from 100% to chance levels (38.57%). Furthermore, we uncover a three-phase layer-wise geometric dynamic and demonstrate that under social pressure prompts, models fail to generate sufficient divergence. This results in a "manifold entanglement" that geometrically explains sycophancy and hallucination. Ultimately, our findings revise the linear-isometric presumption, demonstrating that the emergence of discrete logic in LLMs is purchased at an irreducible cost of topological deformation.

Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated remarkable success in predicting protein structure and function, their application to sequence-based PPI binding affinity prediction remains relatively underexplored. This gap is often attributed to the scarcity of high-quality, rigorously refined datasets and the reliance on simple strategies for concatenating protein representations. In this work, we address these limitations. First, we introduce a meticulously curated version of the PPB-Affinity dataset of a total of 8,207 unique protein-protein interaction entries, by resolving annotation inconsistencies and duplicate entries for multi-chain protein interactions. This dataset incorporates a stringent, less than or equal to 30%, sequence identity threshold to ensure robust splitting into training, validation, and test sets, minimizing data leakage. Second, we propose and systematically evaluate four architectures for adapting PLMs to PPI binding affinity prediction: embeddings concatenation (EC), sequences concatenation (SC), hierarchical pooling (HP), and pooled attention addition (PAD). These architectures were assessed using two training methods: full fine-tuning and a lightweight approach employing ConvBERT heads over frozen PLM features. Our comprehensive experiments across multiple leading PLMs (ProtT5, ESM2, Ankh, Ankh2, and ESM3) demonstrated that the HP and PAD architectures consistently outperform conventional concatenation methods, achieving up to 12% increase in terms of Spearman correlation. These results highlight the necessity of sophisticated architectural designs to fully exploit the capabilities of PLMs for nuanced PPI binding affinity prediction.

The Joint Automated Repository for Various Integrated Simulations (JARVIS) is a unified platform for multiscale, multimodal, forward, and inverse materials design. It integrates diverse theoretical and experimental approaches, including density functional theory, quantum Monte Carlo, tight-binding, classical force fields, machine learning, microscopy, diffraction, and cryogenics, across a wide range of materials. Emphasizing open access and reproducibility, JARVIS provides datasets, tools, benchmarks, and web applications that are widely adopted by the materials community. By bridging computation and experiment, JARVIS accelerates both fundamental research and real-world materials innovation.

Text-to-image (T2I) diffusion models have demonstrated impressive capabilities in generating high-quality images given a text prompt. However, ensuring the prompt-image alignment remains a considerable challenge, i.e., generating images that faithfully align with the prompt's semantics. Recent works attempt to improve the faithfulness by optimizing the latent code, which potentially could cause the latent code to go out-of-distribution and thus produce unrealistic images. In this paper, we propose FRAP, a simple, yet effective approach based on adaptively adjusting the per-token prompt weights to improve prompt-image alignment and authenticity of the generated images. We design an online algorithm to adaptively update each token's weight coefficient, which is achieved by minimizing a unified objective function that encourages object presence and the binding of object-modifier pairs. Through extensive evaluations, we show FRAP generates images with significantly higher prompt-image alignment to prompts from complex datasets, while having a lower average latency compared to recent latent code optimization methods, e.g., 4 seconds faster than D&B on the COCO-Subject dataset. Furthermore, through visual comparisons and evaluation on the CLIP-IQA-Real metric, we show that FRAP not only improves prompt-image alignment but also generates more authentic images with realistic appearances. We also explore combining FRAP with prompt rewriting LLM to recover their degraded prompt-image alignment, where we observe improvements in both prompt-image alignment and image quality.

Recent AI advances have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, alignment, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of modality encoders along protein sequences. It demonstrates strong performance in retrieval tasks and surpasses state-of-the-art methods in various downstream tasks, including metal ion binding classification, gene-ontology annotation, and enzyme function prediction. This work expands multi-modal capabilities in protein models, paving the way for applications in drug discovery, biocatalytic reaction planning, and protein engineering.

Protein language models (pLMs) have emerged as powerful predictors of protein structure and function. However, the computational circuits underlying their predictions remain poorly understood. Recent mechanistic interpretability methods decompose pLM representations into interpretable features, but they treat each layer independently and thus fail to capture cross-layer computation, limiting their ability to approximate the full model. We introduce ProtoMech, a framework for discovering computational circuits in pLMs using cross-layer transcoders that learn sparse latent representations jointly across layers to capture the model's full computational circuitry. Applied to the pLM ESM2, ProtoMech recovers 82-89% of the original performance on protein family classification and function prediction tasks. ProtoMech then identifies compressed circuits that use <1% of the latent space while retaining up to 79% of model accuracy, revealing correspondence with structural and functional motifs, including binding, signaling, and stability. Steering along these circuits enables high-fitness protein design, surpassing baseline methods in more than 70% of cases. These results establish ProtoMech as a principled framework for protein circuit tracing.

This paper introduces the N-Way Self-Evaluating Deliberation (NSED) protocol, a Runtime Mixture-of-Models (MoM) architecture that constructs emergent composite models from a plurality of distinct expert agents. Unlike traditional Mixture-of-Experts (MoE) which rely on static gating networks, NSED employs a Dynamic Expertise Broker - a runtime optimization engine that treats model selection as a variation of the Knapsack Problem, binding heterogeneous checkpoints to functional roles based on live telemetry and cost constraints. At the execution layer, we formalize deliberation as a Macro-Scale Recurrent Neural Network (RNN), where the consensus state loops back through a semantic forget gate to enable iterative refinement without proportional VRAM scaling. Key components include an orchestration fabric for trustless N-to-N peer review, a Quadratic Voting activation function for non-linear consensus, and a feedback-driven state update. Empirical validation on challenging benchmarks (AIME 2025, LiveCodeBench) demonstrates that this topology allows ensembles of small (less than 20B) consumer-grade models to match or exceed the performance of state-of-the-art 100B+ parameter models, establishing a new hardware arbitrage efficiency frontier. Furthermore, testing on the DarkBench safety suite reveals intrinsic alignment properties, with peer-mediated correction reducing sycophancy scores below that of any individual agent.

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our Discrete Walk-Jump Sampling formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the distributional conformity score to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100% of generated samples are successfully expressed and purified and 70% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

Transformer architectures have proven to learn useful representations for protein classification and generation tasks. However, these representations present challenges in interpretability. In this work, we demonstrate a set of methods for analyzing protein Transformer models through the lens of attention. We show that attention: (1) captures the folding structure of proteins, connecting amino acids that are far apart in the underlying sequence, but spatially close in the three-dimensional structure, (2) targets binding sites, a key functional component of proteins, and (3) focuses on progressively more complex biophysical properties with increasing layer depth. We find this behavior to be consistent across three Transformer architectures (BERT, ALBERT, XLNet) and two distinct protein datasets. We also present a three-dimensional visualization of the interaction between attention and protein structure. Code for visualization and analysis is available at https://github.com/salesforce/provis.

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we propose to learn protein-ligand binding representation in a self-supervised learning manner. Different from existing pre-training approaches which treat proteins and ligands individually, we emphasize to discern the intricate binding patterns from fine-grained interactions. Specifically, this self-supervised learning problem is formulated as a prediction of the conclusive binding complex structure given a pocket and ligand with a Transformer based interaction module, which naturally emulates the binding process. To ensure the representation of rich binding information, we introduce two pre-training tasks, i.e.~atomic pairwise distance map prediction and mask ligand reconstruction, which comprehensively model the fine-grained interactions from both structure and feature space. Extensive experiments have demonstrated the superiority of our method across various binding tasks, including protein-ligand affinity prediction, virtual screening and protein-ligand docking.

Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand's bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand's rotatable bonds based on closed-form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

Neural networks have proven to be a highly effective tool for solving complex problems in many areas of life. Recently, their importance and practical usability have further been reinforced with the advent of deep learning. One of the important conditions for the success of neural networks is the choice of an appropriate activation function introducing non-linearity into the model. Many types of these functions have been proposed in the literature in the past, but there is no single comprehensive source containing their exhaustive overview. The absence of this overview, even in our experience, leads to redundancy and the unintentional rediscovery of already existing activation functions. To bridge this gap, our paper presents an extensive survey involving 400 activation functions, which is several times larger in scale than previous surveys. Our comprehensive compilation also references these surveys; however, its main goal is to provide the most comprehensive overview and systematization of previously published activation functions with links to their original sources. The secondary aim is to update the current understanding of this family of functions.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary binding prediction and affinity regression. However, these evaluations provide limited evidence of whether models can localize binding sites or identify the non-covalent interactions underlying molecular recognition. To address this gap, we introduce InteractBind, a large-scale protein-ligand dataset comprising approximately 100k protein-ligand pairs, together with a benchmark for fine-grained evaluation. The core fine-grained task is that of binding-site localization, which uses protein-residue and ligand-atom interaction maps spanning six major types of non-covalent interactions to assess whether model-derived interaction maps localize binding sites. InteractBind further includes binding affinity and protein similarity-controlled splits to support realistic generalization assessment. Using InteractBind, we evaluate eight existing sequence-based and interaction-aware models, assessing binary binding prediction and binding-site localization. Results reveal limited binding-site localization despite strong binary binding prediction, with marked variation across non-covalent interaction types. Overall, InteractBind establishes a benchmark paradigm that encourages the development of more interpretable and physically grounded protein-ligand models.

Protein binder design has largely optimized for affinity alone, leaving conformational selectivity unaddressed: for allosteric targets such as kinases, nuclear receptors, and GPCRs, a binder that engages both active and inactive states provides no functional specificity regardless of how tightly it binds. We introduce AlloGen, a modular framework that decouples backbone generation from a learned state-selectivity scorer Q_θ, an SE(3)-invariant interface graph transformer trained via a two-phase curriculum that first learns interface geometry before imposing conformational discrimination. Because Q_θ is fully differentiable and generator-agnostic, it integrates with any backbone generator as a passive reranker or an active gradient-based guide without retraining. Across a diverse benchmark of proteins spanning multiple families and conformational mechanisms, AlloGen consistently identifies binders that preferentially recognize desired structural states while rejecting alternative conformations. Experimental validation on calmodulin further demonstrates that these computational selectivity signals translate to physical molecules, yielding de novo peptides that bind the desired holo conformation while exhibiting no detectable binding to the apo state. Together, these results establish conformational selectivity as a learnable property and provide a general framework for state-selective protein binder design.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Protein function is often controlled by ligands that bias the direction of state transitions, such as agonists and antagonists, rather than stabilizing a single conformation. This is especially important for clinically relevant G protein-coupled receptors (GPCRs), where therapeutic efficacy depends on functional directionality. Structure-based design methods optimize binding to static conformations and cannot represent non-reversible, directional effects or systematically distinguish agonist from antagonist behavior. To address this gap, we introduce Transition-Directed Discrete Diffusion for Allosteric Binder Design (TD3B), a sequence-based generative framework that designs binders with specified agonist or antagonist behavior via a directional transition control objective. TD3B combines a target-aware Direction Oracle, a soft binding-affinity gate, and amortized fine-tuning of a pre-trained discrete diffusion model, enabling targeted agonist and antagonist generation decoupled from binding affinity and unattainable by equilibrium-based or inference-only guidance baselines. The code and checkpoints are available at https://huggingface.co/ChatterjeeLab/TD3B.

Computational design of protein-binding proteins is a fundamental capability with broad utility in biomedical research and biotechnology. Recent methods have made strides against some target proteins, but on-demand creation of high-affinity binders without multiple rounds of experimental testing remains an unsolved challenge. This technical report introduces AlphaProteo, a family of machine learning models for protein design, and details its performance on the de novo binder design problem. With AlphaProteo, we achieve 3- to 300-fold better binding affinities and higher experimental success rates than the best existing methods on seven target proteins. Our results suggest that AlphaProteo can generate binders "ready-to-use" for many research applications using only one round of medium-throughput screening and no further optimization.

Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can accelerate this process by learning a scoring function with a functional form that allows for more rapid optimization. Specifically, we define the scoring function to be the cross-correlation of multi-channel ligand and protein scalar fields parameterized by equivariant graph neural networks, enabling rapid optimization over rigid-body degrees of freedom with fast Fourier transforms. The runtime of our approach can be amortized at several levels of abstraction, and is particularly favorable for virtual screening settings with a common binding pocket. We benchmark our scoring functions on two simplified docking-related tasks: decoy pose scoring and rigid conformer docking. Our method attains similar but faster performance on crystal structures compared to the widely-used Vina and Gnina scoring functions, and is more robust on computationally predicted structures. Code is available at https://github.com/bjing2016/scalar-fields.

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

The detection of ligand binding sites for proteins is a fundamental step in Structure-Based Drug Design. Despite notable advances in recent years, existing methods, datasets, and evaluation metrics are confronted with several key challenges: (1) current datasets and methods are centered on individual protein-ligand complexes and neglect that diverse binding sites may exist across multiple complexes of the same protein, introducing significant statistical bias; (2) ligand binding site detection is typically modeled as a discontinuous workflow, employing binary segmentation and subsequent clustering algorithms; (3) traditional evaluation metrics do not adequately reflect the actual performance of different binding site prediction methods. To address these issues, we first introduce UniSite-DS, the first UniProt (Unique Protein)-centric ligand binding site dataset, which contains 4.81 times more multi-site data and 2.08 times more overall data compared to the previously most widely used datasets. We then propose UniSite, the first end-to-end ligand binding site detection framework supervised by set prediction loss with bijective matching. In addition, we introduce Average Precision based on Intersection over Union (IoU) as a more accurate evaluation metric for ligand binding site prediction. Extensive experiments on UniSite-DS and several representative benchmark datasets demonstrate that IoU-based Average Precision provides a more accurate reflection of prediction quality, and that UniSite outperforms current state-of-the-art methods in ligand binding site detection. The dataset and codes will be made publicly available at https://github.com/quanlin-wu/unisite.

Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language Models (pLMs) aim to unlock insights from the vast space of unlabeled protein sequences by learning rich, semantic representations from primary sequences via masked language modeling. However, these models typically exhibit limited generative capacity. In this work, we introduce the Diffusion Sequence Model (DSM), a novel pLM trained with masked diffusion to enable both high-quality representation learning and generative protein design. DSM builds upon the ESM2 architecture by incorporating a masked forward diffusion process inspired by the LLaDA framework. After training, DSM is capable of generating diverse, biomimetic sequences that align with expected amino acid compositions, secondary structures, and predicted functions, even with 90\% token corruption. Furthermore, DSM's learned representations match or exceed those of similarly sized pLMs on downstream tasks. We also introduce DSM(ppi), a variant fine-tuned to generate protein binders by attending to target sequences. We demonstrate DSM(ppi)'s effectiveness on the challenging Bench-tested Binder Benchmark (BenchBB), where both DSM and DSM(ppi) produce candidates with superior predicted binding affinity compared to known binders. Our results establish masked diffusion as a powerful paradigm for unifying protein representation and generation in a single framework.

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation. The code is available at https://github.com/prescient-design/funcbind.

Accurate prediction of protein-ligand binding poses is crucial for structure-based drug design, yet existing methods struggle to balance speed, accuracy, and physical plausibility. We introduce Matcha, a novel molecular docking pipeline that combines multi-stage flow matching with learned scoring and physical validity filtering. Our approach consists of three sequential stages applied consecutively to refine docking predictions, each implemented as a flow matching model operating on appropriate geometric spaces (R^3, SO(3), and SO(2)). We enhance the prediction quality through a dedicated scoring model and apply unsupervised physical validity filters to eliminate unrealistic poses. Compared to various approaches, Matcha demonstrates superior performance on Astex and PDBbind test sets in terms of docking success rate and physical plausibility. Moreover, our method works approximately 25 times faster than modern large-scale co-folding models. The model weights and inference code to reproduce our results are available at https://github.com/LigandPro/Matcha.

Weak-to-strong generalization studies how to improve a strong student using supervision from a weaker teacher when reliable labels are scarce. We view this primarily as a data selection problem, where the key challenge is to identify which weak labels are reliable enough to serve as a training signal. To address this, we introduce trust functions that assign each weak label a scalar trust score and use these scores to filter weak supervision. Across several domains, including world knowledge, quantitative reasoning, and strategy games, trust filtering yields students that match and sometimes surpass ground-truth supervision, achieving near-lossless weak-to-strong generalization. Moreover, trust functions enable an iterative weak-to-strong chain that compounds gains by training a student and reusing it as the next teacher, amplifying the gains. There are several mechanisms to which advantage of trust functions can be attributed.

Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative model based on SE(3) flow matching, to predict the structural ensembles of proteins. We specifically designed a valuable prior for the flow process and enhanced the model's ability to distinguish each intermediate state by incorporating an additional dimension to describe the ensemble data, which can reflect the physical laws governing the distribution of ensembles, so that the prior knowledge can effectively guide the generation process. When trained and evaluated on the MD datasets of ATLAS, P2DFlow outperforms other baseline models on extensive experiments, successfully capturing the observable dynamic fluctuations as evidenced in crystal structure and MD simulations. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios. Code is available at https://github.com/BLEACH366/P2DFlow

Most human proteins remain undrugged, over 96% of human proteins remain unexploited by approved therapeutics. While structure-based virtual screening promises to expand the druggable proteome, existing methods lack atomic-level precision and fail to predict binding fitness, limiting translational impact. We present AuroBind, a scalable virtual screening framework that fine-tunes a custom atomic-level structural model on million-scale chemogenomic data. AuroBind integrates direct preference optimization, self-distillation from high-confidence complexes, and a teacher-student acceleration strategy to jointly predict ligand-bound structures and binding fitness. The proposed models outperform state-of-the-art models on structural and functional benchmarks while enabling 100,000-fold faster screening across ultra-large compound libraries. In a prospective screen across ten disease-relevant targets, AuroBind achieved experimental hit rates of 7-69%, with top compounds reaching sub-nanomolar to picomolar potency. For the orphan GPCRs GPR151 and GPR160, AuroBind identified both agonists and antagonists with success rates of 16-30%, and functional assays confirmed GPR160 modulation in liver and prostate cancer models. AuroBind offers a generalizable framework for structure-function learning and high-throughput molecular screening, bridging the gap between structure prediction and therapeutic discovery.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

Activation functions are fundamental in deep neural networks and directly impact gradient flow, optimization stability, and generalization. Although ReLU remains standard because of its simplicity, it suffers from vanishing gradients and lacks adaptability. Alternatives like Swish and GELU introduce smooth transitions, but fail to dynamically adjust to input statistics. We propose VeLU, a Variance-enhanced Learning Unit as an activation function that dynamically scales based on input variance by integrating ArcTan-Sin transformations and Wasserstein-2 regularization, effectively mitigating covariate shifts and stabilizing optimization. Extensive experiments on ViT_B16, VGG19, ResNet50, DenseNet121, MobileNetV2, and EfficientNetB3 confirm VeLU's superiority over ReLU, ReLU6, Swish, and GELU on six vision benchmarks. The codes of VeLU are publicly available on GitHub.

Accurate prediction of protein-ligand binding affinities is crucial in drug discovery, particularly during hit-to-lead and lead optimization phases, however, limitations in ligand force fields continue to impact prediction accuracy. In this work, we validate relative binding free energy (RBFE) accuracy using neural network potentials (NNPs) for the ligands. We utilize a novel NNP model, AceForce 1.0, based on the TensorNet architecture for small molecules that broadens the applicability to diverse drug-like compounds, including all important chemical elements and supporting charged molecules. Using established benchmarks, we show overall improved accuracy and correlation in binding affinity predictions compared with GAFF2 for molecular mechanics and ANI2-x for NNPs. Slightly less accuracy but comparable correlations with OPLS4. We also show that we can run the NNP simulations at 2 fs timestep, at least two times larger than previous NNP models, providing significant speed gains. The results show promise for further evolutions of free energy calculations using NNPs while demonstrating its practical use already with the current generation. The code and NNP model are publicly available for research use.

Absolute Binding Free Energy (ABFE) methods are among the most accurate computational techniques for predicting protein-ligand binding affinities, but their utility is limited by the need for many simulations of alchemically modified intermediate states. We propose Direct Binding Free Energy (DBFE), an end-state ABFE method in implicit solvent that requires no alchemical intermediates. DBFE outperforms OBC2 double decoupling on a host-guest benchmark and performs comparably to OBC2 MM/GBSA on a protein-ligand benchmark. Since receptor and ligand simulations can be precomputed and amortized across compounds, DBFE requires only one complex simulation per ligand compared to the many lambda windows needed for double decoupling, making it a promising candidate for virtual screening workflows. We publicly release the code for this method at https://github.com/molecularmodelinglab/dbfe.

Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector. A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.

The activation function plays a crucial role in model optimisation, yet the optimal choice remains unclear. For example, the Sigmoid activation is the de-facto activation in balanced classification tasks, however, in imbalanced classification, it proves inappropriate due to bias towards frequent classes. In this work, we delve deeper in this phenomenon by performing a comprehensive statistical analysis in the classification and intermediate layers of both balanced and imbalanced networks and we empirically show that aligning the activation function with the data distribution, enhances the performance in both balanced and imbalanced tasks. To this end, we propose the Adaptive Parametric Activation (APA) function, a novel and versatile activation function that unifies most common activation functions under a single formula. APA can be applied in both intermediate layers and attention layers, significantly outperforming the state-of-the-art on several imbalanced benchmarks such as ImageNet-LT, iNaturalist2018, Places-LT, CIFAR100-LT and LVIS and balanced benchmarks such as ImageNet1K, COCO and V3DET. The code is available at https://github.com/kostas1515/AGLU.

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

The computational prediction and design of peptide binders targeting specific linear epitopes is crucial in biological and biomedical research, yet it remains challenging due to their highly dynamic nature and the scarcity of experimentally solved binding data. To address this problem, we built an unprecedentedly large-scale library of peptide pairs within stable secondary structures (beta sheets), leveraging newly available AlphaFold predicted structures. We then developed a machine learning method based on the Transformer architecture for the design of specific linear binders, in analogy to a language translation task. Our method, TransformerBeta, accurately predicts specific beta strand interactions and samples sequences with beta sheet-like molecular properties, while capturing interpretable physico-chemical interaction patterns. As such, it can propose specific candidate binders targeting linear epitope for experimental validation to inform protein design.

Activation functions are core components of all deep learning architectures. Currently, the most popular activation functions are smooth ReLU variants like GELU and SiLU. These are self-gated activation functions where the range of the gating function is between zero and one. In this paper, we explore the viability of using arctan as a gating mechanism. A self-gated activation function that uses arctan as its gating function has a monotonically increasing first derivative. To make this activation function competitive, it is necessary to introduce a trainable parameter for every MLP block to expand the range of the gating function beyond zero and one. We find that this technique also improves existing self-gated activation functions. We conduct an empirical evaluation of Expanded ArcTan Linear Unit (xATLU), Expanded GELU (xGELU), and Expanded SiLU (xSiLU) and show that they outperform existing activation functions within a transformer architecture. Additionally, expanded gating ranges show promising results in improving first-order Gated Linear Units (GLU).

We extend JAX with the capability to automatically differentiate higher-order functions (functionals and operators). By representing functions as a generalization of arrays, we seamlessly use JAX's existing primitive system to implement higher-order functions. We present a set of primitive operators that serve as foundational building blocks for constructing several key types of functionals. For every introduced primitive operator, we derive and implement both linearization and transposition rules, aligning with JAX's internal protocols for forward and reverse mode automatic differentiation. This enhancement allows for functional differentiation in the same syntax traditionally use for functions. The resulting functional gradients are themselves functions ready to be invoked in python. We showcase this tool's efficacy and simplicity through applications where functional derivatives are indispensable. The source code of this work is released at https://github.com/sail-sg/autofd .

We present a novel dual-head deep learning architecture for protein-protein interaction modeling that enables simultaneous prediction of binding affinity (ΔG) and mutation-induced affinity changes (ΔΔG) using only protein sequence information. Our approach offers a significant advancement over existing methods by employing specialized prediction heads that operate on a shared representation network, allowing direct and optimized prediction of both values. To ensure robust generalization, we integrated complementary datasets from SKEMPI v2 and PDBbind with a rigorous protein domain-based splitting strategy that prevents information leakage between training and validation sets. Our architecture combines transformer-based encoders with a novel cross-attention mechanism that processes paired protein sequences directly, without requiring any structural information. The network embeds input sequences using ESM3 representations, then employs a learnable sliced window embedding layer to manage variable-length sequences efficiently. A multi-layer transformer encoder with bidirectional self-attention captures intra-protein patterns, while cross-attention layers enable explicit modeling of interactions between protein pairs. This shared representation network feeds into separate ΔG and ΔΔG prediction heads, allowing task-specific optimization while leveraging common features. The model achieves ΔΔG validation of Pearson correlation at 0.485, while maintaining strong ΔG predictions (Pearson: 0.638). While existing approaches require protein structure data and binding interface information, our model eliminates these constraints. This provides a critical advantage for the numerous proteins with unknown structures or those challenging to crystallize, such as viral and intrinsically disordered proteins.

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.

Recently, influence functions present an apparatus for achieving explainability for deep neural models by quantifying the perturbation of individual train instances that might impact a test prediction. Our objectives in this paper are twofold. First we incorporate influence functions as a feedback into the model to improve its performance. Second, in a dataset extension exercise, using influence functions to automatically identify data points that have been initially `silver' annotated by some existing method and need to be cross-checked (and corrected) by annotators to improve the model performance. To meet these objectives, in this paper, we introduce InfFeed, which uses influence functions to compute the influential instances for a target instance. Toward the first objective, we adjust the label of the target instance based on its influencer(s) label. In doing this, InfFeed outperforms the state-of-the-art baselines (including LLMs) by a maximum macro F1-score margin of almost 4% for hate speech classification, 3.5% for stance classification, and 3% for irony and 2% for sarcasm detection. Toward the second objective we show that manually re-annotating only those silver annotated data points in the extension set that have a negative influence can immensely improve the model performance bringing it very close to the scenario where all the data points in the extension set have gold labels. This allows for huge reduction of the number of data points that need to be manually annotated since out of the silver annotated extension dataset, the influence function scheme picks up ~1/1000 points that need manual correction.

Because learning sometimes involves sensitive data, machine learning algorithms have been extended to offer privacy for training data. In practice, this has been mostly an afterthought, with privacy-preserving models obtained by re-running training with a different optimizer, but using the model architectures that already performed well in a non-privacy-preserving setting. This approach leads to less than ideal privacy/utility tradeoffs, as we show here. Instead, we propose that model architectures are chosen ab initio explicitly for privacy-preserving training. To provide guarantees under the gold standard of differential privacy, one must bound as strictly as possible how individual training points can possibly affect model updates. In this paper, we are the first to observe that the choice of activation function is central to bounding the sensitivity of privacy-preserving deep learning. We demonstrate analytically and experimentally how a general family of bounded activation functions, the tempered sigmoids, consistently outperform unbounded activation functions like ReLU. Using this paradigm, we achieve new state-of-the-art accuracy on MNIST, FashionMNIST, and CIFAR10 without any modification of the learning procedure fundamentals or differential privacy analysis.

Predicting ATP-Protein Binding sites in genes is of great significance in the field of Biology and Medicine. The majority of research in this field has been conducted through time- and resource-intensive 'wet experiments' in laboratories. Over the years, researchers have been investigating computational methods computational methods to accomplish the same goals, utilising the strength of advanced Deep Learning and NLP algorithms. In this paper, we propose to develop methods to classify ATP-Protein binding sites. We conducted various experiments mainly using PSSMs and several word embeddings as features. We used 2D CNNs and LightGBM classifiers as our chief Deep Learning Algorithms. The MP3Vec and BERT models have also been subjected to testing in our study. The outcomes of our experiments demonstrated improvement over the state-of-the-art benchmarks.

Which functions can be used as activations in deep neural networks? This article explores families of functions based on orthonormal bases, including the Hermite polynomial basis and the Fourier trigonometric basis, as well as a basis resulting from the tropicalization of a polynomial basis. Our study shows that, through simple variance-preserving initialization and without additional clamping mechanisms, these activations can successfully be used to train deep models, such as GPT-2 for next-token prediction on OpenWebText and ConvNeXt for image classification on ImageNet. Our work addresses the issue of exploding and vanishing activations and gradients, particularly prevalent with polynomial activations, and opens the door for improving the efficiency of large-scale learning tasks. Furthermore, our approach provides insight into the structure of neural networks, revealing that networks with polynomial activations can be interpreted as multivariate polynomial mappings. Finally, using Hermite interpolation, we show that our activations can closely approximate classical ones in pre-trained models by matching both the function and its derivative, making them especially useful for fine-tuning tasks. These activations are available in the torchortho library, which can be accessed via: https://github.com/K-H-Ismail/torchortho.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

It is often useful to compactly summarize important properties of model parameters and training data so that they can be used later without storing and/or iterating over the entire dataset. As a specific case, we consider estimating the Function Space Distance (FSD) over a training set, i.e. the average discrepancy between the outputs of two neural networks. We propose a Linearized Activation Function TRick (LAFTR) and derive an efficient approximation to FSD for ReLU neural networks. The key idea is to approximate the architecture as a linear network with stochastic gating. Despite requiring only one parameter per unit of the network, our approach outcompetes other parametric approximations with larger memory requirements. Applied to continual learning, our parametric approximation is competitive with state-of-the-art nonparametric approximations, which require storing many training examples. Furthermore, we show its efficacy in estimating influence functions accurately and detecting mislabeled examples without expensive iterations over the entire dataset.

When trying to gain better visibility into a machine learning model in order to understand and mitigate the associated risks, a potentially valuable source of evidence is: which training examples most contribute to a given behavior? Influence functions aim to answer a counterfactual: how would the model's parameters (and hence its outputs) change if a given sequence were added to the training set? While influence functions have produced insights for small models, they are difficult to scale to large language models (LLMs) due to the difficulty of computing an inverse-Hessian-vector product (IHVP). We use the Eigenvalue-corrected Kronecker-Factored Approximate Curvature (EK-FAC) approximation to scale influence functions up to LLMs with up to 52 billion parameters. In our experiments, EK-FAC achieves similar accuracy to traditional influence function estimators despite the IHVP computation being orders of magnitude faster. We investigate two algorithmic techniques to reduce the cost of computing gradients of candidate training sequences: TF-IDF filtering and query batching. We use influence functions to investigate the generalization patterns of LLMs, including the sparsity of the influence patterns, increasing abstraction with scale, math and programming abilities, cross-lingual generalization, and role-playing behavior. Despite many apparently sophisticated forms of generalization, we identify a surprising limitation: influences decay to near-zero when the order of key phrases is flipped. Overall, influence functions give us a powerful new tool for studying the generalization properties of LLMs.

Prediction of protein-ligand (PL) binding affinity remains the key to drug discovery. Popular approaches in recent years involve graph neural networks (GNNs), which are used to learn the topology and geometry of PL complexes. However, GNNs are computationally heavy and have poor scalability to graph sizes. On the other hand, traditional machine learning (ML) approaches, such as gradient-boosted decision trees (GBDTs), are lightweight yet extremely efficient for tabular data. We propose to use PL interaction features along with PL graph-level features in GBDT. We show that this combination outperforms the existing solutions.

Proteins move and deform to ensure their biological functions. Despite significant progress in protein structure prediction, approximating conformational ensembles at physiological conditions remains a fundamental open problem. This paper presents a novel perspective on the problem by directly targeting continuous compact representations of protein motions inferred from sparse experimental observations. We develop a task-specific loss function enforcing data symmetries, including scaling and permutation operations. Our method PETIMOT (Protein sEquence and sTructure-based Inference of MOTions) leverages transfer learning from pre-trained protein language models through an SE(3)-equivariant graph neural network. When trained and evaluated on the Protein Data Bank, PETIMOT shows superior performance in time and accuracy, capturing protein dynamics, particularly large/slow conformational changes, compared to state-of-the-art flow-matching approaches and traditional physics-based models.

The choice of activation functions in deep networks has a significant effect on the training dynamics and task performance. Currently, the most successful and widely-used activation function is the Rectified Linear Unit (ReLU). Although various hand-designed alternatives to ReLU have been proposed, none have managed to replace it due to inconsistent gains. In this work, we propose to leverage automatic search techniques to discover new activation functions. Using a combination of exhaustive and reinforcement learning-based search, we discover multiple novel activation functions. We verify the effectiveness of the searches by conducting an empirical evaluation with the best discovered activation function. Our experiments show that the best discovered activation function, f(x) = x cdot sigmoid(beta x), which we name Swish, tends to work better than ReLU on deeper models across a number of challenging datasets. For example, simply replacing ReLUs with Swish units improves top-1 classification accuracy on ImageNet by 0.9\% for Mobile NASNet-A and 0.6\% for Inception-ResNet-v2. The simplicity of Swish and its similarity to ReLU make it easy for practitioners to replace ReLUs with Swish units in any neural network.

The dynamic nature of proteins is crucial for determining their biological functions and properties, for which Monte Carlo (MC) and molecular dynamics (MD) simulations stand as predominant tools to study such phenomena. By utilizing empirically derived force fields, MC or MD simulations explore the conformational space through numerically evolving the system via Markov chain or Newtonian mechanics. However, the high-energy barrier of the force fields can hamper the exploration of both methods by the rare event, resulting in inadequately sampled ensemble without exhaustive running. Existing learning-based approaches perform direct sampling yet heavily rely on target-specific simulation data for training, which suffers from high data acquisition cost and poor generalizability. Inspired by simulated annealing, we propose Str2Str, a novel structure-to-structure translation framework capable of zero-shot conformation sampling with roto-translation equivariant property. Our method leverages an amortized denoising score matching objective trained on general crystal structures and has no reliance on simulation data during both training and inference. Experimental results across several benchmarking protein systems demonstrate that Str2Str outperforms previous state-of-the-art generative structure prediction models and can be orders of magnitude faster compared to long MD simulations. Our open-source implementation is available at https://github.com/lujiarui/Str2Str

The success of artificial neural networks (ANNs) hinges greatly on the judicious selection of an activation function, introducing non-linearity into network and enabling them to model sophisticated relationships in data. However, the search of activation functions has largely relied on empirical knowledge in the past, lacking theoretical guidance, which has hindered the identification of more effective activation functions. In this work, we offer a proper solution to such issue. Firstly, we theoretically demonstrate the existence of the worst activation function with boundary conditions (WAFBC) from the perspective of information entropy. Furthermore, inspired by the Taylor expansion form of information entropy functional, we propose the Entropy-based Activation Function Optimization (EAFO) methodology. EAFO methodology presents a novel perspective for designing static activation functions in deep neural networks and the potential of dynamically optimizing activation during iterative training. Utilizing EAFO methodology, we derive a novel activation function from ReLU, known as Correction Regularized ReLU (CRReLU). Experiments conducted with vision transformer and its variants on CIFAR-10, CIFAR-100 and ImageNet-1K datasets demonstrate the superiority of CRReLU over existing corrections of ReLU. Extensive empirical studies on task of large language model (LLM) fine-tuning, CRReLU exhibits superior performance compared to GELU, suggesting its broader potential for practical applications.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

Neural networks require a careful design in order to perform properly on a given task. In particular, selecting a good activation function (possibly in a data-dependent fashion) is a crucial step, which remains an open problem in the research community. Despite a large amount of investigations, most current implementations simply select one fixed function from a small set of candidates, which is not adapted during training, and is shared among all neurons throughout the different layers. However, neither two of these assumptions can be supposed optimal in practice. In this paper, we present a principled way to have data-dependent adaptation of the activation functions, which is performed independently for each neuron. This is achieved by leveraging over past and present advances on cubic spline interpolation, allowing for local adaptation of the functions around their regions of use. The resulting algorithm is relatively cheap to implement, and overfitting is counterbalanced by the inclusion of a novel damping criterion, which penalizes unwanted oscillations from a predefined shape. Experimental results validate the proposal over two well-known benchmarks.

Why do brains have inhibitory connections? Why do deep networks have negative weights? We propose an answer from the perspective of representation capacity. We believe representing functions is the primary role of both (i) the brain in natural intelligence, and (ii) deep networks in artificial intelligence. Our answer to why there are inhibitory/negative weights is: to learn more functions. We prove that, in the absence of negative weights, neural networks with non-decreasing activation functions are not universal approximators. While this may be an intuitive result to some, to the best of our knowledge, there is no formal theory, in either machine learning or neuroscience, that demonstrates why negative weights are crucial in the context of representation capacity. Further, we provide insights on the geometric properties of the representation space that non-negative deep networks cannot represent. We expect these insights will yield a deeper understanding of more sophisticated inductive priors imposed on the distribution of weights that lead to more efficient biological and machine learning.

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language models can efficiently process sequential data, offering an alternative approach to molecular representation. In the current study, we introduce BAPULM, an innovative sequence-based framework that leverages the chemical latent representations of proteins via ProtT5-XL-U50 and ligands through MolFormer, eliminating reliance on complex 3D configurations. Our approach was validated extensively on benchmark datasets, achieving scoring power (R) values of 0.925 pm 0.043, 0.914 pm 0.004, and 0.8132 pm 0.001 on benchmark1k2101, Test2016_290, and CSAR-HiQ_36, respectively. These findings indicate the robustness and accuracy of BAPULM across diverse datasets and underscore the potential of sequence-based models in-silico drug discovery, offering a scalable alternative to 3D-centric methods for screening potential ligands.

Catastrophic forgetting remains a significant challenge to continual learning for decades. While recent works have proposed effective methods to mitigate this problem, they mainly focus on the algorithmic side. Meanwhile, we do not fully understand what architectural properties of neural networks lead to catastrophic forgetting. This study aims to fill this gap by studying the role of activation functions in the training dynamics of neural networks and their impact on catastrophic forgetting. Our study reveals that, besides sparse representations, the gradient sparsity of activation functions also plays an important role in reducing forgetting. Based on this insight, we propose a new class of activation functions, elephant activation functions, that can generate both sparse representations and sparse gradients. We show that by simply replacing classical activation functions with elephant activation functions, we can significantly improve the resilience of neural networks to catastrophic forgetting. Our method has broad applicability and benefits for continual learning in regression, class incremental learning, and reinforcement learning tasks. Specifically, we achieves excellent performance on Split MNIST dataset in just one single pass, without using replay buffer, task boundary information, or pre-training.

We propose Mish, a novel self-regularized non-monotonic activation function which can be mathematically defined as: f(x)=xtanh(softplus(x)). As activation functions play a crucial role in the performance and training dynamics in neural networks, we validated experimentally on several well-known benchmarks against the best combinations of architectures and activation functions. We also observe that data augmentation techniques have a favorable effect on benchmarks like ImageNet-1k and MS-COCO across multiple architectures. For example, Mish outperformed Leaky ReLU on YOLOv4 with a CSP-DarkNet-53 backbone on average precision (AP_{50}^{val}) by 2.1% in MS-COCO object detection and ReLU on ResNet-50 on ImageNet-1k in Top-1 accuracy by approx1% while keeping all other network parameters and hyperparameters constant. Furthermore, we explore the mathematical formulation of Mish in relation with the Swish family of functions and propose an intuitive understanding on how the first derivative behavior may be acting as a regularizer helping the optimization of deep neural networks. Code is publicly available at https://github.com/digantamisra98/Mish.

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

In recent years, while natural language processing and multimodal learning have seen rapid advancements, the field of de novo protein design has also experienced significant growth. However, most current methods rely on proprietary datasets and evaluation rubrics, making fair comparisons between different approaches challenging. Moreover, these methods often employ evaluation metrics that capture only a subset of the desired properties of designed proteins, lacking a comprehensive assessment framework. To address these, we introduce PDFBench, the first comprehensive benchmark for evaluating de novo protein design from function. PDFBench supports two tasks: description-guided design and keyword-guided design. To ensure fair and multifaceted evaluation, we compile 22 metrics covering sequence plausibility, structural fidelity, and language-protein alignment, along with measures of novelty and diversity. We evaluate five state-of-the-art baselines, revealing their respective strengths and weaknesses across tasks. Finally, we analyze inter-metric correlations, exploring the relationships between four categories of metrics, and offering guidelines for metric selection. PDFBench establishes a unified framework to drive future advances in function-driven de novo protein design.

Molecular docking is an important tool for structure-based drug design, accelerating the efficiency of drug development. Complex and dynamic binding processes between proteins and small molecules require searching and sampling over a wide spatial range. Traditional docking by searching for possible binding sites and conformations is computationally complex and results poorly under blind docking. Quantum-inspired algorithms combining quantum properties and annealing show great advantages in solving combinatorial optimization problems. Inspired by this, we achieve an improved in blind docking by using quantum-inspired combined with gradients learned by deep learning in the encoded molecular space. Numerical simulation shows that our method outperforms traditional docking algorithms and deep learning-based algorithms over 10\%. Compared to the current state-of-the-art deep learning-based docking algorithm DiffDock, the success rate of Top-1 (RMSD<2) achieves an improvement from 33\% to 35\% in our same setup. In particular, a 6\% improvement is realized in the high-precision region(RMSD<1) on molecules data unseen in DiffDock, which demonstrates the well-generalized of our method.

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing annotation imbalance and instruction deficits in existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by large margins. Moreover, InstructProtein serves as a pioneering step towards text-based protein function prediction and sequence design, effectively bridging the gap between protein and human language understanding.

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce MolCRAFT, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol) with comparable molecular size, outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying deep generative models for three-dimensional (3D) molecular design conditioned on protein pockets to solve SBDD has attracted much attention, but their formulation as probabilistic modeling often leads to unsatisfactory optimization performance. On the other hand, traditional combinatorial optimization methods such as genetic algorithms (GA) have demonstrated state-of-the-art performance in various molecular optimization tasks. However, they do not utilize protein target structure to inform design steps but rely on a random-walk-like exploration, which leads to unstable performance and no knowledge transfer between different tasks despite the similar binding physics. To achieve a more stable and efficient SBDD, we propose Reinforced Genetic Algorithm (RGA) that uses neural models to prioritize the profitable design steps and suppress random-walk behavior. The neural models take the 3D structure of the targets and ligands as inputs and are pre-trained using native complex structures to utilize the knowledge of the shared binding physics from different targets and then fine-tuned during optimization. We conduct thorough empirical studies on optimizing binding affinity to various disease targets and show that RGA outperforms the baselines in terms of docking scores and is more robust to random initializations. The ablation study also indicates that the training on different targets helps improve performance by leveraging the shared underlying physics of the binding processes. The code is available at https://github.com/futianfan/reinforced-genetic-algorithm.

We study the optimisation problem associated with Gaussian process regression using squared loss. The most common approach to this problem is to apply an exact solver, such as conjugate gradient descent, either directly, or to a reduced-order version of the problem. Recently, driven by successes in deep learning, stochastic gradient descent has gained traction as an alternative. In this paper, we show that when done rightx2014by which we mean using specific insights from the optimisation and kernel communitiesx2014this approach is highly effective. We thus introduce a particular stochastic dual gradient descent algorithm, that may be implemented with a few lines of code using any deep learning framework. We explain our design decisions by illustrating their advantage against alternatives with ablation studies and show that the new method is highly competitive. Our evaluations on standard regression benchmarks and a Bayesian optimisation task set our approach apart from preconditioned conjugate gradients, variational Gaussian process approximations, and a previous version of stochastic gradient descent for Gaussian processes. On a molecular binding affinity prediction task, our method places Gaussian process regression on par in terms of performance with state-of-the-art graph neural networks.

Machine Learning Force Fields (MLFFs) are a promising alternative to expensive ab initio quantum mechanical molecular simulations. Given the diversity of chemical spaces that are of interest and the cost of generating new data, it is important to understand how MLFFs generalize beyond their training distributions. In order to characterize and better understand distribution shifts in MLFFs, we conduct diagnostic experiments on chemical datasets, revealing common shifts that pose significant challenges, even for large foundation models trained on extensive data. Based on these observations, we hypothesize that current supervised training methods inadequately regularize MLFFs, resulting in overfitting and learning poor representations of out-of-distribution systems. We then propose two new methods as initial steps for mitigating distribution shifts for MLFFs. Our methods focus on test-time refinement strategies that incur minimal computational cost and do not use expensive ab initio reference labels. The first strategy, based on spectral graph theory, modifies the edges of test graphs to align with graph structures seen during training. Our second strategy improves representations for out-of-distribution systems at test-time by taking gradient steps using an auxiliary objective, such as a cheap physical prior. Our test-time refinement strategies significantly reduce errors on out-of-distribution systems, suggesting that MLFFs are capable of and can move towards modeling diverse chemical spaces, but are not being effectively trained to do so. Our experiments establish clear benchmarks for evaluating the generalization capabilities of the next generation of MLFFs. Our code is available at https://tkreiman.github.io/projects/mlff_distribution_shifts/.

The choice of activation function plays a critical role in neural networks, yet most architectures still rely on fixed, uniform activation functions across all neurons. We introduce SmartMixed, a two-phase training strategy that allows networks to learn optimal per-neuron activation functions while preserving computational efficiency at inference. In the first phase, neurons adaptively select from a pool of candidate activation functions (ReLU, Sigmoid, Tanh, Leaky ReLU, ELU, SELU) using a differentiable hard-mixture mechanism. In the second phase, each neuron's activation function is fixed according to the learned selection, resulting in a computationally efficient network that supports continued training with optimized vectorized operations. We evaluate SmartMixed on the MNIST dataset using feedforward neural networks of varying depths. The analysis shows that neurons in different layers exhibit distinct preferences for activation functions, providing insights into the functional diversity within neural architectures.

We present a unified representation of the most popular neural network activation functions. Adopting Mittag-Leffler functions of fractional calculus, we propose a flexible and compact functional form that is able to interpolate between various activation functions and mitigate common problems in training neural networks such as vanishing and exploding gradients. The presented gated representation extends the scope of fixed-shape activation functions to their adaptive counterparts whose shape can be learnt from the training data. The derivatives of the proposed functional form can also be expressed in terms of Mittag-Leffler functions making it a suitable candidate for gradient-based backpropagation algorithms. By training multiple neural networks of different complexities on various datasets with different sizes, we demonstrate that adopting a unified gated representation of activation functions offers a promising and affordable alternative to individual built-in implementations of activation functions in conventional machine learning frameworks.

Structure-based drug design (SBDD) aims to efficiently discover high-affinity ligands within vast chemical spaces. However, current generative models struggle with objective misalignment and rigid sampling budgets. We present MolFORM, a fast multi-modal flow matching framework for discrete atom types and continuous coordinates. Crucially, to bridge the gap between generative capability and biochemical objectives, we introduce two distinct post-training strategies: (1) Direct Preference Optimization (DPO), which performs offline alignment using ranked preference pairs; and (2) an online reinforcement learning paradigm that optimizes the generative flow directly on the forward process. Both strategies effectively navigate the chemical space toward high-affinity regions. MolFORM achieves state-of-the-art results on the CrossDocked2020 benchmark (Vina Score -7.60, Diversity 0.75), demonstrating that incorporating preference alignment mechanisms-whether via offline optimization or online reinforcement-is crucial for steering generative models toward high-affinity binding regions. The source code for MolFORM is publicly available at https://github.com/daiheng-zhang/SBDD-MolFORM.

Multimodal protein language models deliver strong performance on mutation-effect prediction, but training such models from scratch demands substantial computational resources. In this paper, we propose a fine-tuning framework called InstructPLM-mu and try to answer a question: Can multimodal fine-tuning of a pretrained, sequence-only protein language model match the performance of models trained end-to-end? Surprisingly, our experiments show that fine-tuning ESM2 with structural inputs can reach performance comparable to ESM3. To understand how this is achieved, we systematically compare three different feature-fusion designs and fine-tuning recipes. Our results reveal that both the fusion method and the tuning strategy strongly affect final accuracy, indicating that the fine-tuning process is not trivial. We hope this work offers practical guidance for injecting structure into pretrained protein language models and motivates further research on better fusion mechanisms and fine-tuning protocols.

Recent research in representation learning utilizes large databases of proteins or molecules to acquire knowledge of drug and protein structures through unsupervised learning techniques. These pre-trained representations have proven to significantly enhance the accuracy of subsequent tasks, such as predicting the affinity between drugs and target proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results on established benchmark datasets. We provide preprocessed and integrated data obtained from 7 public sources, which encompass over 30M triples. Additionally, we make available the pre-trained models based on this data, along with the reported outcomes of their performance on three widely-used benchmark datasets for drug-target binding affinity prediction found in the Therapeutic Data Commons (TDC) benchmarks. Additionally, we make the source code for training models on benchmark datasets publicly available. Our objective in releasing these pre-trained models, accompanied by clean data for model pretraining and benchmark results, is to encourage research in knowledge-enhanced representation learning.

D-peptide binders targeting L-proteins have promising therapeutic potential. Despite rapid advances in machine learning-based target-conditioned peptide design, generating D-peptide binders remains largely unexplored. In this work, we show that by injecting axial features to E(3)-equivariant (polar) vector features, it is feasible to achieve cross-chirality generalization from homo-chiral (L--L) training data to hetero-chiral (D--L) design tasks. By implementing this method within a latent diffusion model, we achieved D-peptide binder design that not only outperforms existing tools in in silico benchmarks, but also demonstrates efficacy in wet-lab validation. To our knowledge, our approach represents the first wet-lab validated generative AI for the de novo design of D-peptide binders, offering new perspectives on handling chirality in protein design. Codes are available at https://github.com/YZY010418/PepMirror

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have emerged as the preferred method for this challenge, thanks to their ability to harness large sequence databases. Yet, their reliance on expansive sequence data and parameter sets limits their flexibility and practicality in real-world scenarios. Concurrently, the recent surge in computationally predicted protein structures unlocks new opportunities in protein representation learning. While promising, the computational burden carried by such complex data still hinders widely-adopted practical applications. To address these limitations, we introduce a novel framework that enhances protein language models by integrating protein structural data. Drawing from recent advances in graph transformers, our approach refines the self-attention mechanisms of pretrained language transformers by integrating structural information with structure extractor modules. This refined model, termed Protein Structure Transformer (PST), is further pretrained on a small protein structure database, using the same masked language modeling objective as traditional protein language models. Empirical evaluations of PST demonstrate its superior parameter efficiency relative to protein language models, despite being pretrained on a dataset comprising only 542K structures. Notably, PST consistently outperforms the state-of-the-art foundation model for protein sequences, ESM-2, setting a new benchmark in protein function prediction. Our findings underscore the potential of integrating structural information into protein language models, paving the way for more effective and efficient protein modeling Code and pretrained models are available at https://github.com/BorgwardtLab/PST.

Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding ligands concurrently or have been rigorously benchmarked on pharmacologically relevant drug targets, hindering their widespread adoption in drug discovery efforts. In this work, we propose FlowDock, the first deep geometric generative model based on conditional flow matching that learns to directly map unbound (apo) structures to their bound (holo) counterparts for an arbitrary number of binding ligands. Furthermore, FlowDock provides predicted structural confidence scores and binding affinity values with each of its generated protein-ligand complex structures, enabling fast virtual screening of new (multi-ligand) drug targets. For the well-known PoseBusters Benchmark dataset, FlowDock outperforms single-sequence AlphaFold 3 with a 51% blind docking success rate using unbound (apo) protein input structures and without any information derived from multiple sequence alignments, and for the challenging new DockGen-E dataset, FlowDock outperforms single-sequence AlphaFold 3 and matches single-sequence Chai-1 for binding pocket generalization. Additionally, in the ligand category of the 16th community-wide Critical Assessment of Techniques for Structure Prediction (CASP16), FlowDock ranked among the top-5 methods for pharmacological binding affinity estimation across 140 protein-ligand complexes, demonstrating the efficacy of its learned representations in virtual screening. Source code, data, and pre-trained models are available at https://github.com/BioinfoMachineLearning/FlowDock.

Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level properties. Yet, whether the incorporation of such text data can help protein design tasks has not been explored. To bridge this gap, we propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP that aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that generates the protein sequences from the representation. To train ProteinDT, we construct a large dataset, SwissProtCLAP, with 441K text and protein pairs. We empirically verify the effectiveness of ProteinDT from three aspects: (1) consistently superior performance on four out of six protein property prediction benchmarks; (2) over 90% accuracy for text-guided protein generation; and (3) promising results for zero-shot text-guided protein editing.

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However, most existing methods consider molecular generation for protein pockets independently while neglecting the underlying connections such as subpocket-level similarities. Subpockets are the local protein environments of ligand fragments and pockets with similar subpockets may bind the same molecular fragment (motif) even though their overall structures are different. Therefore, the trained models can hardly generalize to unseen protein pockets in real-world applications. In this paper, we propose a novel method DrugGPS for generalizable structure-based drug design. With the biochemical priors, we propose to learn subpocket prototypes and construct a global interaction graph to model the interactions between subpocket prototypes and molecular motifs. Moreover, a hierarchical graph transformer encoder and motif-based 3D molecule generation scheme are used to improve the model's performance. The experimental results show that our model consistently outperforms baselines in generating realistic drug candidates with high affinities in challenging out-of-distribution settings.

We consider the problem of subset selection where one is given multiple rankings of items and the goal is to select the highest ``quality'' subset. Score functions from the multiwinner voting literature have been used to aggregate rankings into quality scores for subsets. We study this setting of subset selection problems when, in addition, rankings may contain systemic or unconscious biases toward a group of items. For a general model of input rankings and biases, we show that requiring the selected subset to satisfy group fairness constraints can improve the quality of the selection with respect to unbiased rankings. Importantly, we show that for fairness constraints to be effective, different multiwinner score functions may require a drastically different number of rankings: While for some functions, fairness constraints need an exponential number of rankings to recover a close-to-optimal solution, for others, this dependency is only polynomial. This result relies on a novel notion of ``smoothness'' of submodular functions in this setting that quantifies how well a function can ``correctly'' assess the quality of items in the presence of bias. The results in this paper can be used to guide the choice of multiwinner score functions for the subset selection setting considered here; we additionally provide a tool to empirically enable this.

Sequence generative models are transforming protein engineering. However, no principled framework exists for conditioning these models on auxiliary information, such as experimental data, without additional training of a generative model. Herein, we present ProteinGuide, a method for such "on-the-fly" conditioning, amenable to a broad class of protein generative models including Masked Language Models (e.g. ESM3), any-order auto-regressive models (e.g. ProteinMPNN) as well as diffusion and flow matching models (e.g. MultiFlow). ProteinGuide stems from our unifying view of these model classes under a single statistical framework. As proof of principle, we perform several in silico experiments. We first guide pre-trained generative models to design proteins with user-specified properties, such as higher stability or activity. Next, we design for optimizing two desired properties that are in tension with each other. Finally, we apply our method in the wet lab, using ProteinGuide to increase the editing activity of an adenine base editor in vivo with data from only a single pooled library of 2,000 variants. We find that a single round of ProteinGuide achieves a higher editing efficiency than was previously achieved using seven rounds of directed evolution.

Protein biology focuses on the intricate relationships among sequences, structures, and functions. Deciphering protein functions is crucial for understanding biological processes, advancing drug discovery, and enabling synthetic biology applications. Since protein sequences determine tertiary structures, which in turn govern functions, integrating sequence and structure information is essential for accurate prediction of protein functions. Traditional protein language models (pLMs) have advanced protein-related tasks by learning representations from large-scale sequence and structure data. However, pLMs are limited in integrating broader contextual knowledge, particularly regarding functional modalities that are fundamental to protein biology. In contrast, large language models (LLMs) have exhibited outstanding performance in contextual understanding, reasoning, and generation across diverse domains. Leveraging these capabilities, STELLA is proposed as a multimodal LLM integrating protein sequence-structure representations with general knowledge to address protein function prediction. Through multimodal instruction tuning (MMIT) using the proposed OPI-Struc dataset, STELLA achieves state-of-the-art performance in two function-related tasks-functional description prediction (FP) and enzyme-catalyzed reaction prediction (EP). This study highlights the potential of multimodal LLMs as an alternative paradigm to pLMs to advance protein biology research.

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. For a pair of input protein structures, PLASMA outputs a clear alignment matrix with an interpretable overall similarity score. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Reproducibility is ensured via our official implementation at https://github.com/ZW471/PLASMA-Protein-Local-Alignment.git.

Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration overhead. We present an agentic end-to-end drug design framework that leverages a Large Language Model (LLM) in conjunction with the Model Context Protocol (MCP) to dynamically coordinate access to biochemical databases, modular toolchains, and task-specific AI models. The system integrates four state-of-the-art components: MaSIF (MaSIF-site and MaSIF-seed-search) for geometric deep learning-based identification of protein-protein interaction (PPI) sites, Rosetta for grafting protein fragments onto protein backbones to form mini proteins, ProteinMPNN for amino acid sequences redesign, and AlphaFold3 for near-experimental accuracy in complex structure prediction. Starting from a target structure, the framework supports de novo binder generation via surface analysis, scaffold grafting and pose construction, sequence optimization, and structure prediction. Additionally, by replacing rigid, script-based workflows with a protocol-driven, LLM-coordinated architecture, the framework improves reproducibility, reduces manual overhead, and ensures extensibility, portability, and auditability across the entire drug design process.

The RNA structure-function relationship has recently garnered significant attention within the deep learning community, promising to grow in importance as nucleic acid structure models advance. However, the absence of standardized and accessible benchmarks for deep learning on RNA 3D structures has impeded the development of models for RNA functional characteristics. In this work, we introduce a set of seven benchmarking datasets for RNA structure-function prediction, designed to address this gap. Our library builds on the established Python library rnaglib, and offers easy data distribution and encoding, splitters and evaluation methods, providing a convenient all-in-one framework for comparing models. Datasets are implemented in a fully modular and reproducible manner, facilitating for community contributions and customization. Finally, we provide initial baseline results for all tasks using a graph neural network. Source code: https://github.com/cgoliver/rnaglib Documentation: https://rnaglib.org

Influence functions provide crucial insights into model training, but existing methods suffer from large computational costs and limited generalization. Particularly, recent works have proposed various metrics and algorithms to calculate the influence of data using language models, which do not scale well with large models and datasets. This is because of the expensive forward and backward passes required for computation, substantial memory requirements to store large models, and poor generalization of influence estimates to new data. In this paper, we explore the use of small neural networks -- which we refer to as the InfluenceNetwork -- to estimate influence values, achieving up to 99% cost reduction. Our evaluation demonstrates that influence values can be estimated with models just 0.0027% the size of full language models (we use 7B and 8B versions). We apply our algorithm of estimating influence values (called NN-CIFT: Neural Networks for effiCient Instruction Fine-Tuning) to the downstream task of subset selection for general instruction fine-tuning. In our study, we include four state-of-the-art influence functions and show no compromise in performance, despite large speedups, between NN-CIFT and the original influence functions. We provide an in-depth hyperparameter analyses of NN-CIFT. The code for our method can be found here: https://github.com/agarwalishika/NN-CIFT.

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.

Activation functions are fundamental elements of deep learning architectures as they significantly influence training dynamics. ReLU, while widely used, is prone to the dying neuron problem, which has been mitigated by variants such as LeakyReLU, PReLU, and ELU that better handle negative neuron outputs. Recently, self-gated activations like GELU and Swish have emerged as state-of-the-art alternatives, leveraging their smoothness to ensure stable gradient flow and prevent neuron inactivity. In this work, we introduce the Gompertz Linear Unit (GoLU), a novel self-gated activation function defined as GoLU(x) = x , Gompertz(x), where Gompertz(x) = e^{-e^{-x}}. The GoLU activation leverages the asymmetry in the Gompertz function to reduce variance in the latent space more effectively compared to GELU and Swish, while preserving robust gradient flow. Extensive experiments across diverse tasks, including Image Classification, Language Modeling, Semantic Segmentation, Object Detection, Instance Segmentation, and Diffusion, highlight GoLU's superior performance relative to state-of-the-art activation functions, establishing GoLU as a robust alternative to existing activation functions.

Recently, there has been great interest in learning how to best represent proteins, specifically with fixed-length embeddings. Deep learning has become a popular tool for protein representation learning as a model's hidden layers produce potentially useful vector embeddings. TAPE introduced a number of benchmark tasks and showed that semi-supervised learning, via pretraining language models on a large protein corpus, improved performance on downstream tasks. Two of the tasks (fluorescence prediction and stability prediction) involve learning fitness landscapes. In this paper, we show that CNN models trained solely using supervised learning both compete with and sometimes outperform the best models from TAPE that leverage expensive pretraining on large protein datasets. These CNN models are sufficiently simple and small that they can be trained using a Google Colab notebook. We also find for the fluorescence task that linear regression outperforms our models and the TAPE models. The benchmarking tasks proposed by TAPE are excellent measures of a model's ability to predict protein function and should be used going forward. However, we believe it is important to add baselines from simple models to put the performance of the semi-supervised models that have been reported so far into perspective.

Deep generative models are rapidly advancing structure-based drug design, offering substantial promise for generating small molecule ligands that bind to specific protein targets. However, most current approaches assume a rigid protein binding pocket, neglecting the intrinsic flexibility of proteins and the conformational rearrangements induced by ligand binding, limiting their applicability in practical drug discovery. Here, we propose Apo2Mol, a diffusion-based generative framework for 3D molecule design that explicitly accounts for conformational flexibility in protein binding pockets. To support this, we curate a dataset of over 24,000 experimentally resolved apo-holo structure pairs from the Protein Data Bank, enabling the characterization of protein structure changes associated with ligand binding. Apo2Mol employs a full-atom hierarchical graph-based diffusion model that simultaneously generates 3D ligand molecules and their corresponding holo pocket conformations from input apo states. Empirical studies demonstrate that Apo2Mol can achieve state-of-the-art performance in generating high-affinity ligands and accurately capture realistic protein pocket conformational changes.

Generalization beyond training data remains a central challenge in machine learning for biology. A common way to enhance generalization is self-supervised pre-training on large datasets. However, aiming to perform well on all possible proteins can limit a model's capacity to excel on any specific one, whereas experimentalists typically need accurate predictions for individual proteins they study, often not covered in training data. To address this limitation, we propose a method that enables self-supervised customization of protein language models to one target protein at a time, on the fly, and without assuming any additional data. We show that our Protein Test-Time Training (ProteinTTT) method consistently enhances generalization across different models, their sizes, and datasets. ProteinTTT improves structure prediction for challenging targets, achieves new state-of-the-art results on protein fitness prediction, and enhances function prediction on two tasks. Through two challenging case studies, we also show that customization via ProteinTTT achieves more accurate antibody-antigen loop modeling and enhances 19% of structures in the Big Fantastic Virus Database, delivering improved predictions where general-purpose AlphaFold2 and ESMFold struggle.

Large language models (LLMs) have exhibited the ability to effectively utilize external tools to address user queries. However, their performance may be limited in complex, multi-turn interactions involving users and multiple tools. To address this, we propose Magnet, a principled framework for synthesizing high-quality training trajectories to enhance the function calling capability of large language model agents in multi-turn conversations with humans. The framework is based on automatic and iterative translations from a function signature path to a sequence of queries and executable function calls. We model the complicated function interactions in multi-turn cases with graph and design novel node operations to build reliable signature paths. Motivated by context distillation, when guiding the generation of positive and negative trajectories using a teacher model, we provide reference function call sequences as positive hints in context and contrastive, incorrect function calls as negative hints. Experiments show that training with the positive trajectories with supervised fine-tuning and preference optimization against negative trajectories, our 14B model, Magnet-14B-mDPO, obtains 68.01 on BFCL-v3 and 73.30 on ToolQuery, surpassing the performance of the teacher model Gemini-1.5-pro-002 by a large margin in function calling.

Activation Functions introduce non-linearity in the deep neural networks. This nonlinearity helps the neural networks learn faster and efficiently from the dataset. In deep learning, many activation functions are developed and used based on the type of problem statement. ReLU's variants, SWISH, and MISH are goto activation functions. MISH function is considered having similar or even better performance than SWISH, and much better than ReLU. In this paper, we propose an activation function named APTx which behaves similar to MISH, but requires lesser mathematical operations to compute. The lesser computational requirements of APTx does speed up the model training, and thus also reduces the hardware requirement for the deep learning model. Source code: https://github.com/mr-ravin/aptx_activation

Predicting protein function from amino acid sequence remains a central challenge in data-scarce (low-N) regimes, limiting machine learning-guided protein design when only small amounts of assay-labeled sequence-function data are available. Protein language models (pLMs) have advanced the field by providing evolutionary-informed embeddings and sparse autoencoders (SAEs) have enabled decomposition of these embeddings into interpretable latent variables that capture structural and functional features. However, the effectiveness of SAEs for low-N function prediction and protein design has not been systematically studied. Herein, we evaluate SAEs trained on fine-tuned ESM2 embeddings across diverse fitness extrapolation and protein engineering tasks. We show that SAEs, with as few as 24 sequences, consistently outperform or compete with their ESM2 baselines in fitness prediction, indicating that their sparse latent space encodes compact and biologically meaningful representations that generalize more effectively from limited data. Moreover, steering predictive latents exploits biological motifs in pLM representations, yielding top-fitness variants in 83% of cases compared to designing with ESM2 alone.

Set function learning has emerged as a crucial area in machine learning, addressing the challenge of modeling functions that take sets as inputs. Unlike traditional machine learning that involves fixed-size input vectors where the order of features matters, set function learning demands methods that are invariant to permutations of the input set, presenting a unique and complex problem. This survey provides a comprehensive overview of the current development in set function learning, covering foundational theories, key methodologies, and diverse applications. We categorize and discuss existing approaches, focusing on deep learning approaches, such as DeepSets and Set Transformer based methods, as well as other notable alternative methods beyond deep learning, offering a complete view of current models. We also introduce various applications and relevant datasets, such as point cloud processing and multi-label classification, highlighting the significant progress achieved by set function learning methods in these domains. Finally, we conclude by summarizing the current state of set function learning approaches and identifying promising future research directions, aiming to guide and inspire further advancements in this promising field.

The widely used ReLU is favored for its hardware efficiency, {as the implementation at inference is a one bit sign case,} yet suffers from issues such as the ``dying ReLU'' problem, where during training, neurons fail to activate and constantly remain at zero, as highlighted by Lu et al. Traditional approaches to mitigate this issue often introduce more complex and less hardware-friendly activation functions. In this work, we propose a Hysteresis Rectified Linear Unit (HeLU), an efficient activation function designed to address the ``dying ReLU'' problem with minimal complexity. Unlike traditional activation functions with fixed thresholds for training and inference, HeLU employs a variable threshold that refines the backpropagation. This refined mechanism allows simpler activation functions to achieve competitive performance comparable to their more complex counterparts without introducing unnecessary complexity or requiring inductive biases. Empirical evaluations demonstrate that HeLU enhances model generalization across diverse datasets, offering a promising solution for efficient and effective inference suitable for a wide range of neural network architectures.

The performance of deep network learning strongly depends on the choice of the non-linear activation function associated with each neuron. However, deciding on the best activation is non-trivial, and the choice depends on the architecture, hyper-parameters, and even on the dataset. Typically these activations are fixed by hand before training. Here, we demonstrate how to eliminate the reliance on first picking fixed activation functions by using flexible parametric rational functions instead. The resulting Pad\'e Activation Units (PAUs) can both approximate common activation functions and also learn new ones while providing compact representations. Our empirical evidence shows that end-to-end learning deep networks with PAUs can increase the predictive performance. Moreover, PAUs pave the way to approximations with provable robustness. https://github.com/ml-research/pau

The tradeoff between precision and performance in molecular simulations can nowadays be addressed by machine-learned force fields (MLFF), which combine ab initio accuracy with force field numerical efficiency. Different from conventional force fields however, incorporating relevant electronic degrees of freedom into MLFFs becomes important. Here, we implement an equivariant transformer that embeds molecular net charge and spin state without additional neural network parameters. The model trained on a singlet/triplet non-correlated CH2 dataset can identify different spin states and shows state-of-the-art extrapolation capability. Therein, self-attention sensibly captures non-local effects, which, as we show, can be finely tuned over the network hyper-parameters. We indeed found that Softmax activation functions utilised in the self-attention mechanism of graph networks outperformed ReLU-like functions in prediction accuracy. Increasing the attention temperature from τ= d to 2d further improved the extrapolation capability, indicating a weighty role of nonlocality. Additionally, a weight initialisation method was purposed that sensibly accelerated the training process.

Machine learning-based antibody design is emerging as one of the most promising approaches to combat infectious diseases, due to significant advancements in the field of artificial intelligence and an exponential surge in experimental antibody data (in particular related to COVID-19). The ability of an antibody to bind to an antigens (called binding affinity) is one of the the most critical properties in designing neutralizing antibodies. In this study we introduce Ab-Affinity, a new large language model that can accurately predict the binding affinity of antibodies against a target peptide, e.g., the SARS-CoV-2 spike protein. Code and model are available at https://github.com/ucrbioinfo/AbAffinity.

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological alternatives, but still require small molecule docking at binding pockets for targeted protein degradation (TPD). The computational design of protein-based binders presents unique opportunities to access undruggable targets, but have often relied on stable 3D structures or predictions for effective binder generation. Recently, we have leveraged the expressive latent spaces of protein language models (pLMs) for the prioritization of peptide binders from sequence alone, which we have then fused to E3 ubiquitin ligase domains, creating a CRISPR-analogous TPD system for target proteins. However, our methods rely on training discriminator models for ranking heuristically or unconditionally-derived guide peptides for their target binding capability. In this work, we introduce PepMLM, a purely target sequence-conditioned de novo generator of linear peptide binders. By employing a novel masking strategy that uniquely positions cognate peptide sequences at the terminus of target protein sequences, PepMLM tasks the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon previously-validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of target substrates in cellular models. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream programmable proteome editing applications.

Pre-trained large language models (LLMs) are commonly fine-tuned to adapt to downstream tasks. Since the majority of knowledge is acquired during pre-training, attributing the predictions of fine-tuned LLMs to their pre-training data may provide valuable insights. Influence functions have been proposed as a means to explain model predictions based on training data. However, existing approaches fail to compute ``multi-stage'' influence and lack scalability to billion-scale LLMs. In this paper, we propose the multi-stage influence function to attribute the downstream predictions of fine-tuned LLMs to pre-training data under the full-parameter fine-tuning paradigm. To enhance the efficiency and practicality of our multi-stage influence function, we leverage Eigenvalue-corrected Kronecker-Factored (EK-FAC) parameterization for efficient approximation. Empirical results validate the superior scalability of EK-FAC approximation and the effectiveness of our multi-stage influence function. Additionally, case studies on a real-world LLM, dolly-v2-3b, demonstrate its interpretive power, with exemplars illustrating insights provided by multi-stage influence estimates. Our code is public at https://github.com/colored-dye/multi_stage_influence_function.

Predicting vulnerable source code helps to focus attention on those parts of the code that need to be examined with more scrutiny. Recent work proposed the use of function names as semantic cues that can be learned by a deep neural network (DNN) to aid in the hunt for vulnerability of functions. Combining identifier splitting, which splits each function name into its constituent words, with a novel frequency-based algorithm, we explore the extent to which the words that make up a function's name can predict potentially vulnerable functions. In contrast to *lightweight* predictions by a DNN that considers only function names, avoiding the use of a DNN provides *featherweight* predictions. The underlying idea is that function names that contain certain "dangerous" words are more likely to accompany vulnerable functions. Of course, this assumes that the frequency-based algorithm can be properly tuned to focus on truly dangerous words. Because it is more transparent than a DNN, the frequency-based algorithm enables us to investigate the inner workings of the DNN. If successful, this investigation into what the DNN does and does not learn will help us train more effective future models. We empirically evaluate our approach on a heterogeneous dataset containing over 73000 functions labeled vulnerable, and over 950000 functions labeled benign. Our analysis shows that words alone account for a significant portion of the DNN's classification ability. We also find that words are of greatest value in the datasets with a more homogeneous vocabulary. Thus, when working within the scope of a given project, where the vocabulary is unavoidably homogeneous, our approach provides a cheaper, potentially complementary, technique to aid in the hunt for source-code vulnerabilities. Finally, this approach has the advantage that it is viable with orders of magnitude less training data.

Function calling is a core capability of large language models, essential for AI agents. Existing benchmarks such as the Berkeley Function Calling Leaderboard (BFCL), tau^2-Bench (arXiv:2506.07982), and ACEBench (arXiv:2501.12851) evaluate argument correctness but do not test adherence to format instructions embedded in parameter descriptions, such as enclosing values in double quotes or using ISO date formats. We introduce IFEval-FC, a benchmark inspired by IFEval (arXiv:2311.07911) that assesses precise instruction following in function calling. IFEval-FC encodes verifiable formats directly within JSON schema descriptions, for example specifying that a value must not contain punctuation. It includes 750 test cases, each consisting of a function with an embedded format for one of its input parameters and a corresponding user query. Evaluation is fully algorithmic, ensuring objectivity, reproducibility, and scalability. Our results show that even state-of-the-art proprietary models, including GPT-5 and Claude 4.1 Opus, frequently fail to follow basic formatting rules, highlighting a practical limitation for real-world agent systems. The complete codebase and data are publicly available at https://github.com/Skripkon/IFEval-FC.